DC-Build-Header: vg 1.23.0+ds-2 / 2020-05-03 02:13:24 +0000 DC-Task: type:rebuild-binarch-only source:vg version:1.23.0+ds-2 chroot:unstable esttime: logfile:/tmp/vg_1.23.0+ds-2_unstable_clang10.log modes:clang10:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 vg_1.23.0+ds-2' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-3-251.eu-central-1.compute.internal +==============================================================================+ | vg 1.23.0+ds-2 (amd64) Sun, 03 May 2020 02:13:25 +0000 | +==============================================================================+ Package: vg Version: 1.23.0+ds-2 Source Version: 1.23.0+ds-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-6efd42d2-1dfe-43d7-9095-3d2c1b83312e' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang10 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=10 + echo 'Install of clang-10' Install of clang-10 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:12 http://127.0.0.1:12990/debian sid/main Translation-en [6192 kB] Fetched 6459 kB in 2s (3901 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc4 libomp5-10 libz3-4 Suggested packages: clang-10-doc libomp-10-doc Recommended packages: llvm-10-dev python3 The following NEW packages will be installed: clang-10 lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 49.8 MB of archives. After this operation, 259 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200418-1 [41.7 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200418-1 [49.4 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200418-1 [1100 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200418-1 [510 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.8 MB in 0s (133 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12123 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20191231-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../02-libz3-4_4.8.7-4_amd64.deb ... Unpacking libz3-4:amd64 (4.8.7-4) ... Selecting previously unselected package libllvm10:amd64. Preparing to unpack .../03-libllvm10_1%3a10.0.0-4_amd64.deb ... Unpacking libllvm10:amd64 (1:10.0.0-4) ... Selecting previously unselected package libclang-cpp10. Preparing to unpack .../04-libclang-cpp10_1%3a10.0.0-4_amd64.deb ... Unpacking libclang-cpp10 (1:10.0.0-4) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../05-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../06-libobjc4_10-20200418-1_amd64.deb ... Unpacking libobjc4:amd64 (10-20200418-1) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../07-libobjc-9-dev_9.3.0-11_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.3.0-11) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../08-libc6-i386_2.30-4_amd64.deb ... Unpacking libc6-i386 (2.30-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../09-lib32gcc-s1_10-20200418-1_amd64.deb ... Unpacking lib32gcc-s1 (10-20200418-1) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../10-lib32gcc1_1%3a10-20200418-1_amd64.deb ... Unpacking lib32gcc1 (1:10-20200418-1) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../11-lib32stdc++6_10-20200418-1_amd64.deb ... Unpacking lib32stdc++6 (10-20200418-1) ... Selecting previously unselected package libclang-common-10-dev. Preparing to unpack .../12-libclang-common-10-dev_1%3a10.0.0-4_amd64.deb ... Unpacking libclang-common-10-dev (1:10.0.0-4) ... Selecting previously unselected package libclang1-10. Preparing to unpack .../13-libclang1-10_1%3a10.0.0-4_amd64.deb ... Unpacking libclang1-10 (1:10.0.0-4) ... Selecting previously unselected package clang-10. Preparing to unpack .../14-clang-10_1%3a10.0.0-4_amd64.deb ... Unpacking clang-10 (1:10.0.0-4) ... Selecting previously unselected package libomp5-10:amd64. Preparing to unpack .../15-libomp5-10_1%3a10.0.0-4_amd64.deb ... Unpacking libomp5-10:amd64 (1:10.0.0-4) ... Selecting previously unselected package libomp-10-dev. Preparing to unpack .../16-libomp-10-dev_1%3a10.0.0-4_amd64.deb ... Unpacking libomp-10-dev (1:10.0.0-4) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libobjc4:amd64 (10-20200418-1) ... Setting up libz3-4:amd64 (4.8.7-4) ... Setting up libobjc-9-dev:amd64 (9.3.0-11) ... Setting up libomp5-10:amd64 (1:10.0.0-4) ... Setting up libc6-i386 (2.30-4) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libomp-10-dev (1:10.0.0-4) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up libllvm10:amd64 (1:10.0.0-4) ... Setting up lib32gcc-s1 (10-20200418-1) ... Setting up libclang1-10 (1:10.0.0-4) ... Setting up lib32gcc1 (1:10-20200418-1) ... Setting up libclang-cpp10 (1:10.0.0-4) ... Setting up lib32stdc++6 (10-20200418-1) ... Setting up libclang-common-10-dev (1:10.0.0-4) ... Setting up clang-10 (1:10.0.0-4) ... Processing triggers for libc-bin (2.30-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-10 g++-4.6 + ln -s clang-10 gcc-4.6 + ln -s clang-10 cpp-4.6 + ln -s clang-10 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-10 g++-4.7 + ln -s clang-10 gcc-4.7 + ln -s clang-10 cpp-4.7 + ln -s clang-10 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-10 g++-4.8 + ln -s clang-10 gcc-4.8 + ln -s clang-10 cpp-4.8 + ln -s clang-10 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-10 g++-4.9 + ln -s clang-10 gcc-4.9 + ln -s clang-10 cpp-4.9 + ln -s clang-10 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-10 g++-5 + ln -s clang-10 gcc-5 + ln -s clang-10 cpp-5 + ln -s clang-10 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-10 g++-6 + ln -s clang-10 gcc-6 + ln -s clang-10 cpp-6 + ln -s clang-10 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-10 g++-7 + ln -s clang-10 gcc-7 + ln -s clang-10 cpp-7 + ln -s clang-10 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-10 g++-8 + ln -s clang-10 gcc-8 + ln -s clang-10 cpp-8 + ln -s clang-10 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-10 g++-9 + ln -s clang-10 gcc-9 + ln -s clang-10 cpp-9 + ln -s clang-10 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-10 g++-10 + ln -s clang-10 gcc-10 + ln -s clang-10 cpp-10 + ln -s clang-10 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/vg-jhrgZ9 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-10 clang++ + ln -s clang-10 clang + clang++ --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/vg-jhrgZ9 + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 1270 kB of archives. After this operation, 4788 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.12.5+dfsg-10 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1270 kB in 0s (56.2 MB/s) Selecting previously unselected package qt5-qmake-bin. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12968 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ... Setting up qt5-qmake-bin (5.12.5+dfsg-10) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 May 3 02:13 . drwxr-xr-x 75 root root 4096 May 3 02:13 .. -rw-r--r-- 1 root root 276 May 3 02:13 qmake.conf -rw-r--r-- 1 root root 3218 May 3 02:13 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang10'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/vg-jhrgZ9/resolver-uBXDty' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 88.4 MB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main vg 1.23.0+ds-2 (dsc) [2878 B] Get:2 http://127.0.0.1:12990/debian sid/main vg 1.23.0+ds-2 (tar) [88.3 MB] Get:3 http://127.0.0.1:12990/debian sid/main vg 1.23.0+ds-2 (diff) [42.6 kB] Fetched 88.4 MB in 1s (119 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/vg-jhrgZ9/vg-1.23.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/vg-jhrgZ9' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, librocksdb-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, build-essential, fakeroot, doxygen, graphviz Filtered Build-Depends: debhelper-compat (= 12), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, librocksdb-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, build-essential, fakeroot, doxygen, graphviz dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [753 B] Get:5 copy:/<>/apt_archive ./ Packages [799 B] Fetched 2515 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdmainutils bwa ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man docbook-xml docbook-xsl doxygen dwz elfutils fastahack file flex fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base graphviz groff-base gtk-doc-tools help2man icu-devtools intltool-debian jq libann0 libarchive-zip-perl libarchive13 libasm1 libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost1.67-dev libbrotli1 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcdt5 libcgraph6 libclang1-9 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgd3 libgflags2.2 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhts-dev libhts3 libice-dev libice6 libicu-dev libicu63 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg62-turbo libjq1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 liblapack3 libldap-2.4-2 libldap-common libllvm9 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec2 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpng16-16 libprocps8 libprotobuf-dev libprotobuf-lite22 libprotobuf22 libprotoc-dev libprotoc22 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev libreadline8 librhash0 librocksdb-dev librocksdb5.17 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 libsnappy1v5 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libtsl-hopscotch-map-dev libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libx11-dev libxapian30 libxau-dev libxau6 libxaw7 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft2 libxml2 libxml2-dev libxmu6 libxpm4 libxrender-dev libxrender1 libxslt1-dev libxslt1.1 libxss1 libxt6 libyajl-dev libyajl2 littler m4 man-db mime-support opensp openssl pkg-config po-debconf procps protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pkg-resources python3-pygments python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rapidjson-dev raptor2-utils rasqal-utils readline-common rs samtools sensible-utils sgml-base sgml-data ucf unzip uuid-dev x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make docbook-defguide docbook-dsssl psgml dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan doxygen-latex doxygen-doc doxygen-gui flex-doc gawk-doc gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff dblatex lrzip binutils-dev libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-contract1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev libcairo2-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev freetype2-doc libgd-tools libgirepository1.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils gmp-doc libgmp10-doc libmpfr-dev krb5-doc krb5-user libice-doc icu-doc liblzma-doc ncurses-doc libraptor2-doc librasqal3-doc librdf-storage-postgresql librdf-storage-mysql librdf-storage-sqlite librdf-storage-virtuoso redland-utils librdf-perl python-librdf librdf-ruby libsm-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma libx11-doc xapian-tools libxcb-doc libxext-doc m4-doc apparmor less www-browser doc-base libmail-box-perl protobuf-mode-el python3-doc python3-tk python3-venv python3-lxml-dbg python-lxml-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis libgdal-dev r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-getopt r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-curl r-cran-inline r-cran-mockr r-cran-dichromat r-cran-devtools r-cran-usethis r-cran-bit64 r-cran-blob r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-xml2 r-cran-zeallot readline-doc sgml-base-doc perlsgml w3-recs Recommended packages: libfl-dev curl | wget | lynx fonts-liberation bzip2-doc libarchive-cpio-perl shared-mime-info xdg-user-dirs libgts-bin krb5-locales libgpm2 libpng-tools publicsuffix redland-utils libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc python3-bs4 python3-html5lib r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-xml2 r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics r-cran-dbi cwltool libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdmainutils bwa ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man docbook-xml docbook-xsl doxygen dwz elfutils fastahack file flex fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base graphviz groff-base gtk-doc-tools help2man icu-devtools intltool-debian jq libann0 libarchive-zip-perl libarchive13 libasm1 libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost1.67-dev libbrotli1 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcdt5 libcgraph6 libclang1-9 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgd3 libgflags2.2 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhts-dev libhts3 libice-dev libice6 libicu-dev libicu63 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg62-turbo libjq1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 liblapack3 libldap-2.4-2 libldap-common libllvm9 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec2 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpng16-16 libprocps8 libprotobuf-dev libprotobuf-lite22 libprotobuf22 libprotoc-dev libprotoc22 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev libreadline8 librhash0 librocksdb-dev librocksdb5.17 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 libsnappy1v5 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libtsl-hopscotch-map-dev libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libx11-dev libxapian30 libxau-dev libxau6 libxaw7 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft2 libxml2 libxml2-dev libxmu6 libxpm4 libxrender-dev libxrender1 libxslt1-dev libxslt1.1 libxss1 libxt6 libyajl-dev libyajl2 littler m4 man-db mime-support opensp openssl pkg-config po-debconf procps protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pkg-resources python3-pygments python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rapidjson-dev raptor2-utils rasqal-utils readline-common rs samtools sbuild-build-depends-main-dummy sensible-utils sgml-base sgml-data ucf unzip uuid-dev x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev zip zlib1g-dev 0 upgraded, 342 newly installed, 0 to remove and 0 not upgraded. Need to get 227 MB of archives. After this operation, 1044 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1228 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 flex amd64 2.6.4-6.2 [456 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 gawk amd64 1:5.0.1+dfsg-1 [610 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-minimal amd64 3.8.3~rc1-1 [760 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 python3.8-minimal amd64 3.8.3~rc1-1 [1944 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-3 [84.1 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.3~rc1-1 [1667 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 python3.8 amd64 3.8.3~rc1-1 [415 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 sgml-base all 1.30 [15.1 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.2-1 [102 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-4 [62.7 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-4 [262 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-1 [775 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 bc amd64 1.07.1-2+b2 [109 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 bison amd64 2:3.5.3+dfsg-1 [967 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 bwa amd64 0.7.17-5 [220 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1g-1 [846 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.16.3-2 [1628 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libarchive13 amd64 3.4.0-2 [335 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6.1 [267 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-7 [64.4 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-7 [115 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-7 [366 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-7 [156 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.50+dfsg-1 [228 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.21.0-1 [55.1 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.68.0-1 [321 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.3.9-1 [123 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.35.0-2 [128 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.16.3-2 [3675 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 sgml-data all 2.0.11 [179 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 docbook all 4.5-6 [129 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libosp5 amd64 1.5.2-13+b1 [948 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 opensp amd64 1.5.2-13+b1 [449 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 docbook-to-man amd64 1:2.0.0-42+b1 [76.8 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 docbook-xml all 4.5-9 [84.4 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 docbook-xsl all 1.79.1+dfsg-2 [1249 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libllvm9 amd64 1:9.0.1-12 [15.0 MB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libclang1-9 amd64 1:9.0.1-12 [6713 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libxapian30 amd64 1.4.15-1 [1085 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 doxygen amd64 1.8.17-1 [9482 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libdw1 amd64 0.176-1.1 [235 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libasm1 amd64 0.176-1.1 [29.3 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 elfutils amd64 0.176-1.1 [280 kB] Get:98 http://127.0.0.1:12990/debian sid/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-1 [4264 B] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libfastahack0 amd64 1.0.0+dfsg-5 [23.8 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 fastahack amd64 1.0.0+dfsg-5 [12.2 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 libpng16-16 amd64 1.6.37-2 [292 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6 amd64 2.10.1-2 [392 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 fontconfig-config all 2.13.1-4 [281 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig1 amd64 2.13.1-4 [347 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 fontconfig amd64 2.13.1-4 [416 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 libann0 amd64 1.1.2+doc-7 [25.3 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 libcdt5 amd64 2.42.2-4 [60.7 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libcgraph6 amd64 2.42.2-4 [85.0 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:111 http://127.0.0.1:12990/debian sid/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:112 http://127.0.0.1:12990/debian sid/main amd64 libwebp6 amd64 0.6.1-2+b1 [261 kB] Get:113 http://127.0.0.1:12990/debian sid/main amd64 libtiff5 amd64 4.1.0+git191117-2 [271 kB] Get:114 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:115 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:116 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:117 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.6.9-2 [298 kB] Get:118 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.6.9-2 [759 kB] Get:119 http://127.0.0.1:12990/debian sid/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:120 http://127.0.0.1:12990/debian sid/main amd64 libgd3 amd64 2.3.0-1 [137 kB] Get:121 http://127.0.0.1:12990/debian sid/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4+b1 [158 kB] Get:122 http://127.0.0.1:12990/debian sid/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:123 http://127.0.0.1:12990/debian sid/main amd64 libxcb-render0 amd64 1.14-2 [111 kB] Get:124 http://127.0.0.1:12990/debian sid/main amd64 libxcb-shm0 amd64 1.14-2 [101 kB] Get:125 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:126 http://127.0.0.1:12990/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:127 http://127.0.0.1:12990/debian sid/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:128 http://127.0.0.1:12990/debian sid/main amd64 libltdl7 amd64 2.4.6-14 [390 kB] Get:129 http://127.0.0.1:12990/debian sid/main amd64 libfribidi0 amd64 1.0.8-2 [64.8 kB] Get:130 http://127.0.0.1:12990/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:131 http://127.0.0.1:12990/debian sid/main amd64 libharfbuzz0b amd64 2.6.4-1 [1360 kB] Get:132 http://127.0.0.1:12990/debian sid/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:133 http://127.0.0.1:12990/debian sid/main amd64 libdatrie1 amd64 0.2.12-3 [39.5 kB] Get:134 http://127.0.0.1:12990/debian sid/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:135 http://127.0.0.1:12990/debian sid/main amd64 libpango-1.0-0 amd64 1.44.7-4 [183 kB] Get:136 http://127.0.0.1:12990/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.44.7-4 [59.0 kB] Get:137 http://127.0.0.1:12990/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.44.7-4 [48.9 kB] Get:138 http://127.0.0.1:12990/debian sid/main amd64 libpathplan4 amd64 2.42.2-4 [63.9 kB] Get:139 http://127.0.0.1:12990/debian sid/main amd64 libgvc6 amd64 2.42.2-4 [691 kB] Get:140 http://127.0.0.1:12990/debian sid/main amd64 libgvpr2 amd64 2.42.2-4 [211 kB] Get:141 http://127.0.0.1:12990/debian sid/main amd64 liblab-gamut1 amd64 2.42.2-4 [221 kB] Get:142 http://127.0.0.1:12990/debian sid/main amd64 x11-common all 1:7.7+20 [252 kB] Get:143 http://127.0.0.1:12990/debian sid/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:144 http://127.0.0.1:12990/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:145 http://127.0.0.1:12990/debian sid/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:146 http://127.0.0.1:12990/debian sid/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:147 http://127.0.0.1:12990/debian sid/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:148 http://127.0.0.1:12990/debian sid/main amd64 graphviz amd64 2.42.2-4 [630 kB] Get:149 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get:150 http://127.0.0.1:12990/debian sid/main amd64 libxslt1.1 amd64 1.1.34-4 [239 kB] Get:151 http://127.0.0.1:12990/debian sid/main amd64 python3-lxml amd64 4.5.0-1.1 [1425 kB] Get:152 http://127.0.0.1:12990/debian sid/main amd64 python3-pkg-resources all 46.1.3-1 [183 kB] Get:153 http://127.0.0.1:12990/debian sid/main amd64 python3-pygments all 2.3.1+dfsg-3 [596 kB] Get:154 http://127.0.0.1:12990/debian sid/main amd64 xsltproc amd64 1.1.34-4 [124 kB] Get:155 http://127.0.0.1:12990/debian sid/main amd64 gtk-doc-tools all 1.32-4 [371 kB] Get:156 http://127.0.0.1:12990/debian sid/main amd64 help2man amd64 1.47.15 [181 kB] Get:157 http://127.0.0.1:12990/debian sid/main amd64 icu-devtools amd64 63.2-3 [189 kB] Get:158 http://127.0.0.1:12990/debian sid/main amd64 libonig5 amd64 6.9.5-2 [182 kB] Get:159 http://127.0.0.1:12990/debian sid/main amd64 libjq1 amd64 1.6-1 [133 kB] Get:160 http://127.0.0.1:12990/debian sid/main amd64 jq amd64 1.6-1 [63.4 kB] Get:161 http://127.0.0.1:12990/debian sid/main amd64 libbackward-cpp-dev all 1.5-1 [31.7 kB] Get:162 http://127.0.0.1:12990/debian sid/main amd64 libblas3 amd64 3.9.0-2 [153 kB] Get:163 http://127.0.0.1:12990/debian sid/main amd64 uuid-dev amd64 2.34-0.1 [93.5 kB] Get:164 http://127.0.0.1:12990/debian sid/main amd64 libblkid-dev amd64 2.34-0.1 [226 kB] Get:165 http://127.0.0.1:12990/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-17+b1 [8389 kB] Get:166 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67.0 amd64 1.67.0-17+b1 [356 kB] Get:167 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67-dev amd64 1.67.0-17+b1 [381 kB] Get:168 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options-dev amd64 1.67.0.2+b1 [4288 B] Get:169 http://127.0.0.1:12990/debian sid/main amd64 libbz2-dev amd64 1.0.8-2 [30.1 kB] Get:170 http://127.0.0.1:12990/debian sid/main amd64 libcairo-gobject2 amd64 1.16.0-4 [124 kB] Get:171 http://127.0.0.1:12990/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:172 http://127.0.0.1:12990/debian sid/main amd64 libcairo-script-interpreter2 amd64 1.16.0-4 [160 kB] Get:173 http://127.0.0.1:12990/debian sid/main amd64 libexpat1-dev amd64 2.2.9-1 [136 kB] Get:174 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:175 http://127.0.0.1:12990/debian sid/main amd64 libpng-dev amd64 1.6.37-2 [295 kB] Get:176 http://127.0.0.1:12990/debian sid/main amd64 libfreetype-dev amd64 2.10.1-2 [545 kB] Get:177 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6-dev amd64 2.10.1-2 [63.8 kB] Get:178 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig-dev amd64 2.13.1-4 [369 kB] Get:179 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig1-dev amd64 2.13.1-4 [238 kB] Get:180 http://127.0.0.1:12990/debian sid/main amd64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get:181 http://127.0.0.1:12990/debian sid/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get:182 http://127.0.0.1:12990/debian sid/main amd64 x11proto-core-dev all 2020.1-1 [3404 B] Get:183 http://127.0.0.1:12990/debian sid/main amd64 libxau-dev amd64 1:1.0.8-1+b2 [23.1 kB] Get:184 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:185 http://127.0.0.1:12990/debian sid/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:186 http://127.0.0.1:12990/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:187 http://127.0.0.1:12990/debian sid/main amd64 libxcb1-dev amd64 1.14-2 [176 kB] Get:188 http://127.0.0.1:12990/debian sid/main amd64 libx11-dev amd64 2:1.6.9-2 [830 kB] Get:189 http://127.0.0.1:12990/debian sid/main amd64 libxrender-dev amd64 1:0.9.10-1 [40.8 kB] Get:190 http://127.0.0.1:12990/debian sid/main amd64 x11proto-xext-dev all 2020.1-1 [3404 B] Get:191 http://127.0.0.1:12990/debian sid/main amd64 libxext-dev amd64 2:1.3.3-1+b2 [107 kB] Get:192 http://127.0.0.1:12990/debian sid/main amd64 libice-dev amd64 2:1.0.9-2 [66.8 kB] Get:193 http://127.0.0.1:12990/debian sid/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get:194 http://127.0.0.1:12990/debian sid/main amd64 libpixman-1-dev amd64 0.36.0-1 [554 kB] Get:195 http://127.0.0.1:12990/debian sid/main amd64 libxcb-render0-dev amd64 1.14-2 [114 kB] Get:196 http://127.0.0.1:12990/debian sid/main amd64 libxcb-shm0-dev amd64 1.14-2 [102 kB] Get:197 http://127.0.0.1:12990/debian sid/main amd64 libffi-dev amd64 3.3-4 [56.4 kB] Get:198 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-data all 2.64.2-1 [1158 kB] Get:199 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-bin amd64 2.64.2-1 [135 kB] Get:200 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.8.2-2 [78.4 kB] Get:201 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.8.2-2 [145 kB] Get:202 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-dev-bin amd64 2.64.2-1 [172 kB] Get:203 http://127.0.0.1:12990/debian sid/main amd64 libmount-dev amd64 2.34-0.1 [236 kB] Get:204 http://127.0.0.1:12990/debian sid/main amd64 libpcre16-3 amd64 2:8.39-12+b1 [259 kB] Get:205 http://127.0.0.1:12990/debian sid/main amd64 libpcre32-3 amd64 2:8.39-12+b1 [250 kB] Get:206 http://127.0.0.1:12990/debian sid/main amd64 libpcrecpp0v5 amd64 2:8.39-12+b1 [152 kB] Get:207 http://127.0.0.1:12990/debian sid/main amd64 libpcre3-dev amd64 2:8.39-12+b1 [653 kB] Get:208 http://127.0.0.1:12990/debian sid/main amd64 libsepol1-dev amd64 3.0-1 [336 kB] Get:209 http://127.0.0.1:12990/debian sid/main amd64 libpcre2-16-0 amd64 10.34-7 [219 kB] Get:210 http://127.0.0.1:12990/debian sid/main amd64 libpcre2-32-0 amd64 10.34-7 [208 kB] Get:211 http://127.0.0.1:12990/debian sid/main amd64 libpcre2-posix2 amd64 10.34-7 [45.2 kB] Get:212 http://127.0.0.1:12990/debian sid/main amd64 libpcre2-dev amd64 10.34-7 [709 kB] Get:213 http://127.0.0.1:12990/debian sid/main amd64 libselinux1-dev amd64 3.0-1+b3 [171 kB] Get:214 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-dev amd64 2.64.2-1 [1561 kB] Get:215 http://127.0.0.1:12990/debian sid/main amd64 libcairo2-dev amd64 1.16.0-4 [734 kB] Get:216 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB] Get:217 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1 [408 kB] Get:218 http://127.0.0.1:12990/debian sid/main amd64 libdeflate0 amd64 1.5-3 [55.8 kB] Get:219 http://127.0.0.1:12990/debian sid/main amd64 libdeflate-dev amd64 1.5-3 [46.0 kB] Get:220 http://127.0.0.1:12990/debian sid/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-1 [4212 B] Get:221 http://127.0.0.1:12990/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB] Get:222 http://127.0.0.1:12990/debian sid/main amd64 libdivsufsort-dev amd64 2.0.1-4 [27.4 kB] Get:223 http://127.0.0.1:12990/debian sid/main amd64 libelf-dev amd64 0.176-1.1 [72.1 kB] Get:224 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:225 http://127.0.0.1:12990/debian sid/main amd64 libdw-dev amd64 0.176-1.1 [218 kB] Get:226 http://127.0.0.1:12990/debian sid/main amd64 libfastahack-dev amd64 1.0.0+dfsg-5 [25.3 kB] Get:227 http://127.0.0.1:12990/debian sid/main amd64 libfml0 amd64 0.1-13 [70.8 kB] Get:228 http://127.0.0.1:12990/debian sid/main amd64 libfml-dev amd64 0.1-13 [82.1 kB] Get:229 http://127.0.0.1:12990/debian sid/main amd64 libgflags2.2 amd64 2.2.2-1+b1 [83.7 kB] Get:230 http://127.0.0.1:12990/debian sid/main amd64 libgfortran5 amd64 10-20200418-1 [727 kB] Get:231 http://127.0.0.1:12990/debian sid/main amd64 libgmpxx4ldbl amd64 2:6.2.0+dfsg-4 [23.0 kB] Get:232 http://127.0.0.1:12990/debian sid/main amd64 libgmp-dev amd64 2:6.2.0+dfsg-4 [643 kB] Get:233 http://127.0.0.1:12990/debian sid/main amd64 libhts3 amd64 1.10.2-3 [370 kB] Get:234 http://127.0.0.1:12990/debian sid/main amd64 libhts-dev amd64 1.10.2-3 [4846 kB] Get:235 http://127.0.0.1:12990/debian sid/main amd64 libicu-dev amd64 63.2-3 [9184 kB] Get:236 http://127.0.0.1:12990/debian sid/main amd64 libjansson4 amd64 2.12-1 [38.0 kB] Get:237 http://127.0.0.1:12990/debian sid/main amd64 libjansson-dev amd64 2.12-1 [40.5 kB] Get:238 http://127.0.0.1:12990/debian sid/main amd64 libjemalloc2 amd64 5.2.1-1 [259 kB] Get:239 http://127.0.0.1:12990/debian sid/main amd64 libjemalloc-dev amd64 5.2.1-1 [452 kB] Get:240 http://127.0.0.1:12990/debian sid/main amd64 liblapack3 amd64 3.9.0-2 [2169 kB] Get:241 http://127.0.0.1:12990/debian sid/main amd64 liblz4-dev amd64 1.9.2-2 [76.7 kB] Get:242 http://127.0.0.1:12990/debian sid/main amd64 libmhash2 amd64 0.9.9.9-8 [93.9 kB] Get:243 http://127.0.0.1:12990/debian sid/main amd64 libncurses-dev amd64 6.2-1 [337 kB] Get:244 http://127.0.0.1:12990/debian sid/main amd64 libncurses5-dev amd64 6.2-1 [932 B] Get:245 http://127.0.0.1:12990/debian sid/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:246 http://127.0.0.1:12990/debian sid/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:247 http://127.0.0.1:12990/debian sid/main amd64 libprotobuf22 amd64 3.11.4-4 [899 kB] Get:248 http://127.0.0.1:12990/debian sid/main amd64 libprotobuf-lite22 amd64 3.11.4-4 [237 kB] Get:249 http://127.0.0.1:12990/debian sid/main amd64 libprotobuf-dev amd64 3.11.4-4 [1243 kB] Get:250 http://127.0.0.1:12990/debian sid/main amd64 libprotoc22 amd64 3.11.4-4 [807 kB] Get:251 http://127.0.0.1:12990/debian sid/main amd64 libprotoc-dev amd64 3.11.4-4 [22.8 MB] Get:252 http://127.0.0.1:12990/debian sid/main amd64 libyajl2 amd64 2.1.0-3 [23.8 kB] Get:253 http://127.0.0.1:12990/debian sid/main amd64 libraptor2-0 amd64 2.0.14-1+b1 [167 kB] Get:254 http://127.0.0.1:12990/debian sid/main amd64 libxml2-dev amd64 2.9.10+dfsg-5 [806 kB] Get:255 http://127.0.0.1:12990/debian sid/main amd64 libxslt1-dev amd64 1.1.34-4 [329 kB] Get:256 http://127.0.0.1:12990/debian sid/main amd64 libyajl-dev amd64 2.1.0-3 [32.6 kB] Get:257 http://127.0.0.1:12990/debian sid/main amd64 libraptor2-dev amd64 2.0.14-1+b1 [208 kB] Get:258 http://127.0.0.1:12990/debian sid/main amd64 librasqal3 amd64 0.9.33-0.1 [192 kB] Get:259 http://127.0.0.1:12990/debian sid/main amd64 librasqal3-dev amd64 0.9.33-0.1 [228 kB] Get:260 http://127.0.0.1:12990/debian sid/main amd64 librdf0 amd64 1.0.17-1.1+b1 [110 kB] Get:261 http://127.0.0.1:12990/debian sid/main amd64 librdf0-dev amd64 1.0.17-1.1+b1 [242 kB] Get:262 http://127.0.0.1:12990/debian sid/main amd64 libsnappy1v5 amd64 1.1.8-1 [17.9 kB] Get:263 http://127.0.0.1:12990/debian sid/main amd64 librocksdb5.17 amd64 5.17.2-3 [1744 kB] Get:264 http://127.0.0.1:12990/debian sid/main amd64 librocksdb-dev amd64 5.17.2-3 [2752 kB] Get:265 http://127.0.0.1:12990/debian sid/main amd64 libsimde-dev all 0.0.0.git.20200424-1 [87.6 kB] Get:266 http://127.0.0.1:12990/debian sid/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-7 [36.0 kB] Get:267 http://127.0.0.1:12990/debian sid/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-7 [38.9 kB] Get:268 http://127.0.0.1:12990/debian sid/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:269 http://127.0.0.1:12990/debian sid/main amd64 libssw0 amd64 1.1-9 [19.2 kB] Get:270 http://127.0.0.1:12990/debian sid/main amd64 libssw-dev amd64 1.1-9 [22.0 kB] Get:271 http://127.0.0.1:12990/debian sid/main amd64 libtabixpp0 amd64 1.1.0-3 [8712 B] Get:272 http://127.0.0.1:12990/debian sid/main amd64 libtabixpp-dev amd64 1.1.0-3 [7824 B] Get:273 http://127.0.0.1:12990/debian sid/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [1007 kB] Get:274 http://127.0.0.1:12990/debian sid/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:275 http://127.0.0.1:12990/debian sid/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:276 http://127.0.0.1:12990/debian sid/main amd64 libtk8.6 amd64 8.6.10-1 [773 kB] Get:277 http://127.0.0.1:12990/debian sid/main amd64 libtsl-hopscotch-map-dev all 2.2.1-3 [35.1 kB] Get:278 http://127.0.0.1:12990/debian sid/main amd64 libvcflib1 amd64 1.0.1+dfsg-3 [152 kB] Get:279 http://127.0.0.1:12990/debian sid/main amd64 libvcflib-dev amd64 1.0.1+dfsg-3 [28.7 kB] Get:280 http://127.0.0.1:12990/debian sid/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:281 http://127.0.0.1:12990/debian sid/main amd64 unzip amd64 6.0-25 [172 kB] Get:282 http://127.0.0.1:12990/debian sid/main amd64 xdg-utils all 1.1.3-2 [74.6 kB] Get:283 http://127.0.0.1:12990/debian sid/main amd64 r-base-core amd64 3.6.3-2 [24.6 MB] Get:284 http://127.0.0.1:12990/debian sid/main amd64 r-cran-littler amd64 0.3.9-1 [312 kB] Get:285 http://127.0.0.1:12990/debian sid/main amd64 littler all 0.3.9-1 [14.6 kB] Get:286 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgkitten all 0.1.5-1 [23.8 kB] Get:287 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rcpp amd64 1.0.4.6-1 [1953 kB] Get:288 http://127.0.0.1:12990/debian sid/main amd64 r-cran-plyr amd64 1.8.6-1 [828 kB] Get:289 http://127.0.0.1:12990/debian sid/main amd64 r-cran-digest amd64 0.6.25-1 [180 kB] Get:290 http://127.0.0.1:12990/debian sid/main amd64 r-cran-glue amd64 1.4.0-1 [141 kB] Get:291 http://127.0.0.1:12990/debian sid/main amd64 r-cran-gtable all 0.3.0+dfsg-1 [164 kB] Get:292 http://127.0.0.1:12990/debian sid/main amd64 r-cran-assertthat all 0.2.1-1 [56.7 kB] Get:293 http://127.0.0.1:12990/debian sid/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:294 http://127.0.0.1:12990/debian sid/main amd64 r-cran-fansi amd64 0.4.1-1 [346 kB] Get:295 http://127.0.0.1:12990/debian sid/main amd64 r-cran-cli all 2.0.2-1 [393 kB] Get:296 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rlang amd64 0.4.5-2 [1121 kB] Get:297 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ellipsis amd64 0.3.0-1 [30.4 kB] Get:298 http://127.0.0.1:12990/debian sid/main amd64 r-cran-evaluate all 0.14-1 [81.2 kB] Get:299 http://127.0.0.1:12990/debian sid/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:300 http://127.0.0.1:12990/debian sid/main amd64 r-cran-r6 all 2.4.1-1 [79.4 kB] Get:301 http://127.0.0.1:12990/debian sid/main amd64 r-cran-backports amd64 1.1.6-1 [67.0 kB] Get:302 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rprojroot all 1.3-2-2 [96.9 kB] Get:303 http://127.0.0.1:12990/debian sid/main amd64 r-cran-desc all 1.2.0-2 [290 kB] Get:304 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ps amd64 1.3.2-2 [213 kB] Get:305 http://127.0.0.1:12990/debian sid/main amd64 r-cran-processx amd64 3.4.2-1 [270 kB] Get:306 http://127.0.0.1:12990/debian sid/main amd64 r-cran-callr all 3.4.3-1 [387 kB] Get:307 http://127.0.0.1:12990/debian sid/main amd64 r-cran-prettyunits all 1.1.1-1 [39.6 kB] Get:308 http://127.0.0.1:12990/debian sid/main amd64 r-cran-withr all 2.2.0-1 [210 kB] Get:309 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgbuild all 1.0.7-1 [141 kB] Get:310 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rstudioapi all 0.11-1 [252 kB] Get:311 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgload amd64 1.0.2-1 [160 kB] Get:312 http://127.0.0.1:12990/debian sid/main amd64 r-cran-praise all 1.0.0-3 [19.7 kB] Get:313 http://127.0.0.1:12990/debian sid/main amd64 r-cran-testthat amd64 2.3.2-1 [1091 kB] Get:314 http://127.0.0.1:12990/debian sid/main amd64 r-cran-isoband amd64 0.2.1-1 [2491 kB] Get:315 http://127.0.0.1:12990/debian sid/main amd64 r-cran-mass amd64 7.3-51.6-1 [1117 kB] Get:316 http://127.0.0.1:12990/debian sid/main amd64 r-cran-lattice amd64 0.20-41-1 [1168 kB] Get:317 http://127.0.0.1:12990/debian sid/main amd64 r-cran-nlme amd64 3.1.147-1 [2221 kB] Get:318 http://127.0.0.1:12990/debian sid/main amd64 r-cran-matrix amd64 1.2-18-1 [3500 kB] Get:319 http://127.0.0.1:12990/debian sid/main amd64 r-cran-mgcv amd64 1.8-31-1 [2778 kB] Get:320 http://127.0.0.1:12990/debian sid/main amd64 r-cran-farver amd64 2.0.3-1 [1395 kB] Get:321 http://127.0.0.1:12990/debian sid/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:322 http://127.0.0.1:12990/debian sid/main amd64 r-cran-colorspace amd64 1.4-1+dfsg-1 [1587 kB] Get:323 http://127.0.0.1:12990/debian sid/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:324 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:325 http://127.0.0.1:12990/debian sid/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:326 http://127.0.0.1:12990/debian sid/main amd64 r-cran-lifecycle all 0.2.0-1 [93.2 kB] Get:327 http://127.0.0.1:12990/debian sid/main amd64 r-cran-scales all 1.1.0-1 [553 kB] Get:328 http://127.0.0.1:12990/debian sid/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:329 http://127.0.0.1:12990/debian sid/main amd64 r-cran-vctrs amd64 0.2.4-1 [895 kB] Get:330 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pillar all 1.4.3-1 [228 kB] Get:331 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-1 [19.7 kB] Get:332 http://127.0.0.1:12990/debian sid/main amd64 r-cran-tibble amd64 3.0.1-1 [424 kB] Get:333 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ggplot2 all 3.3.0+dfsg-1 [3090 kB] Get:334 http://127.0.0.1:12990/debian sid/main amd64 r-cran-gridbase all 0.4-7-4 [170 kB] Get:335 http://127.0.0.1:12990/debian sid/main amd64 libvcflib-tools amd64 1.0.1+dfsg-3 [637 kB] Get:336 http://127.0.0.1:12990/debian sid/main amd64 protobuf-compiler amd64 3.11.4-4 [72.5 kB] Get:337 http://127.0.0.1:12990/debian sid/main amd64 pv amd64 1.6.6-1+b1 [49.5 kB] Get:338 http://127.0.0.1:12990/debian sid/main amd64 rapidjson-dev all 1.1.0+dfsg2-5 [98.7 kB] Get:339 http://127.0.0.1:12990/debian sid/main amd64 raptor2-utils amd64 2.0.14-1+b1 [35.6 kB] Get:340 http://127.0.0.1:12990/debian sid/main amd64 rasqal-utils amd64 0.9.33-0.1 [45.4 kB] Get:341 http://127.0.0.1:12990/debian sid/main amd64 rs amd64 20200313-1 [15.5 kB] Get:342 http://127.0.0.1:12990/debian sid/main amd64 samtools amd64 1.10-3 [523 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 227 MB in 2s (108 MB/s) Selecting previously unselected package bsdmainutils. 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Setting up libboost1.67-dev:amd64 (1.67.0-17+b1) ... Setting up libboost-program-options1.67.0:amd64 (1.67.0-17+b1) ... Setting up libpcrecpp0v5:amd64 (2:8.39-12+b1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up libsimde-dev (0.0.0.git.20200424-1) ... Setting up libdisorder0:amd64 (0.0.2+git20130809.8062ee1-1) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up libxapian30:amd64 (1.4.15-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libpsl5:amd64 (0.21.0-1) ... Setting up libxcb1:amd64 (1.14-2) ... Setting up libpixman-1-dev:amd64 (0.36.0-1) ... Setting up mime-support (3.64) ... Setting up libpcre16-3:amd64 (2:8.39-12+b1) ... Setting up libdatrie1:amd64 (0.2.12-3) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up gawk (1:5.0.1+dfsg-1) ... Setting up libxcb-render0:amd64 (1.14-2) ... 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Setting up docbook-to-man (1:2.0.0-42+b1) ... Setting up gtk-doc-tools (1.32-4) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200418-1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 bc_1.07.1-2+b2 binutils_2.34-6 binutils-common_2.34-6 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Crusoe Homepage: https://github.com/vgteam/vg#vg Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/vg Vcs-Git: https://salsa.debian.org/med-team/vg.git Testsuite: autopkgtest Testsuite-Triggers: libvcflib-tools Build-Depends: debhelper-compat (= 12), pv , bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa , protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools , unzip, librdf-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils , rasqal-utils , bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, librocksdb-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack , libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools , libhts-dev, help2man , python3:any, libsimde-dev Build-Depends-Indep: doxygen , graphviz Package-List: vg deb science optional arch=any vg-docs deb doc optional arch=all Checksums-Sha1: efbfd87a1af0062d53134c340dece51a20f27093 88323764 vg_1.23.0+ds.orig.tar.xz df84623d3879612b23374748a2454ce274fcab80 42636 vg_1.23.0+ds-2.debian.tar.xz Checksums-Sha256: 318c11871d93ea0e62e466f06a0ab825d41a8233c439c8a6f836f7a773277026 88323764 vg_1.23.0+ds.orig.tar.xz cb639d1e811fa79a448594af36c46e559818d42c3efbbc56a897a9e976cced71 42636 vg_1.23.0+ds-2.debian.tar.xz Files: 1a35f53ff30a3fd969f543f7ea1ef37e 88323764 vg_1.23.0+ds.orig.tar.xz b8c4b230638a13cd06aa6d742c0d815e 42636 vg_1.23.0+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl6dd/8ACgkQPCZ2P2xn 5uJdThAAy7fqw6W+7uA5t7PO6xmJZc6uA7uWgap3Q8ssenEsCFUi4fZJ6C2qlFUh 4d02Yaji25EiqXB/lUcxLh24j+3u6ooHPJCeCGJlBkX6GQ+F+9dPM56e/wQaRN+M uogtZElFkY9kHIQikork6TAu75QOZDlJusc+kZpxPBdm2mZHHXUvqqrz4+13z3BA LEKRRaZSpMpz45ByeNxQ78lzdxRLmDIxrSjq/O4TYXA2IYcpeWcFNKDiwt/98+cu ixLowZEcvj9sod5UtFnOCMUo/lOdwiy+arNDibiy+osfB1LAEQNzsmYjlSg8lIJ5 /5Ks65yICaEvKjXOJ2kZl20vQ1ucE29yrTfE9Oar40+1GLp7HCZb7acB0FijY48V m0N16IuAi/KcHXwj/2BD8+oUa3M5cmlVuc0cX9xsKw6+mzvVjLbgdynzpdcKNJcA mCFbklTTXNy18PGmr6J8YlPZ7Dtet2nSwRlJWiCsoI/JV7CAfKmPZUHvhj/FG6As CVET3ZHkqErnl2EMbn2fKOWZ4vsh/IOwMGuhNTvewFnOIea4lFaUAO33vnif14yA j65ZmqkrYiqeaUXKdgnAHVWNCFNWX1xfL5WpghljManiodcFqstcZJeEG/BXIalE vj+IWbI0UkRjxZCt2/eM0sxv/q+4ib94iBMWG1Rnts43G/UJu5M= =5kfN -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Apr 20 10:22:55 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./vg_1.23.0+ds-2.dsc dpkg-source: info: extracting vg in /<> dpkg-source: info: unpacking vg_1.23.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.23.0+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_boost dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_rocksdb dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-6efd42d2-1dfe-43d7-9095-3d2c1b83312e SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.23.0+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' mv include/vg_git_version.hpp debian/ rm -Rf include/* mv debian/vg_git_version.hpp include/ dh_auto_clean || true make -j4 clean make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/C' make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean cd quicktree_1.1 && make clean rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/<>/deps/gcsa2' make[2]: *** [Makefile:608: clean] Error 2 make[2]: Leaving directory '/<>' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' dh_autoreconf --sourcedirectory=/<>/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/<>' dh_auto_configure debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>' mkdir -p /<>/debian/help mkdir -p /<>/debian/vg/usr mkdir -p /<>/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ export CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/<>/deps/gcsa2' make[2]: *** [Makefile:608: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib make[3]: Entering directory '/<>/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/<>' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] -- The C compiler identification is Clang 10.0.0 -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The CXX compiler identification is Clang 10.0.0 -- Check for working C compiler: /usr/bin/gcc -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done 2 warnings generated. -- Check for working C compiler: /usr/bin/gcc gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Detecting CXX compiler ABI info - done gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks -- Detecting C compiler ABI info - done make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_objs -- Detecting C compile features make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build -- Detecting C compile features - done make[5]: Entering directory '/<>/deps/libhandlegraph' -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c:393:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success 9 warnings generated. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' make[5]: Leaving directory '/<>/deps/libhandlegraph' error: invalid argument '-std=c++14' not allowed with 'C' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= error: invalid argument '-std=c++14' not allowed with 'C' Scanning dependencies of target handlegraph_static make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake error: invalid argument '-std=c++14' not allowed with 'C' /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 -- Looking for C++ include cstdio - found /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o error: invalid argument '-std=c++14' not allowed with 'C' /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= error: invalid argument '-std=c++14' not allowed with 'C' Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot make[5]: Entering directory '/<>/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so error: invalid argument '-std=c++14' not allowed with 'C' /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' make[5]: Leaving directory '/<>/deps/libhandlegraph' error: invalid argument '-std=c++14' not allowed with 'C' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ error: invalid argument '-std=c++14' not allowed with 'C' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* -- Configuring done make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o error: invalid argument '-std=c++14' not allowed with 'C' clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o error: invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/include/sdsl/bit_vector_il.hpp -- 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/<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend lcp.o build_gcsa.o algorithms.o utils.o files.o support.o gcsa_format.o dbg.o try_extend.o gcsa.o convert_graph.o path_graph.o internal.o libgcsa2.a make[3]: Leaving directory '/<>/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/<>/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o build_gbwt.o bwtmerge.o utils.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/<>/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/<>/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/<>/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/<>/deps/progress_bar' make[3]: Leaving directory '/<>/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/sbuild-nonexistent/lib' and '/sbuild-nonexistent/include' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -P /<>/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/<>/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/<>/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/<>/include/sdsl/bit_vectors.hpp" - found -- Looking for "/<>/include/sdsl/bits.hpp" - found -- Looking for "/<>/include/sdsl/bp_support.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_g.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/coder.hpp" - found -- Looking for "/<>/include/sdsl/coder_comma.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/<>/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/<>/include/sdsl/config.hpp" - found -- Looking for "/<>/include/sdsl/construct.hpp" - found -- Looking for "/<>/include/sdsl/construct_bwt.hpp" - found -- Looking for "/<>/include/sdsl/construct_config.hpp" - found -- Looking for "/<>/include/sdsl/construct_isa.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/<>/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/csa_sada.hpp" - found -- Looking for "/<>/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_wt.hpp" - found -- Looking for "/<>/include/sdsl/cst_fully.hpp" - found -- Looking for "/<>/include/sdsl/cst_iterators.hpp" - found -- Looking for "/<>/include/sdsl/cst_sada.hpp" - found -- Looking for "/<>/include/sdsl/cst_sct3.hpp" - found -- Looking for "/<>/include/sdsl/dac_vector.hpp" - found -- Looking for "/<>/include/sdsl/enc_vector.hpp" - found -- Looking for "/<>/include/sdsl/fast_cache.hpp" - found -- Looking for "/<>/include/sdsl/hyb_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/<>/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/<>/include/sdsl/io.hpp" - found -- Looking for "/<>/include/sdsl/iterators.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/lcp.hpp" - found -- Looking for "/<>/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/lcp_byte.hpp" - found -- Looking for "/<>/include/sdsl/lcp_dac.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/<>/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/<>/include/sdsl/lcp_wt.hpp" - found -- Looking for "/<>/include/sdsl/louds_tree.hpp" - found -- Looking for "/<>/include/sdsl/memory_management.hpp" - found -- Looking for "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/<>/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/<>/include/sdsl/qsufsort.hpp" - found -- Looking for "/<>/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/<>/include/sdsl/ram_fs.hpp" - found -- Looking for "/<>/include/sdsl/rank_support.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/<>/include/sdsl/raster_img.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/<>/include/sdsl/rrr_helper.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/<>/include/sdsl/sd_vector.hpp" - found -- Looking for "/<>/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/<>/include/sdsl/select_support.hpp" - found -- Looking for "/<>/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/<>/include/sdsl/select_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/sfstream.hpp" - found -- Looking for "/<>/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/<>/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/structure_tree.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_trees.hpp" - found -- Looking for "/<>/include/sdsl/uint128_t.hpp" - found -- Looking for "/<>/include/sdsl/uint256_t.hpp" - found -- Looking for "/<>/include/sdsl/uintx_t.hpp" - found -- Looking for "/<>/include/sdsl/util.hpp" - found -- Looking for "/<>/include/sdsl/vectors.hpp" - found -- Looking for "/<>/include/sdsl/vlc_vector.hpp" - found -- Looking for "/<>/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/<>/include/sdsl/wm_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/wt_ap.hpp" - found -- Looking for "/<>/include/sdsl/wt_blcd.hpp" - found -- Looking for "/<>/include/sdsl/wt_gmr.hpp" - found -- Looking for "/<>/include/sdsl/wt_helper.hpp" - found -- Looking for "/<>/include/sdsl/wt_huff.hpp" - found -- Looking for "/<>/include/sdsl/wt_hutu.hpp" - found -- Looking for "/<>/include/sdsl/wt_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_pc.hpp" - found -- Looking for "/<>/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/<>/lib/libsdsl.a" - not found -- Uninstalling "/<>/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/<>/include/sdsl/bit_vectors.hpp" -- Uninstalling "/<>/include/sdsl/bits.hpp" -- Uninstalling "/<>/include/sdsl/bp_support.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_g.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/coder.hpp" -- Uninstalling "/<>/include/sdsl/coder_comma.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/<>/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/<>/include/sdsl/config.hpp" -- Uninstalling "/<>/include/sdsl/construct.hpp" -- Uninstalling "/<>/include/sdsl/construct_bwt.hpp" -- Uninstalling "/<>/include/sdsl/construct_config.hpp" -- Uninstalling "/<>/include/sdsl/construct_isa.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/<>/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/csa_sada.hpp" -- Uninstalling "/<>/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_wt.hpp" -- Uninstalling "/<>/include/sdsl/cst_fully.hpp" -- Uninstalling "/<>/include/sdsl/cst_iterators.hpp" -- Uninstalling "/<>/include/sdsl/cst_sada.hpp" -- Uninstalling "/<>/include/sdsl/cst_sct3.hpp" -- Uninstalling "/<>/include/sdsl/dac_vector.hpp" -- Uninstalling "/<>/include/sdsl/enc_vector.hpp" -- Uninstalling "/<>/include/sdsl/fast_cache.hpp" -- Uninstalling "/<>/include/sdsl/hyb_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/<>/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/<>/include/sdsl/io.hpp" -- Uninstalling "/<>/include/sdsl/iterators.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/lcp.hpp" -- Uninstalling "/<>/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/lcp_byte.hpp" -- Uninstalling "/<>/include/sdsl/lcp_dac.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/<>/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/<>/include/sdsl/lcp_wt.hpp" -- Uninstalling "/<>/include/sdsl/louds_tree.hpp" -- Uninstalling "/<>/include/sdsl/memory_management.hpp" -- Uninstalling "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/<>/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/<>/include/sdsl/qsufsort.hpp" -- Uninstalling "/<>/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/<>/include/sdsl/ram_fs.hpp" -- Uninstalling "/<>/include/sdsl/rank_support.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/<>/include/sdsl/raster_img.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/<>/include/sdsl/rrr_helper.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/<>/include/sdsl/sd_vector.hpp" -- Uninstalling "/<>/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/<>/include/sdsl/select_support.hpp" -- Uninstalling "/<>/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/<>/include/sdsl/select_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/sfstream.hpp" -- Uninstalling "/<>/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/<>/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/structure_tree.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_trees.hpp" -- Uninstalling "/<>/include/sdsl/uint128_t.hpp" -- Uninstalling "/<>/include/sdsl/uint256_t.hpp" -- Uninstalling "/<>/include/sdsl/uintx_t.hpp" -- Uninstalling "/<>/include/sdsl/util.hpp" -- Uninstalling "/<>/include/sdsl/vectors.hpp" -- Uninstalling "/<>/include/sdsl/vlc_vector.hpp" -- Uninstalling "/<>/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/<>/include/sdsl/wm_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/wt_ap.hpp" -- Uninstalling "/<>/include/sdsl/wt_blcd.hpp" -- Uninstalling "/<>/include/sdsl/wt_gmr.hpp" -- Uninstalling "/<>/include/sdsl/wt_helper.hpp" -- Uninstalling "/<>/include/sdsl/wt_huff.hpp" -- Uninstalling "/<>/include/sdsl/wt_hutu.hpp" -- Uninstalling "/<>/include/sdsl/wt_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_pc.hpp" -- Uninstalling "/<>/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/<>/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/<>/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/<>/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/<>/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/<>/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/<>/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/<>/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/<>/deps/vowpal_wabbit' cd vowpalwabbit && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/vowpalwabbit' echo \#define PACKAGE_VERSION \"`grep AC_INIT ../configure.ac | cut -d '[' -f 3 | cut -d ']' -f 1`\" > config.h /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM classweight.cc > classweight.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM baseline.cc > baseline.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example_json.cc > parse_example_json.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM OjaNewton.cc > OjaNewton.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore_adf.cc > cb_explore_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM action_score.cc > action_score.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore.cc > cb_explore.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gen_cs_example.cc > gen_cs_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM audit_regressor.cc > audit_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_validate.cc > vw_validate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_exception.cc > vw_exception.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interactions.cc > interactions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM comp_io.cc > comp_io.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interact.cc > interact.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrqfa.cc > lrqfa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM svrg.cc > svrg.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ftrl.cc > ftrl.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM best_constant.cc > best_constant.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM kernel_svm.cc > kernel_svm.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cs_active.cc > cs_active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active_cover.cc > active_cover.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active.cc > active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM recall_tree.cc > recall_tree.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM log_multi.cc > log_multi.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM stagewise_poly.cc > stagewise_poly.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM topk.cc > topk.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM explore_eval.cc > explore_eval.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cbify.cc > cbify.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bs.cc > bs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM confidence.cc > confidence.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM nn.cc > nn.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM sender.cc > sender.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM loss_functions.cc > loss_functions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser.cc > parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM example.cc > example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM print.cc > print.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM noop.cc > noop.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bfgs.cc > bfgs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mf.cc > mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd_mf.cc > gd_mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lda_core.cc > lda_core.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mwt.cc > mwt.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM learner.cc > learner.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd.cc > gd.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM accumulate.cc > accumulate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_args.cc > parse_args.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM network.cc > network.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM scorer.cc > scorer.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example.cc > parse_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_graph.cc > search_graph.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_entityrelationtask.cc > search_entityrelationtask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_multiclasstask.cc > search_multiclasstask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_hooktask.cc > search_hooktask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_dep_parser.cc > search_dep_parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_sequencetask.cc > search_sequencetask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_meta.cc > search_meta.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search.cc > search.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_algs.cc > cb_algs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_adf.cc > cb_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb.cc > cb.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM csoaa.cc > csoaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM label_dictionary.cc > label_dictionary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel.cc > multilabel.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cost_sensitive.cc > cost_sensitive.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrq.cc > lrq.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM binary.cc > binary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM autolink.cc > autolink.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM marginal.cc > marginal.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ect.cc > ect.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM boosting.cc > boosting.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel_oaa.cc > multilabel_oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM oaa.cc > oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multiclass.cc > multiclass.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM simple_label.cc > simple_label.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM rand48.cc > rand48.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cache.cc > cache.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM unique_sort.cc > unique_sort.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_primitives.cc > parse_primitives.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_regressor.cc > parse_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM io_buf.cc > io_buf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM global_data.cc > global_data.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser_helper.cc > parser_helper.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM hash.cc > hash.d rm -f *.o *.d vw active_interactor *~ vw.1 libvw.a liballreduce.a make[4]: Leaving directory '/<>/deps/vowpal_wabbit/vowpalwabbit' cd cluster && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/cluster' rm -f *.o vw active_interactor *~ vw.1 make[4]: Leaving directory '/<>/deps/vowpal_wabbit/cluster' cd library && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/library' rm -f *.o ezexample_predict ezexample_train library_example test_search recommend ezexample_predict_threaded make[4]: Leaving directory '/<>/deps/vowpal_wabbit/library' cd python && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/python' rm -f *.o pylibvw.so make[4]: Leaving directory '/<>/deps/vowpal_wabbit/python' cd java && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/java' rm -f target/libvw_jni.so rm -f src/main/c++/vowpalWabbit_learner_VWScalarLearner.o src/main/c++/vowpalWabbit_learner_VWScalarsLearner.o src/main/c++/vowpalWabbit_VW.o src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.o src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.o src/main/c++/vowpalWabbit_learner_VWLearners.o src/main/c++/jni_base_learner.o src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.o src/main/c++/vowpalWabbit_learner_VWProbLearner.o src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.o make[4]: Leaving directory '/<>/deps/vowpal_wabbit/java' make[3]: Leaving directory '/<>/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make[4]: Leaving directory '/<>/deps/libhandlegraph' make[3]: Leaving directory '/<>/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/<>/deps/libvgio' make[3]: *** No rule to make target 'clean'. Stop. make[3]: Leaving directory '/<>/deps/libvgio' make[2]: *** [Makefile:620: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib make[3]: Entering directory '/<>/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all Library will be installed in '/<>' make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] -- Configuring done -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc 2 warnings generated. gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o ./src/tree.c:393:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ make[5]: Leaving directory '/<>/deps/libhandlegraph' -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] 9 warnings generated. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Looking for C++ include cstdio - found error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Configuring done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 sdsl error: invalid argument '-std=c++14' not allowed with 'C' make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 error: invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o 1 warning generated. cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/include/sdsl/bit_vector_il.hpp -- Installing: /<>/include/sdsl/bit_vectors.hpp -- Installing: /<>/include/sdsl/bits.hpp -- Installing: /<>/include/sdsl/bp_support.hpp -- Installing: /<>/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/include/sdsl/bp_support_g.hpp -- Installing: /<>/include/sdsl/bp_support_gg.hpp -- Installing: /<>/include/sdsl/bp_support_sada.hpp -- Installing: /<>/include/sdsl/coder.hpp -- Installing: /<>/include/sdsl/coder_comma.hpp -- Installing: /<>/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/include/sdsl/coder_elias_gamma.hpp -- Installing: /<>/include/sdsl/coder_fibonacci.hpp -- Installing: /<>/include/sdsl/config.hpp -- Installing: /<>/include/sdsl/construct.hpp -- Installing: /<>/include/sdsl/construct_bwt.hpp -- Installing: /<>/include/sdsl/construct_config.hpp -- Installing: /<>/include/sdsl/construct_isa.hpp -- Installing: /<>/include/sdsl/construct_lcp.hpp -- Installing: /<>/include/sdsl/construct_lcp_helper.hpp -- Installing: /<>/include/sdsl/construct_sa.hpp -- Installing: /<>/include/sdsl/construct_sa_se.hpp -- Installing: /<>/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /<>/include/sdsl/csa_bitcompressed.hpp -- Installing: /<>/include/sdsl/csa_sada.hpp -- Installing: /<>/include/sdsl/csa_sampling_strategy.hpp -- Installing: /<>/include/sdsl/csa_wt.hpp -- Installing: /<>/include/sdsl/cst_fully.hpp -- Installing: /<>/include/sdsl/cst_iterators.hpp -- Installing: /<>/include/sdsl/cst_sada.hpp -- Installing: /<>/include/sdsl/cst_sct3.hpp -- Installing: /<>/include/sdsl/dac_vector.hpp -- Installing: /<>/include/sdsl/enc_vector.hpp -- Installing: /<>/include/sdsl/fast_cache.hpp -- Installing: /<>/include/sdsl/hyb_vector.hpp -- Installing: /<>/include/sdsl/int_vector.hpp -- Installing: /<>/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/include/sdsl/inv_perm_support.hpp -- Installing: /<>/include/sdsl/io.hpp -- Installing: /<>/include/sdsl/iterators.hpp -- Installing: /<>/include/sdsl/k2_treap.hpp -- Installing: /<>/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/include/sdsl/k2_tree.hpp -- Installing: /<>/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/include/sdsl/lcp.hpp -- Installing: /<>/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/include/sdsl/lcp_byte.hpp -- Installing: /<>/include/sdsl/lcp_dac.hpp -- Installing: /<>/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/include/sdsl/lcp_vlc.hpp -- Installing: /<>/include/sdsl/lcp_wt.hpp -- Installing: /<>/include/sdsl/louds_tree.hpp -- Installing: /<>/include/sdsl/memory_management.hpp -- Installing: /<>/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/include/sdsl/qsufsort.hpp -- Installing: /<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend lcp.o build_gcsa.o algorithms.o utils.o files.o support.o gcsa_format.o dbg.o try_extend.o gcsa.o convert_graph.o path_graph.o internal.o libgcsa2.a make[3]: Leaving directory '/<>/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/<>/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o build_gbwt.o bwtmerge.o utils.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/<>/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/<>/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/<>/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/<>/deps/progress_bar' make[3]: Leaving directory '/<>/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/sbuild-nonexistent/lib' and '/sbuild-nonexistent/include' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -P /<>/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/<>/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/<>/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/<>/include/sdsl/bit_vectors.hpp" - found -- Looking for "/<>/include/sdsl/bits.hpp" - found -- Looking for "/<>/include/sdsl/bp_support.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_g.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/coder.hpp" - found -- Looking for "/<>/include/sdsl/coder_comma.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/<>/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/<>/include/sdsl/config.hpp" - found -- Looking for "/<>/include/sdsl/construct.hpp" - found -- Looking for "/<>/include/sdsl/construct_bwt.hpp" - found -- Looking for "/<>/include/sdsl/construct_config.hpp" - found -- 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"/<>/include/sdsl/fast_cache.hpp" - found -- Looking for "/<>/include/sdsl/hyb_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/<>/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/<>/include/sdsl/io.hpp" - found -- Looking for "/<>/include/sdsl/iterators.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/lcp.hpp" - found -- Looking for "/<>/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/lcp_byte.hpp" - found -- Looking for "/<>/include/sdsl/lcp_dac.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/<>/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/<>/include/sdsl/lcp_wt.hpp" - found -- Looking for "/<>/include/sdsl/louds_tree.hpp" - found -- Looking for "/<>/include/sdsl/memory_management.hpp" - found -- Looking for "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/<>/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/<>/include/sdsl/qsufsort.hpp" - found -- Looking for "/<>/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/<>/include/sdsl/ram_fs.hpp" - found -- Looking for "/<>/include/sdsl/rank_support.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/<>/include/sdsl/raster_img.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/<>/include/sdsl/rrr_helper.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/<>/include/sdsl/sd_vector.hpp" - found -- Looking for "/<>/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/<>/include/sdsl/select_support.hpp" - found -- Looking for "/<>/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/<>/include/sdsl/select_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/sfstream.hpp" - found -- Looking for "/<>/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/<>/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/structure_tree.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_trees.hpp" - found -- Looking for "/<>/include/sdsl/uint128_t.hpp" - found -- Looking for "/<>/include/sdsl/uint256_t.hpp" - found -- Looking for "/<>/include/sdsl/uintx_t.hpp" - found -- Looking for "/<>/include/sdsl/util.hpp" - found -- Looking for "/<>/include/sdsl/vectors.hpp" - found -- Looking for "/<>/include/sdsl/vlc_vector.hpp" - found -- Looking for "/<>/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/<>/include/sdsl/wm_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/wt_ap.hpp" - found -- Looking for "/<>/include/sdsl/wt_blcd.hpp" - found -- Looking for "/<>/include/sdsl/wt_gmr.hpp" - found -- Looking for "/<>/include/sdsl/wt_helper.hpp" - found -- Looking for "/<>/include/sdsl/wt_huff.hpp" - found -- Looking for "/<>/include/sdsl/wt_hutu.hpp" - found -- Looking for "/<>/include/sdsl/wt_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_pc.hpp" - found -- Looking for "/<>/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/<>/lib/libsdsl.a" - not found -- Uninstalling "/<>/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/<>/include/sdsl/bit_vectors.hpp" -- Uninstalling "/<>/include/sdsl/bits.hpp" -- Uninstalling "/<>/include/sdsl/bp_support.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_g.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_gg.hpp" -- 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"/<>/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_wt.hpp" -- Uninstalling "/<>/include/sdsl/cst_fully.hpp" -- Uninstalling "/<>/include/sdsl/cst_iterators.hpp" -- Uninstalling "/<>/include/sdsl/cst_sada.hpp" -- Uninstalling "/<>/include/sdsl/cst_sct3.hpp" -- Uninstalling "/<>/include/sdsl/dac_vector.hpp" -- Uninstalling "/<>/include/sdsl/enc_vector.hpp" -- Uninstalling "/<>/include/sdsl/fast_cache.hpp" -- Uninstalling "/<>/include/sdsl/hyb_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/<>/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/<>/include/sdsl/io.hpp" -- Uninstalling "/<>/include/sdsl/iterators.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling 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"/<>/include/sdsl/rank_support.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/<>/include/sdsl/raster_img.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/<>/include/sdsl/rrr_helper.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/<>/include/sdsl/sd_vector.hpp" -- Uninstalling "/<>/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/<>/include/sdsl/select_support.hpp" -- Uninstalling "/<>/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/<>/include/sdsl/select_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/sfstream.hpp" -- Uninstalling "/<>/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/<>/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/structure_tree.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_trees.hpp" -- Uninstalling "/<>/include/sdsl/uint128_t.hpp" -- Uninstalling "/<>/include/sdsl/uint256_t.hpp" -- Uninstalling "/<>/include/sdsl/uintx_t.hpp" -- Uninstalling "/<>/include/sdsl/util.hpp" -- Uninstalling "/<>/include/sdsl/vectors.hpp" -- Uninstalling "/<>/include/sdsl/vlc_vector.hpp" -- Uninstalling "/<>/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/<>/include/sdsl/wm_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/wt_ap.hpp" -- Uninstalling "/<>/include/sdsl/wt_blcd.hpp" -- Uninstalling "/<>/include/sdsl/wt_gmr.hpp" -- Uninstalling "/<>/include/sdsl/wt_helper.hpp" -- Uninstalling "/<>/include/sdsl/wt_huff.hpp" -- Uninstalling "/<>/include/sdsl/wt_hutu.hpp" -- Uninstalling "/<>/include/sdsl/wt_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_pc.hpp" -- Uninstalling "/<>/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/<>/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/<>/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/<>/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/<>/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/<>/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/<>/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/<>/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/<>/deps/vowpal_wabbit' cd vowpalwabbit && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/vowpalwabbit' /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM classweight.cc > classweight.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM baseline.cc > baseline.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example_json.cc > parse_example_json.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM OjaNewton.cc > OjaNewton.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore_adf.cc > cb_explore_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM action_score.cc > action_score.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore.cc > cb_explore.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gen_cs_example.cc > gen_cs_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM audit_regressor.cc > audit_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_validate.cc > vw_validate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_exception.cc > vw_exception.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interactions.cc > interactions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM comp_io.cc > comp_io.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interact.cc > interact.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrqfa.cc > lrqfa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM svrg.cc > svrg.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ftrl.cc > ftrl.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM best_constant.cc > best_constant.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM kernel_svm.cc > kernel_svm.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cs_active.cc > cs_active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active_cover.cc > active_cover.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active.cc > active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM recall_tree.cc > recall_tree.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM log_multi.cc > log_multi.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM stagewise_poly.cc > stagewise_poly.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM topk.cc > topk.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM explore_eval.cc > explore_eval.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cbify.cc > cbify.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bs.cc > bs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM confidence.cc > confidence.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM nn.cc > nn.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM sender.cc > sender.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM loss_functions.cc > loss_functions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser.cc > parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM example.cc > example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM print.cc > print.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM noop.cc > noop.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bfgs.cc > bfgs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mf.cc > mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd_mf.cc > gd_mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lda_core.cc > lda_core.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mwt.cc > mwt.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM learner.cc > learner.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd.cc > gd.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM accumulate.cc > accumulate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_args.cc > parse_args.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM network.cc > network.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM scorer.cc > scorer.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example.cc > parse_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_graph.cc > search_graph.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_entityrelationtask.cc > search_entityrelationtask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_multiclasstask.cc > search_multiclasstask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_hooktask.cc > search_hooktask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_dep_parser.cc > search_dep_parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_sequencetask.cc > search_sequencetask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_meta.cc > search_meta.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search.cc > search.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_algs.cc > cb_algs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_adf.cc > cb_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb.cc > cb.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM csoaa.cc > csoaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM label_dictionary.cc > label_dictionary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel.cc > multilabel.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cost_sensitive.cc > cost_sensitive.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrq.cc > lrq.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM binary.cc > binary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM autolink.cc > autolink.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM marginal.cc > marginal.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ect.cc > ect.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM boosting.cc > boosting.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel_oaa.cc > multilabel_oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM oaa.cc > oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multiclass.cc > multiclass.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM simple_label.cc > simple_label.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM rand48.cc > rand48.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cache.cc > cache.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM unique_sort.cc > unique_sort.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_primitives.cc > parse_primitives.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_regressor.cc > parse_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM io_buf.cc > io_buf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM global_data.cc > global_data.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser_helper.cc > parser_helper.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM hash.cc > hash.d rm -f *.o *.d vw active_interactor *~ vw.1 libvw.a liballreduce.a make[4]: Leaving directory '/<>/deps/vowpal_wabbit/vowpalwabbit' cd cluster && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/cluster' rm -f *.o vw active_interactor *~ vw.1 make[4]: Leaving directory '/<>/deps/vowpal_wabbit/cluster' cd library && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/library' rm -f *.o ezexample_predict ezexample_train library_example test_search recommend ezexample_predict_threaded make[4]: Leaving directory '/<>/deps/vowpal_wabbit/library' cd python && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/python' rm -f *.o pylibvw.so make[4]: Leaving directory '/<>/deps/vowpal_wabbit/python' cd java && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/java' rm -f target/libvw_jni.so rm -f src/main/c++/vowpalWabbit_learner_VWScalarLearner.o src/main/c++/vowpalWabbit_learner_VWScalarsLearner.o src/main/c++/vowpalWabbit_VW.o src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.o src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.o src/main/c++/vowpalWabbit_learner_VWLearners.o src/main/c++/jni_base_learner.o src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.o src/main/c++/vowpalWabbit_learner_VWProbLearner.o src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.o make[4]: Leaving directory '/<>/deps/vowpal_wabbit/java' make[3]: Leaving directory '/<>/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make[4]: Leaving directory '/<>/deps/libhandlegraph' make[3]: Leaving directory '/<>/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/<>/deps/libvgio' make[3]: *** No rule to make target 'clean'. Stop. make[3]: Leaving directory '/<>/deps/libvgio' make[2]: *** [Makefile:620: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib make[3]: Entering directory '/<>/deps/gssw' Library will be installed in '/<>' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- Configuring done clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc 2 warnings generated. gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' ./src/tree.c:393:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ [100%] Linking CXX shared library libhandlegraph.so ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success make[5]: Leaving directory '/<>/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o 9 warnings generated. clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] errorclang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] : invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Looking for C++ include cstdio - found error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Configuring done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: 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/<>/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/include/sdsl/qsufsort.hpp -- Installing: /<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend lcp.o build_gcsa.o algorithms.o utils.o files.o support.o gcsa_format.o dbg.o try_extend.o gcsa.o convert_graph.o path_graph.o internal.o libgcsa2.a make[3]: Leaving directory '/<>/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/<>/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o build_gbwt.o bwtmerge.o utils.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/<>/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/<>/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/<>/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/<>/deps/progress_bar' make[3]: Leaving directory '/<>/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/sbuild-nonexistent/lib' and '/sbuild-nonexistent/include' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -P /<>/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/<>/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/<>/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/<>/include/sdsl/bit_vectors.hpp" - found -- Looking for "/<>/include/sdsl/bits.hpp" - found -- Looking for "/<>/include/sdsl/bp_support.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_g.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/coder.hpp" - found -- Looking for "/<>/include/sdsl/coder_comma.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/<>/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/<>/include/sdsl/config.hpp" - found -- Looking for "/<>/include/sdsl/construct.hpp" - found -- Looking for "/<>/include/sdsl/construct_bwt.hpp" - found -- Looking for "/<>/include/sdsl/construct_config.hpp" - found -- 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for "/<>/include/sdsl/lcp_dac.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/<>/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/<>/include/sdsl/lcp_wt.hpp" - found -- Looking for "/<>/include/sdsl/louds_tree.hpp" - found -- Looking for "/<>/include/sdsl/memory_management.hpp" - found -- Looking for "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/<>/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/<>/include/sdsl/qsufsort.hpp" - found -- Looking for "/<>/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/<>/include/sdsl/ram_fs.hpp" - found -- Looking for "/<>/include/sdsl/rank_support.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v.hpp" - found -- Looking for 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Uninstalling "/<>/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/coder.hpp" -- Uninstalling "/<>/include/sdsl/coder_comma.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/<>/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/<>/include/sdsl/config.hpp" -- Uninstalling "/<>/include/sdsl/construct.hpp" -- Uninstalling "/<>/include/sdsl/construct_bwt.hpp" -- Uninstalling "/<>/include/sdsl/construct_config.hpp" -- Uninstalling "/<>/include/sdsl/construct_isa.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/<>/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/csa_sada.hpp" -- Uninstalling "/<>/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_wt.hpp" -- Uninstalling "/<>/include/sdsl/cst_fully.hpp" -- Uninstalling "/<>/include/sdsl/cst_iterators.hpp" -- Uninstalling "/<>/include/sdsl/cst_sada.hpp" -- Uninstalling "/<>/include/sdsl/cst_sct3.hpp" -- Uninstalling "/<>/include/sdsl/dac_vector.hpp" -- Uninstalling "/<>/include/sdsl/enc_vector.hpp" -- Uninstalling "/<>/include/sdsl/fast_cache.hpp" -- Uninstalling "/<>/include/sdsl/hyb_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/<>/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/<>/include/sdsl/io.hpp" -- Uninstalling "/<>/include/sdsl/iterators.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling 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"/<>/include/sdsl/rank_support.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/<>/include/sdsl/raster_img.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/<>/include/sdsl/rrr_helper.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/<>/include/sdsl/sd_vector.hpp" -- Uninstalling "/<>/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/<>/include/sdsl/select_support.hpp" -- Uninstalling "/<>/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/<>/include/sdsl/select_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/sfstream.hpp" -- Uninstalling "/<>/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/<>/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/structure_tree.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_trees.hpp" -- Uninstalling "/<>/include/sdsl/uint128_t.hpp" -- Uninstalling "/<>/include/sdsl/uint256_t.hpp" -- Uninstalling "/<>/include/sdsl/uintx_t.hpp" -- Uninstalling "/<>/include/sdsl/util.hpp" -- Uninstalling "/<>/include/sdsl/vectors.hpp" -- Uninstalling "/<>/include/sdsl/vlc_vector.hpp" -- Uninstalling "/<>/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/<>/include/sdsl/wm_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/wt_ap.hpp" -- Uninstalling "/<>/include/sdsl/wt_blcd.hpp" -- Uninstalling "/<>/include/sdsl/wt_gmr.hpp" -- Uninstalling "/<>/include/sdsl/wt_helper.hpp" -- Uninstalling "/<>/include/sdsl/wt_huff.hpp" -- Uninstalling "/<>/include/sdsl/wt_hutu.hpp" -- Uninstalling "/<>/include/sdsl/wt_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_pc.hpp" -- Uninstalling "/<>/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/<>/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/<>/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/<>/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/<>/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/<>/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/<>/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/<>/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/<>/deps/vowpal_wabbit' cd vowpalwabbit && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/vowpalwabbit' /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM classweight.cc > classweight.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM baseline.cc > baseline.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example_json.cc > parse_example_json.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM OjaNewton.cc > OjaNewton.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore_adf.cc > cb_explore_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM action_score.cc > action_score.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore.cc > cb_explore.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gen_cs_example.cc > gen_cs_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM audit_regressor.cc > audit_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_validate.cc > vw_validate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_exception.cc > vw_exception.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interactions.cc > interactions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM comp_io.cc > comp_io.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interact.cc > interact.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrqfa.cc > lrqfa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM svrg.cc > svrg.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ftrl.cc > ftrl.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM best_constant.cc > best_constant.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM kernel_svm.cc > kernel_svm.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cs_active.cc > cs_active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active_cover.cc > active_cover.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active.cc > active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM recall_tree.cc > recall_tree.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM log_multi.cc > log_multi.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM stagewise_poly.cc > stagewise_poly.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM topk.cc > topk.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM explore_eval.cc > explore_eval.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cbify.cc > cbify.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bs.cc > bs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM confidence.cc > confidence.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM nn.cc > nn.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM sender.cc > sender.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM loss_functions.cc > loss_functions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser.cc > parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM example.cc > example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM print.cc > print.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM noop.cc > noop.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bfgs.cc > bfgs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mf.cc > mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd_mf.cc > gd_mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lda_core.cc > lda_core.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mwt.cc > mwt.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM learner.cc > learner.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd.cc > gd.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM accumulate.cc > accumulate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_args.cc > parse_args.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM network.cc > network.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM scorer.cc > scorer.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example.cc > parse_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_graph.cc > search_graph.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_entityrelationtask.cc > search_entityrelationtask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_multiclasstask.cc > search_multiclasstask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_hooktask.cc > search_hooktask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_dep_parser.cc > search_dep_parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_sequencetask.cc > search_sequencetask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_meta.cc > search_meta.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search.cc > search.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_algs.cc > cb_algs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_adf.cc > cb_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb.cc > cb.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM csoaa.cc > csoaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM label_dictionary.cc > label_dictionary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel.cc > multilabel.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cost_sensitive.cc > cost_sensitive.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrq.cc > lrq.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM binary.cc > binary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM autolink.cc > autolink.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM marginal.cc > marginal.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ect.cc > ect.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM boosting.cc > boosting.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel_oaa.cc > multilabel_oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM oaa.cc > oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multiclass.cc > multiclass.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM simple_label.cc > simple_label.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM rand48.cc > rand48.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cache.cc > cache.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM unique_sort.cc > unique_sort.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_primitives.cc > parse_primitives.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_regressor.cc > parse_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM io_buf.cc > io_buf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM global_data.cc > global_data.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser_helper.cc > parser_helper.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM hash.cc > hash.d rm -f *.o *.d vw active_interactor *~ vw.1 libvw.a liballreduce.a make[4]: Leaving directory '/<>/deps/vowpal_wabbit/vowpalwabbit' cd cluster && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/cluster' rm -f *.o vw active_interactor *~ vw.1 make[4]: Leaving directory '/<>/deps/vowpal_wabbit/cluster' cd library && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/library' rm -f *.o ezexample_predict ezexample_train library_example test_search recommend ezexample_predict_threaded make[4]: Leaving directory '/<>/deps/vowpal_wabbit/library' cd python && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/python' rm -f *.o pylibvw.so make[4]: Leaving directory '/<>/deps/vowpal_wabbit/python' cd java && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/java' rm -f target/libvw_jni.so rm -f src/main/c++/vowpalWabbit_learner_VWScalarLearner.o src/main/c++/vowpalWabbit_learner_VWScalarsLearner.o src/main/c++/vowpalWabbit_VW.o src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.o src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.o src/main/c++/vowpalWabbit_learner_VWLearners.o src/main/c++/jni_base_learner.o src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.o src/main/c++/vowpalWabbit_learner_VWProbLearner.o src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.o make[4]: Leaving directory '/<>/deps/vowpal_wabbit/java' make[3]: Leaving directory '/<>/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make[4]: Leaving directory '/<>/deps/libhandlegraph' make[3]: Leaving directory '/<>/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/<>/deps/libvgio' make[3]: *** No rule to make target 'clean'. Stop. make[3]: Leaving directory '/<>/deps/libvgio' make[2]: *** [Makefile:620: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib make[3]: Entering directory '/<>/deps/gssw' Library will be installed in '/<>' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- Configuring done clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc 2 warnings generated. gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' ./src/tree.c:393:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o make[5]: Leaving directory '/<>/deps/libhandlegraph' -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o 9 warnings generated. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o error: invalid argument '-std=c++14' not allowed with 'C' clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success error: invalid argument '-std=c++14' not allowed with 'C' -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Looking for C++ include cstdio - found error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Configuring done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 errormake -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all : invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/include/sdsl/bit_vector_il.hpp -- Installing: /<>/include/sdsl/bit_vectors.hpp -- Installing: /<>/include/sdsl/bits.hpp -- Installing: /<>/include/sdsl/bp_support.hpp -- Installing: /<>/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/include/sdsl/bp_support_g.hpp -- Installing: /<>/include/sdsl/bp_support_gg.hpp -- Installing: /<>/include/sdsl/bp_support_sada.hpp -- Installing: /<>/include/sdsl/coder.hpp -- Installing: /<>/include/sdsl/coder_comma.hpp -- Installing: /<>/include/sdsl/coder_elias_delta.hpp -- Installing: 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/<>/include/sdsl/dac_vector.hpp -- Installing: /<>/include/sdsl/enc_vector.hpp -- Installing: /<>/include/sdsl/fast_cache.hpp -- Installing: /<>/include/sdsl/hyb_vector.hpp -- Installing: /<>/include/sdsl/int_vector.hpp -- Installing: /<>/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/include/sdsl/inv_perm_support.hpp -- Installing: /<>/include/sdsl/io.hpp -- Installing: /<>/include/sdsl/iterators.hpp -- Installing: /<>/include/sdsl/k2_treap.hpp -- Installing: /<>/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/include/sdsl/k2_tree.hpp -- Installing: /<>/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/include/sdsl/lcp.hpp -- Installing: /<>/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/include/sdsl/lcp_byte.hpp -- Installing: /<>/include/sdsl/lcp_dac.hpp -- Installing: /<>/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/include/sdsl/lcp_vlc.hpp -- Installing: /<>/include/sdsl/lcp_wt.hpp -- Installing: /<>/include/sdsl/louds_tree.hpp -- Installing: /<>/include/sdsl/memory_management.hpp -- Installing: /<>/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/include/sdsl/qsufsort.hpp -- Installing: /<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend lcp.o build_gcsa.o algorithms.o utils.o files.o support.o gcsa_format.o dbg.o try_extend.o gcsa.o convert_graph.o path_graph.o internal.o libgcsa2.a make[3]: Leaving directory '/<>/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/<>/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o build_gbwt.o bwtmerge.o utils.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/<>/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/<>/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/<>/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/<>/deps/progress_bar' make[3]: Leaving directory '/<>/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/sbuild-nonexistent/lib' and '/sbuild-nonexistent/include' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -P /<>/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/<>/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/<>/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/<>/include/sdsl/bit_vectors.hpp" - found -- Looking for "/<>/include/sdsl/bits.hpp" - found -- Looking for "/<>/include/sdsl/bp_support.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_g.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/coder.hpp" - found -- Looking for "/<>/include/sdsl/coder_comma.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/<>/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/<>/include/sdsl/config.hpp" - found -- Looking for "/<>/include/sdsl/construct.hpp" - found -- Looking for "/<>/include/sdsl/construct_bwt.hpp" - found -- Looking for "/<>/include/sdsl/construct_config.hpp" - found -- Looking for "/<>/include/sdsl/construct_isa.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/<>/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/csa_sada.hpp" - found -- Looking for "/<>/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_wt.hpp" - found -- Looking for "/<>/include/sdsl/cst_fully.hpp" - found -- Looking for "/<>/include/sdsl/cst_iterators.hpp" - found -- Looking for "/<>/include/sdsl/cst_sada.hpp" - found -- Looking for "/<>/include/sdsl/cst_sct3.hpp" - found -- Looking for "/<>/include/sdsl/dac_vector.hpp" - found -- Looking for "/<>/include/sdsl/enc_vector.hpp" - found -- Looking for "/<>/include/sdsl/fast_cache.hpp" - found -- Looking for "/<>/include/sdsl/hyb_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/<>/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/<>/include/sdsl/io.hpp" - found -- Looking for "/<>/include/sdsl/iterators.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/lcp.hpp" - found -- Looking for "/<>/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/lcp_byte.hpp" - found -- Looking for "/<>/include/sdsl/lcp_dac.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/<>/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/<>/include/sdsl/lcp_wt.hpp" - found -- Looking for "/<>/include/sdsl/louds_tree.hpp" - found -- Looking for "/<>/include/sdsl/memory_management.hpp" - found -- Looking for "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/<>/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/<>/include/sdsl/qsufsort.hpp" - found -- Looking for "/<>/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/<>/include/sdsl/ram_fs.hpp" - found -- Looking for "/<>/include/sdsl/rank_support.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/<>/include/sdsl/raster_img.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/<>/include/sdsl/rrr_helper.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/<>/include/sdsl/sd_vector.hpp" - found -- Looking for "/<>/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/<>/include/sdsl/select_support.hpp" - found -- Looking for "/<>/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/<>/include/sdsl/select_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/sfstream.hpp" - found -- Looking for "/<>/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/<>/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/structure_tree.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_trees.hpp" - found -- Looking for "/<>/include/sdsl/uint128_t.hpp" - found -- Looking for "/<>/include/sdsl/uint256_t.hpp" - found -- Looking for "/<>/include/sdsl/uintx_t.hpp" - found -- Looking for "/<>/include/sdsl/util.hpp" - found -- Looking for "/<>/include/sdsl/vectors.hpp" - found -- Looking for "/<>/include/sdsl/vlc_vector.hpp" - found -- Looking for "/<>/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/<>/include/sdsl/wm_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/wt_ap.hpp" - found -- Looking for "/<>/include/sdsl/wt_blcd.hpp" - found -- Looking for "/<>/include/sdsl/wt_gmr.hpp" - found -- Looking for "/<>/include/sdsl/wt_helper.hpp" - found -- Looking for "/<>/include/sdsl/wt_huff.hpp" - found -- Looking for "/<>/include/sdsl/wt_hutu.hpp" - found -- Looking for "/<>/include/sdsl/wt_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_pc.hpp" - found -- Looking for "/<>/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/<>/lib/libsdsl.a" - not found -- Uninstalling "/<>/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/<>/include/sdsl/bit_vectors.hpp" -- Uninstalling "/<>/include/sdsl/bits.hpp" -- Uninstalling "/<>/include/sdsl/bp_support.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_g.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/coder.hpp" -- Uninstalling "/<>/include/sdsl/coder_comma.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/<>/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/<>/include/sdsl/config.hpp" -- Uninstalling "/<>/include/sdsl/construct.hpp" -- Uninstalling "/<>/include/sdsl/construct_bwt.hpp" -- Uninstalling "/<>/include/sdsl/construct_config.hpp" -- Uninstalling "/<>/include/sdsl/construct_isa.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/<>/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/csa_sada.hpp" -- Uninstalling "/<>/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_wt.hpp" -- Uninstalling "/<>/include/sdsl/cst_fully.hpp" -- Uninstalling "/<>/include/sdsl/cst_iterators.hpp" -- Uninstalling "/<>/include/sdsl/cst_sada.hpp" -- Uninstalling "/<>/include/sdsl/cst_sct3.hpp" -- Uninstalling "/<>/include/sdsl/dac_vector.hpp" -- Uninstalling "/<>/include/sdsl/enc_vector.hpp" -- Uninstalling "/<>/include/sdsl/fast_cache.hpp" -- Uninstalling "/<>/include/sdsl/hyb_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/<>/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/<>/include/sdsl/io.hpp" -- Uninstalling "/<>/include/sdsl/iterators.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/lcp.hpp" -- Uninstalling "/<>/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/lcp_byte.hpp" -- Uninstalling "/<>/include/sdsl/lcp_dac.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/<>/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/<>/include/sdsl/lcp_wt.hpp" -- Uninstalling "/<>/include/sdsl/louds_tree.hpp" -- Uninstalling "/<>/include/sdsl/memory_management.hpp" -- Uninstalling "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/<>/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/<>/include/sdsl/qsufsort.hpp" -- Uninstalling "/<>/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/<>/include/sdsl/ram_fs.hpp" -- Uninstalling "/<>/include/sdsl/rank_support.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/<>/include/sdsl/raster_img.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/<>/include/sdsl/rrr_helper.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/<>/include/sdsl/sd_vector.hpp" -- Uninstalling "/<>/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/<>/include/sdsl/select_support.hpp" -- Uninstalling "/<>/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/<>/include/sdsl/select_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/sfstream.hpp" -- Uninstalling "/<>/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/<>/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/structure_tree.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_trees.hpp" -- Uninstalling "/<>/include/sdsl/uint128_t.hpp" -- Uninstalling "/<>/include/sdsl/uint256_t.hpp" -- Uninstalling "/<>/include/sdsl/uintx_t.hpp" -- Uninstalling "/<>/include/sdsl/util.hpp" -- Uninstalling "/<>/include/sdsl/vectors.hpp" -- Uninstalling "/<>/include/sdsl/vlc_vector.hpp" -- Uninstalling "/<>/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/<>/include/sdsl/wm_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/wt_ap.hpp" -- Uninstalling "/<>/include/sdsl/wt_blcd.hpp" -- Uninstalling "/<>/include/sdsl/wt_gmr.hpp" -- Uninstalling "/<>/include/sdsl/wt_helper.hpp" -- Uninstalling "/<>/include/sdsl/wt_huff.hpp" -- Uninstalling "/<>/include/sdsl/wt_hutu.hpp" -- Uninstalling "/<>/include/sdsl/wt_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_pc.hpp" -- Uninstalling "/<>/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/<>/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/<>/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/<>/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/<>/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/<>/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/<>/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/<>/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/<>/deps/vowpal_wabbit' cd vowpalwabbit && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/vowpalwabbit' /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM classweight.cc > classweight.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM baseline.cc > baseline.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example_json.cc > parse_example_json.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM OjaNewton.cc > OjaNewton.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore_adf.cc > cb_explore_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM action_score.cc > action_score.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore.cc > cb_explore.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gen_cs_example.cc > gen_cs_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM audit_regressor.cc > audit_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_validate.cc > vw_validate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_exception.cc > vw_exception.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interactions.cc > interactions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM comp_io.cc > comp_io.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interact.cc > interact.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrqfa.cc > lrqfa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM svrg.cc > svrg.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ftrl.cc > ftrl.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM best_constant.cc > best_constant.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM kernel_svm.cc > kernel_svm.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cs_active.cc > cs_active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active_cover.cc > active_cover.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active.cc > active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM recall_tree.cc > recall_tree.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM log_multi.cc > log_multi.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM stagewise_poly.cc > stagewise_poly.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM topk.cc > topk.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM explore_eval.cc > explore_eval.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cbify.cc > cbify.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bs.cc > bs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM confidence.cc > confidence.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM nn.cc > nn.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM sender.cc > sender.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM loss_functions.cc > loss_functions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser.cc > parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM example.cc > example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM print.cc > print.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM noop.cc > noop.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bfgs.cc > bfgs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mf.cc > mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd_mf.cc > gd_mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lda_core.cc > lda_core.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mwt.cc > mwt.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM learner.cc > learner.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd.cc > gd.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM accumulate.cc > accumulate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_args.cc > parse_args.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM network.cc > network.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM scorer.cc > scorer.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example.cc > parse_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_graph.cc > search_graph.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_entityrelationtask.cc > search_entityrelationtask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_multiclasstask.cc > search_multiclasstask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_hooktask.cc > search_hooktask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_dep_parser.cc > search_dep_parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_sequencetask.cc > search_sequencetask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_meta.cc > search_meta.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search.cc > search.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_algs.cc > cb_algs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_adf.cc > cb_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb.cc > cb.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM csoaa.cc > csoaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM label_dictionary.cc > label_dictionary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel.cc > multilabel.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cost_sensitive.cc > cost_sensitive.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrq.cc > lrq.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM binary.cc > binary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM autolink.cc > autolink.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM marginal.cc > marginal.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ect.cc > ect.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM boosting.cc > boosting.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel_oaa.cc > multilabel_oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM oaa.cc > oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multiclass.cc > multiclass.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM simple_label.cc > simple_label.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM rand48.cc > rand48.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cache.cc > cache.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM unique_sort.cc > unique_sort.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_primitives.cc > parse_primitives.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_regressor.cc > parse_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM io_buf.cc > io_buf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM global_data.cc > global_data.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser_helper.cc > parser_helper.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM hash.cc > hash.d rm -f *.o *.d vw active_interactor *~ vw.1 libvw.a liballreduce.a make[4]: Leaving directory '/<>/deps/vowpal_wabbit/vowpalwabbit' cd cluster && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/cluster' rm -f *.o vw active_interactor *~ vw.1 make[4]: Leaving directory '/<>/deps/vowpal_wabbit/cluster' cd library && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/library' rm -f *.o ezexample_predict ezexample_train library_example test_search recommend ezexample_predict_threaded make[4]: Leaving directory '/<>/deps/vowpal_wabbit/library' cd python && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/python' rm -f *.o pylibvw.so make[4]: Leaving directory '/<>/deps/vowpal_wabbit/python' cd java && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/java' rm -f target/libvw_jni.so rm -f src/main/c++/vowpalWabbit_learner_VWScalarLearner.o src/main/c++/vowpalWabbit_learner_VWScalarsLearner.o src/main/c++/vowpalWabbit_VW.o src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.o src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.o src/main/c++/vowpalWabbit_learner_VWLearners.o src/main/c++/jni_base_learner.o src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.o src/main/c++/vowpalWabbit_learner_VWProbLearner.o src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.o make[4]: Leaving directory '/<>/deps/vowpal_wabbit/java' make[3]: Leaving directory '/<>/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make[4]: Leaving directory '/<>/deps/libhandlegraph' make[3]: Leaving directory '/<>/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/<>/deps/libvgio' make[3]: *** No rule to make target 'clean'. Stop. make[3]: Leaving directory '/<>/deps/libvgio' make[2]: *** [Makefile:620: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib make[3]: Entering directory '/<>/deps/gssw' Library will be installed in '/<>' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all The pre-commit hook is not installed. make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- Configuring done clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features 2 warnings generated. -- Detecting CXX compile features - done gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Check for working C compiler: /usr/bin/gcc gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build ./src/tree.c:393:3: warningmake[5]: Entering directory '/<>/deps/libhandlegraph' : ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o make[5]: Leaving directory '/<>/deps/libhandlegraph' -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o 9 warnings generated. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o error: invalid argument '-std=c++14' not allowed with 'C' clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Looking for C++ include cstdio - found error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Configuring done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build error: invalid argument '-std=c++14' not allowed with 'C' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl error: invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/include/sdsl/bit_vector_il.hpp -- Installing: /<>/include/sdsl/bit_vectors.hpp -- Installing: /<>/include/sdsl/bits.hpp -- Installing: /<>/include/sdsl/bp_support.hpp -- Installing: /<>/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/include/sdsl/bp_support_g.hpp -- Installing: /<>/include/sdsl/bp_support_gg.hpp -- Installing: /<>/include/sdsl/bp_support_sada.hpp -- Installing: /<>/include/sdsl/coder.hpp -- Installing: /<>/include/sdsl/coder_comma.hpp -- Installing: /<>/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/include/sdsl/coder_elias_gamma.hpp -- 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/<>/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/include/sdsl/lcp_vlc.hpp -- Installing: /<>/include/sdsl/lcp_wt.hpp -- Installing: /<>/include/sdsl/louds_tree.hpp -- Installing: /<>/include/sdsl/memory_management.hpp -- Installing: /<>/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/include/sdsl/qsufsort.hpp -- Installing: /<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/<>' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/deps/sonLib' cd C && make clean make[4]: Entering directory '/<>/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/<>/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend lcp.o build_gcsa.o algorithms.o utils.o files.o support.o gcsa_format.o dbg.o try_extend.o gcsa.o convert_graph.o path_graph.o internal.o libgcsa2.a make[3]: Leaving directory '/<>/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/<>/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o build_gbwt.o bwtmerge.o utils.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/<>/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/<>/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/<>/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/<>/deps/progress_bar' make[3]: Leaving directory '/<>/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/sbuild-nonexistent/lib' and '/sbuild-nonexistent/include' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -P /<>/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/<>/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/<>/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/<>/include/sdsl/bit_vectors.hpp" - found -- Looking for "/<>/include/sdsl/bits.hpp" - found -- Looking for "/<>/include/sdsl/bp_support.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_g.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/<>/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/coder.hpp" - found -- Looking for "/<>/include/sdsl/coder_comma.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/<>/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/<>/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/<>/include/sdsl/config.hpp" - found -- Looking for "/<>/include/sdsl/construct.hpp" - found -- Looking for "/<>/include/sdsl/construct_bwt.hpp" - found -- Looking for "/<>/include/sdsl/construct_config.hpp" - found -- Looking for "/<>/include/sdsl/construct_isa.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp.hpp" - found -- Looking for "/<>/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa.hpp" - found -- Looking for "/<>/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/<>/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/csa_sada.hpp" - found -- Looking for "/<>/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/<>/include/sdsl/csa_wt.hpp" - found -- Looking for "/<>/include/sdsl/cst_fully.hpp" - found -- Looking for "/<>/include/sdsl/cst_iterators.hpp" - found -- Looking for "/<>/include/sdsl/cst_sada.hpp" - found -- Looking for "/<>/include/sdsl/cst_sct3.hpp" - found -- Looking for "/<>/include/sdsl/dac_vector.hpp" - found -- Looking for "/<>/include/sdsl/enc_vector.hpp" - found -- Looking for "/<>/include/sdsl/fast_cache.hpp" - found -- Looking for "/<>/include/sdsl/hyb_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/<>/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/<>/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/<>/include/sdsl/io.hpp" - found -- Looking for "/<>/include/sdsl/iterators.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree.hpp" - found -- Looking for "/<>/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/lcp.hpp" - found -- Looking for "/<>/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/<>/include/sdsl/lcp_byte.hpp" - found -- Looking for "/<>/include/sdsl/lcp_dac.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/<>/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/<>/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/<>/include/sdsl/lcp_wt.hpp" - found -- Looking for "/<>/include/sdsl/louds_tree.hpp" - found -- Looking for "/<>/include/sdsl/memory_management.hpp" - found -- Looking for "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/<>/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/<>/include/sdsl/qsufsort.hpp" - found -- Looking for "/<>/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/<>/include/sdsl/ram_fs.hpp" - found -- Looking for "/<>/include/sdsl/rank_support.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v.hpp" - found -- Looking for "/<>/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/<>/include/sdsl/raster_img.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/<>/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support.hpp" - found -- Looking for "/<>/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/<>/include/sdsl/rrr_helper.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector.hpp" - found -- Looking for "/<>/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/<>/include/sdsl/sd_vector.hpp" - found -- Looking for "/<>/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/<>/include/sdsl/select_support.hpp" - found -- Looking for "/<>/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/<>/include/sdsl/select_support_scan.hpp" - found -- Looking for "/<>/include/sdsl/sfstream.hpp" - found -- Looking for "/<>/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/<>/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/<>/include/sdsl/structure_tree.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/<>/include/sdsl/suffix_trees.hpp" - found -- Looking for "/<>/include/sdsl/uint128_t.hpp" - found -- Looking for "/<>/include/sdsl/uint256_t.hpp" - found -- Looking for "/<>/include/sdsl/uintx_t.hpp" - found -- Looking for "/<>/include/sdsl/util.hpp" - found -- Looking for "/<>/include/sdsl/vectors.hpp" - found -- Looking for "/<>/include/sdsl/vlc_vector.hpp" - found -- Looking for "/<>/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/<>/include/sdsl/wm_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/<>/include/sdsl/wt_ap.hpp" - found -- Looking for "/<>/include/sdsl/wt_blcd.hpp" - found -- Looking for "/<>/include/sdsl/wt_gmr.hpp" - found -- Looking for "/<>/include/sdsl/wt_helper.hpp" - found -- Looking for "/<>/include/sdsl/wt_huff.hpp" - found -- Looking for "/<>/include/sdsl/wt_hutu.hpp" - found -- Looking for "/<>/include/sdsl/wt_int.hpp" - found -- Looking for "/<>/include/sdsl/wt_pc.hpp" - found -- Looking for "/<>/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/<>/lib/libsdsl.a" - not found -- Uninstalling "/<>/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/<>/include/sdsl/bit_vectors.hpp" -- Uninstalling "/<>/include/sdsl/bits.hpp" -- Uninstalling "/<>/include/sdsl/bp_support.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_g.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/<>/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/coder.hpp" -- Uninstalling "/<>/include/sdsl/coder_comma.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/<>/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/<>/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/<>/include/sdsl/config.hpp" -- Uninstalling "/<>/include/sdsl/construct.hpp" -- Uninstalling "/<>/include/sdsl/construct_bwt.hpp" -- Uninstalling "/<>/include/sdsl/construct_config.hpp" -- Uninstalling "/<>/include/sdsl/construct_isa.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp.hpp" -- Uninstalling "/<>/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa.hpp" -- Uninstalling "/<>/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/<>/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/csa_sada.hpp" -- Uninstalling "/<>/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/<>/include/sdsl/csa_wt.hpp" -- Uninstalling "/<>/include/sdsl/cst_fully.hpp" -- Uninstalling "/<>/include/sdsl/cst_iterators.hpp" -- Uninstalling "/<>/include/sdsl/cst_sada.hpp" -- Uninstalling "/<>/include/sdsl/cst_sct3.hpp" -- Uninstalling "/<>/include/sdsl/dac_vector.hpp" -- Uninstalling "/<>/include/sdsl/enc_vector.hpp" -- Uninstalling "/<>/include/sdsl/fast_cache.hpp" -- Uninstalling "/<>/include/sdsl/hyb_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/<>/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/<>/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/<>/include/sdsl/io.hpp" -- Uninstalling "/<>/include/sdsl/iterators.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree.hpp" -- Uninstalling "/<>/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/lcp.hpp" -- Uninstalling "/<>/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/<>/include/sdsl/lcp_byte.hpp" -- Uninstalling "/<>/include/sdsl/lcp_dac.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/<>/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/<>/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/<>/include/sdsl/lcp_wt.hpp" -- Uninstalling "/<>/include/sdsl/louds_tree.hpp" -- Uninstalling "/<>/include/sdsl/memory_management.hpp" -- Uninstalling "/<>/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/<>/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/<>/include/sdsl/qsufsort.hpp" -- Uninstalling "/<>/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/<>/include/sdsl/ram_fs.hpp" -- Uninstalling "/<>/include/sdsl/rank_support.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v.hpp" -- Uninstalling "/<>/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/<>/include/sdsl/raster_img.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/<>/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support.hpp" -- Uninstalling "/<>/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/<>/include/sdsl/rrr_helper.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector.hpp" -- Uninstalling "/<>/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/<>/include/sdsl/sd_vector.hpp" -- Uninstalling "/<>/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/<>/include/sdsl/select_support.hpp" -- Uninstalling "/<>/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/<>/include/sdsl/select_support_scan.hpp" -- Uninstalling "/<>/include/sdsl/sfstream.hpp" -- Uninstalling "/<>/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/<>/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/<>/include/sdsl/structure_tree.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/<>/include/sdsl/suffix_trees.hpp" -- Uninstalling "/<>/include/sdsl/uint128_t.hpp" -- Uninstalling "/<>/include/sdsl/uint256_t.hpp" -- Uninstalling "/<>/include/sdsl/uintx_t.hpp" -- Uninstalling "/<>/include/sdsl/util.hpp" -- Uninstalling "/<>/include/sdsl/vectors.hpp" -- Uninstalling "/<>/include/sdsl/vlc_vector.hpp" -- Uninstalling "/<>/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/<>/include/sdsl/wm_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/<>/include/sdsl/wt_ap.hpp" -- Uninstalling "/<>/include/sdsl/wt_blcd.hpp" -- Uninstalling "/<>/include/sdsl/wt_gmr.hpp" -- Uninstalling "/<>/include/sdsl/wt_helper.hpp" -- Uninstalling "/<>/include/sdsl/wt_huff.hpp" -- Uninstalling "/<>/include/sdsl/wt_hutu.hpp" -- Uninstalling "/<>/include/sdsl/wt_int.hpp" -- Uninstalling "/<>/include/sdsl/wt_pc.hpp" -- Uninstalling "/<>/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/<>/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/<>/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/<>/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/<>/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/<>/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/<>/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/<>/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/<>/deps/vowpal_wabbit' cd vowpalwabbit && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/vowpalwabbit' /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM classweight.cc > classweight.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM baseline.cc > baseline.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example_json.cc > parse_example_json.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM OjaNewton.cc > OjaNewton.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore_adf.cc > cb_explore_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM action_score.cc > action_score.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_explore.cc > cb_explore.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gen_cs_example.cc > gen_cs_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM audit_regressor.cc > audit_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_validate.cc > vw_validate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM vw_exception.cc > vw_exception.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interactions.cc > interactions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM comp_io.cc > comp_io.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM interact.cc > interact.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrqfa.cc > lrqfa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM svrg.cc > svrg.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ftrl.cc > ftrl.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM best_constant.cc > best_constant.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM kernel_svm.cc > kernel_svm.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cs_active.cc > cs_active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active_cover.cc > active_cover.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM active.cc > active.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM recall_tree.cc > recall_tree.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM log_multi.cc > log_multi.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM stagewise_poly.cc > stagewise_poly.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM topk.cc > topk.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM explore_eval.cc > explore_eval.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cbify.cc > cbify.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bs.cc > bs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM confidence.cc > confidence.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM nn.cc > nn.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM sender.cc > sender.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM loss_functions.cc > loss_functions.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser.cc > parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM example.cc > example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM print.cc > print.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM noop.cc > noop.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM bfgs.cc > bfgs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mf.cc > mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd_mf.cc > gd_mf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lda_core.cc > lda_core.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM mwt.cc > mwt.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM learner.cc > learner.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM gd.cc > gd.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM accumulate.cc > accumulate.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_args.cc > parse_args.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM network.cc > network.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM scorer.cc > scorer.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_example.cc > parse_example.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_graph.cc > search_graph.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_entityrelationtask.cc > search_entityrelationtask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_multiclasstask.cc > search_multiclasstask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_hooktask.cc > search_hooktask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_dep_parser.cc > search_dep_parser.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_sequencetask.cc > search_sequencetask.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search_meta.cc > search_meta.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM search.cc > search.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_algs.cc > cb_algs.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb_adf.cc > cb_adf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cb.cc > cb.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM csoaa.cc > csoaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM label_dictionary.cc > label_dictionary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel.cc > multilabel.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cost_sensitive.cc > cost_sensitive.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM lrq.cc > lrq.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM binary.cc > binary.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM autolink.cc > autolink.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM marginal.cc > marginal.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM ect.cc > ect.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM boosting.cc > boosting.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multilabel_oaa.cc > multilabel_oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM oaa.cc > oaa.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM multiclass.cc > multiclass.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM simple_label.cc > simple_label.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM rand48.cc > rand48.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM cache.cc > cache.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM unique_sort.cc > unique_sort.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_primitives.cc > parse_primitives.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parse_regressor.cc > parse_regressor.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM io_buf.cc > io_buf.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM global_data.cc > global_data.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM parser_helper.cc > parser_helper.d /usr/bin/g++ -std=c++0x -I /usr/include/rapidjson -MM hash.cc > hash.d rm -f *.o *.d vw active_interactor *~ vw.1 libvw.a liballreduce.a make[4]: Leaving directory '/<>/deps/vowpal_wabbit/vowpalwabbit' cd cluster && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/cluster' rm -f *.o vw active_interactor *~ vw.1 make[4]: Leaving directory '/<>/deps/vowpal_wabbit/cluster' cd library && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/library' rm -f *.o ezexample_predict ezexample_train library_example test_search recommend ezexample_predict_threaded make[4]: Leaving directory '/<>/deps/vowpal_wabbit/library' cd python && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/python' rm -f *.o pylibvw.so make[4]: Leaving directory '/<>/deps/vowpal_wabbit/python' cd java && make clean make[4]: Entering directory '/<>/deps/vowpal_wabbit/java' rm -f target/libvw_jni.so rm -f src/main/c++/vowpalWabbit_learner_VWScalarLearner.o src/main/c++/vowpalWabbit_learner_VWScalarsLearner.o src/main/c++/vowpalWabbit_VW.o src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.o src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.o src/main/c++/vowpalWabbit_learner_VWLearners.o src/main/c++/jni_base_learner.o src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.o src/main/c++/vowpalWabbit_learner_VWProbLearner.o src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.o make[4]: Leaving directory '/<>/deps/vowpal_wabbit/java' make[3]: Leaving directory '/<>/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake 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Stop. make[3]: Leaving directory '/<>/deps/libvgio' make[2]: *** [Makefile:620: clean] Error 2 make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" SFX=-sse2 all test/build_graph bin/shuf make[2]: Entering directory '/<>' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp" ./install.sh /<> . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/lib && cp -r src/include/handlegraph /<>/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/lib/ && cp obj/* /<>/obj && cp src/*.h /<>/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/lib/libsonlib.a && mkdir -p /<>/include/sonLib && cp lib/*.h /<>/include/sonLib Library will be installed in '/<>' make[3]: Entering directory '/<>/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/<>/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[4]: Entering directory '/<>/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- Configuring done -- Generating done -- Build files have been written to: /<>/deps/libhandlegraph clang: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] make[3]: Entering directory '/<>/deps/libhandlegraph' /usr/bin/cmake -S/<>/deps/libhandlegraph -B/<>/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles /<>/deps/libhandlegraph/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/deps/libhandlegraph/src/handle.cpp -- The CXX compiler identification is Clang 10.0.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The C compiler identification is Clang 10.0.0 -- Check for working CXX compiler: /usr/bin/g++ gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c:390:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%s", identifier ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%lf", &dist); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc 2 warnings generated. gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CLANG_STD=C__11__DNDEBUG - Success -- Performing Test HAVE_CLANG_STDLIB=LIBC__ make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' -- Performing Test HAVE_CLANG_STDLIB=LIBC__ - Failed -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/deps/libhandlegraph' cd /<>/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph /<>/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= gcc -std=c99 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[5]: Leaving directory '/<>/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o ./src/tree.c:393:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be ) */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); /* should be : */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:468:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "("); ^~~~~~ ~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c ); /* should be , */ ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf( handle, "%1s", &c); ^~~~~~ ~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CLANG_O3__FFAST_MATH__FUNROLL_LOOPS__D__EXTERN_ALWAYS_INLINE="EXTERN___ALWAYS_INLINE"_ - Success make[5]: Leaving directory '/<>/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/include" make libs && cp lib/libsublinearLS.a /<>/lib/ && mkdir -p /<>/include/sublinearLS && cp src/*.hpp /<>/include/sublinearLS/ make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' rm -f /<>/deps/sublinear-Li-Stephens/bin/* /<>/deps/sublinear-Li-Stephens/obj/*.o /<>/deps/sublinear-Li-Stephens/obj/test/*.o /<>/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/deps/sublinear-Li-Stephens' if [ ! -d /<>/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/deps/sublinear-Li-Stephens/obj/math.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] 9 warnings generated. gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/<>/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/deps/sonLib/externalTools' cd C && make all -- Performing Test HAVE_CXA_DEMANGLE make[4]: Entering directory '/<>/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference.o mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] cp inc/stSafeC.h ../lib/stSafeC.h.tmp clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -I inc -I ../lib/ -c impl/*.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Performing Test HAVE_CLANG_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Looking for C++ include cstdio - found error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Configuring done error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' error: invalid argument '-std=c++14' not allowed with 'C' -- Generating done error: invalid argument '-std=c++14' not allowed with 'C' -- Build files have been written to: /<>/deps/sdsl-lite/build make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 sdsl error: invalid argument '-std=c++14' not allowed with 'C' make[4]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 7 error: invalid argument '-std=c++14' not allowed with 'C' make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= error: invalid argument '-std=c++14' not allowed with 'C' make[4]: *** [Makefile:55: ../lib/sonLib.a] Error 1 make[4]: Leaving directory '/<>/deps/sonLib/C' make[3]: *** [Makefile:12: cP] Error 2 make[3]: Leaving directory '/<>/deps/sonLib' make[2]: *** [Makefile:424: lib/libsonlib.a] Error 2 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/deps/sublinear-Li-Stephens/obj/probability.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/deps/sdsl-lite/lib/bits.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/deps/sdsl-lite/lib/bp_support_algorithm.cpp /<>/deps/sublinear-Li-Stephens/src/probability.cpp:130:9: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:152:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/probability.cpp:189:11: warning: expression result unused [-Wunused-value] for(it; it != end; ++it) { ^~ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/deps/gssw' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_delta.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/deps/sdsl-lite/lib/coder_elias_gamma.cpp /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:126:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:256:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ /<>/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp:262:7: warning: expression result unused [-Wunused-value] for(it; it != rows_end; ++it) { ^~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/deps/sdsl-lite/lib/coder_fibonacci.cpp 3 warnings generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: warning: equality comparison result unused [-Wunused-comparison] constant == 0; ~~~~~~~~~^~~~ /<>/deps/sublinear-Li-Stephens/src/DP_map.cpp:8:12: note: use '=' to turn this equality comparison into an assignment constant == 0; ^~ = g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/deps/sublinear-Li-Stephens/obj/allele.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/deps/sdsl-lite/lib/config.cpp /<>/deps/sublinear-Li-Stephens/src/penalty_set.cpp:9:29: warning: field 'rho' is uninitialized when used here [-Wuninitialized] H(H), mu(mu), rho(rho - log(H - 1)) { ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/deps/sublinear-Li-Stephens/obj/row_set.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/deps/sdsl-lite/lib/construct_config.cpp /<>/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_isa.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: warning: equality comparison result unused [-Wunused-comparison] current_node == nullptr; ~~~~~~~~~~~~~^~~~~~~~~~ /<>/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp:60:22: note: use '=' to turn this equality comparison into an assignment current_node == nullptr; ^~ = [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp.cpp 1 warning generated. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/include -I/<>/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -g -I/<>/include -L. -L/<>/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o clang: warning: -lhts: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L.' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/<>/deps/sublinear-Li-Stephens/deps/htslib/' [-Wunused-command-line-argument] [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ /<>/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<'\x08'>' requested here construct_lcp_PHI<8>(config); ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here static const char* KEY_TEXT; ^ /<>/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\x08'>::KEY_TEXT' is explicitly instantiated in another translation unit const char* KEY_TEXT = key_text_trait::KEY_TEXT; ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa.cpp ar rc /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/deps/sublinear-Li-Stephens/obj/math.o /<>/deps/sublinear-Li-Stephens/obj/reference.o /<>/deps/sublinear-Li-Stephens/obj/probability.o /<>/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/deps/sublinear-Li-Stephens/obj/allele.o /<>/deps/sublinear-Li-Stephens/obj/row_set.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/deps/sublinear-Li-Stephens' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/deps/sdsl-lite/lib/io.cpp cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/deps/sdsl-lite/lib/memory_management.cpp 1 warning generated. [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/deps/sdsl-lite/build/lib/../include -I/<>/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2 -fopenmp -std=c++11 -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/deps/sdsl-lite/lib/wt_helper.cpp [100%] Linking CXX static library libsdsl.a cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/deps/sdsl-lite/build' Removing old files rm -rf '/<>/include/sdsl/*' rm -f '/<>/lib/libsdsl*' make[3]: Entering directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/deps/sdsl-lite -B/<>/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles /<>/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/deps/sdsl-lite/build' cd /<>/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/deps/sdsl-lite /<>/deps/sdsl-lite/lib /<>/deps/sdsl-lite/build /<>/deps/sdsl-lite/build/lib /<>/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/include/sdsl/bit_vector_il.hpp -- Installing: /<>/include/sdsl/bit_vectors.hpp -- Installing: /<>/include/sdsl/bits.hpp -- Installing: /<>/include/sdsl/bp_support.hpp -- Installing: /<>/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/include/sdsl/bp_support_g.hpp -- Installing: /<>/include/sdsl/bp_support_gg.hpp -- Installing: /<>/include/sdsl/bp_support_sada.hpp -- Installing: /<>/include/sdsl/coder.hpp -- Installing: /<>/include/sdsl/coder_comma.hpp -- Installing: /<>/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/include/sdsl/coder_elias_gamma.hpp -- Installing: /<>/include/sdsl/coder_fibonacci.hpp -- Installing: /<>/include/sdsl/config.hpp -- Installing: /<>/include/sdsl/construct.hpp -- Installing: /<>/include/sdsl/construct_bwt.hpp -- Installing: /<>/include/sdsl/construct_config.hpp -- Installing: /<>/include/sdsl/construct_isa.hpp -- Installing: /<>/include/sdsl/construct_lcp.hpp -- Installing: /<>/include/sdsl/construct_lcp_helper.hpp -- Installing: /<>/include/sdsl/construct_sa.hpp -- Installing: /<>/include/sdsl/construct_sa_se.hpp -- Installing: /<>/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /<>/include/sdsl/csa_bitcompressed.hpp -- Installing: /<>/include/sdsl/csa_sada.hpp -- Installing: /<>/include/sdsl/csa_sampling_strategy.hpp -- Installing: /<>/include/sdsl/csa_wt.hpp -- Installing: /<>/include/sdsl/cst_fully.hpp -- Installing: /<>/include/sdsl/cst_iterators.hpp -- Installing: /<>/include/sdsl/cst_sada.hpp -- Installing: /<>/include/sdsl/cst_sct3.hpp -- Installing: /<>/include/sdsl/dac_vector.hpp -- Installing: /<>/include/sdsl/enc_vector.hpp -- Installing: /<>/include/sdsl/fast_cache.hpp -- Installing: /<>/include/sdsl/hyb_vector.hpp -- Installing: /<>/include/sdsl/int_vector.hpp -- Installing: /<>/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/include/sdsl/inv_perm_support.hpp -- Installing: /<>/include/sdsl/io.hpp -- Installing: /<>/include/sdsl/iterators.hpp -- Installing: /<>/include/sdsl/k2_treap.hpp -- Installing: /<>/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/include/sdsl/k2_tree.hpp -- Installing: /<>/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/include/sdsl/lcp.hpp -- Installing: /<>/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/include/sdsl/lcp_byte.hpp -- Installing: /<>/include/sdsl/lcp_dac.hpp -- Installing: /<>/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/include/sdsl/lcp_vlc.hpp -- Installing: /<>/include/sdsl/lcp_wt.hpp -- Installing: /<>/include/sdsl/louds_tree.hpp -- Installing: /<>/include/sdsl/memory_management.hpp -- Installing: /<>/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/include/sdsl/qsufsort.hpp -- Installing: /<>/include/sdsl/ram_filebuf.hpp -- Installing: /<>/include/sdsl/ram_fs.hpp -- Installing: /<>/include/sdsl/rank_support.hpp -- Installing: /<>/include/sdsl/rank_support_scan.hpp -- Installing: /<>/include/sdsl/rank_support_v.hpp -- Installing: /<>/include/sdsl/rank_support_v5.hpp -- Installing: /<>/include/sdsl/raster_img.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/include/sdsl/rmq_support.hpp -- Installing: /<>/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/include/sdsl/rrr_helper.hpp -- Installing: /<>/include/sdsl/rrr_vector.hpp -- Installing: /<>/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/include/sdsl/sd_vector.hpp -- Installing: /<>/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/include/sdsl/select_support.hpp -- Installing: /<>/include/sdsl/select_support_mcl.hpp -- Installing: /<>/include/sdsl/select_support_scan.hpp -- Installing: /<>/include/sdsl/sfstream.hpp -- Installing: /<>/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/include/sdsl/structure_tree.hpp -- Installing: /<>/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/include/sdsl/suffix_arrays.hpp -- Installing: /<>/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/include/sdsl/suffix_trees.hpp -- Installing: /<>/include/sdsl/uint128_t.hpp -- Installing: /<>/include/sdsl/uint256_t.hpp -- Installing: /<>/include/sdsl/uintx_t.hpp -- Installing: /<>/include/sdsl/util.hpp -- Installing: /<>/include/sdsl/vectors.hpp -- Installing: /<>/include/sdsl/vlc_vector.hpp -- Installing: /<>/include/sdsl/wavelet_trees.hpp -- Installing: /<>/include/sdsl/wm_int.hpp -- Installing: /<>/include/sdsl/wt_algorithm.hpp -- Installing: /<>/include/sdsl/wt_ap.hpp -- Installing: /<>/include/sdsl/wt_blcd.hpp -- Installing: /<>/include/sdsl/wt_gmr.hpp -- Installing: /<>/include/sdsl/wt_helper.hpp -- Installing: /<>/include/sdsl/wt_huff.hpp -- Installing: /<>/include/sdsl/wt_hutu.hpp -- Installing: /<>/include/sdsl/wt_int.hpp -- Installing: /<>/include/sdsl/wt_pc.hpp -- Installing: /<>/include/sdsl/wt_rlmn.hpp -- Installing: /<>/lib/libsdsl.a make[3]: Leaving directory '/<>/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/include'. The library files are located in '/<>/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" SFX=-sse2 all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:34: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:19: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T02:21:51Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 277420 Build-Time: 344 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 144 Job: vg_1.23.0+ds-2 Machine Architecture: amd64 Package: vg Package-Time: 506 Source-Version: 1.23.0+ds-2 Space: 277420 Status: attempted Version: 1.23.0+ds-2 -------------------------------------------------------------------------------- Finished at 2020-05-03T02:21:51Z Build needed 00:08:26, 277420k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 507.985288416s DC-Time-Estimation: 507.985288416 versus expected 1 (r/m: 506.985288416 ; m: 1.0)