DC-Build-Header: canu 2.0+dfsg-1 / 2020-05-03 04:18:43 +0000 DC-Task: type:rebuild-binarch-only source:canu version:2.0+dfsg-1 chroot:unstable esttime:403 logfile:/tmp/canu_2.0+dfsg-1_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 canu_2.0+dfsg-1' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-9-59.eu-central-1.compute.internal +==============================================================================+ | canu 2.0+dfsg-1 (amd64) Sun, 03 May 2020 04:18:43 +0000 | +==============================================================================+ Package: canu Version: 2.0+dfsg-1 Source Version: 2.0+dfsg-1 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-19a1575d-86fb-4897-8c0d-565d8f7c2055' 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:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6185 kB] Fetched 6480 kB in 2s (3844 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: gcc-10-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libatomic1 libbsd0 libc6-i386 libcc1-0 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libgcc-s1 libgomp1 libitm1 libllvm10 liblsan0 libobjc4 libomp5-10 libquadmath0 libstdc++6 libtsan0 libubsan1 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 The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 11 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 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 libatomic1 amd64 10-20200502-1 [9048 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libubsan1 amd64 10-20200502-1 [134 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libtsan0 amd64 10-20200502-1 [313 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 gcc-10-base amd64 10-20200502-1 [197 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libstdc++6 amd64 10-20200502-1 [492 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libquadmath0 amd64 10-20200502-1 [145 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblsan0 amd64 10-20200502-1 [141 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libitm1 amd64 10-20200502-1 [25.7 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgomp1 amd64 10-20200502-1 [99.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libcc1-0 amd64 10-20200502-1 [39.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libgcc-s1 amd64 10-20200502-1 [41.2 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200502-1 [41.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200502-1 [49.4 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200502-1 [1100 B] Get:23 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200502-1 [510 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:28 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 51.4 MB in 0s (139 MB/s) (Reading database ... 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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/canu-FZQXw1 + 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/canu-FZQXw1 + 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 (54.6 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 04:18 . drwxr-xr-x 75 root root 4096 May 3 04:18 .. -rw-r--r-- 1 root root 276 May 3 04:18 qmake.conf -rw-r--r-- 1 root root 3218 May 3 04:18 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/canu-FZQXw1/resolver-aMenoN' 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: 'canu' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/canu.git Please use: git clone https://salsa.debian.org/med-team/canu.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1262 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main canu 2.0+dfsg-1 (dsc) [1945 B] Get:2 http://127.0.0.1:12990/debian sid/main canu 2.0+dfsg-1 (tar) [1254 kB] Get:3 http://127.0.0.1:12990/debian sid/main canu 2.0+dfsg-1 (diff) [5976 B] Fetched 1262 kB in 0s (14.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/canu-FZQXw1/canu-2.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/canu-FZQXw1' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3), build-essential, fakeroot 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [409 B] Get:5 copy:/<>/apt_archive ./ Packages [488 B] Fetched 1854 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 binfmt-support bsdmainutils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libcommons-compress-java libcommons-parent-java libcroco3 libcups2 libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63 libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libsqlite3-0 libssl1.1 libssw-java libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mhap openjdk-11-jre-headless openssl po-debconf sensible-utils ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libboost-doc 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-program-options1.67-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 libxz-java cups-common krb5-doc krb5-user libjsr305-java-doc liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl Recommended packages: curl | wget | lynx alsa-ucm-conf alsa-topology-conf dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bsdmainutils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libcommons-compress-java libcommons-parent-java libcroco3 libcups2 libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63 libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libsqlite3-0 libssl1.1 libssw-java libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mhap openjdk-11-jre-headless openssl po-debconf sbuild-build-depends-main-dummy sensible-utils ucf x11-common 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 94.7 MB of archives. After this operation, 423 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 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 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-1 [775 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 binfmt-support amd64 2.2.1-1 [66.1 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1g-1 [846 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 java-common all 0.72 [14.5 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libavahi-common-data amd64 0.7-5 [122 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libavahi-common3 amd64 0.7-5 [54.6 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libdbus-1-3 amd64 1.12.16-2 [214 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libavahi-client3 amd64 0.7-5 [58.2 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-7 [64.4 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-7 [115 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-7 [366 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-7 [156 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 libcups2 amd64 2.3.3-1 [349 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 liblcms2-2 amd64 2.9-4+b1 [146 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libpng16-16 amd64 1.6.37-2 [292 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6 amd64 2.10.1-2 [392 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 fontconfig-config all 2.13.1-4 [281 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig1 amd64 2.13.1-4 [347 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libnspr4 amd64 2:4.25-1 [112 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libnss3 amd64 2:3.51-1 [1192 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libasound2-data all 1.2.2-2.1 [37.8 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libasound2 amd64 1.2.2-2.1 [349 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libpcsclite1 amd64 1.8.26-3 [59.0 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.6.9-2 [298 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.6.9-2 [759 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 x11-common all 1:7.7+20 [252 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.7+10-3 [37.4 MB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates-java all 20190909 [15.7 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 fastjar amd64 2:0.98-6+b1 [81.0 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 jaligner all 1.0+dfsg-6 [131 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 jarwrapper all 0.72.11 [21.2 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libapache-pom-java all 18-1 [4676 B] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-17+b1 [8389 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libboost-dev amd64 1.67.0.2+b1 [4496 B] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libcommons-compress-java all 1.20-1 [574 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 libfastutil-java all 8.3.1-1 [15.4 MB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 libfilesys-df-perl amd64 0.92-6+b5 [12.6 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 libguava-java all 19.0-1 [2028 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libmeryl-dev amd64 0~20150903+r2013-7 [53.9 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libssw-java amd64 1.1-9 [16.3 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 mhap all 2.1.3+dfsg-2 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.7 MB in 1s (131 MB/s) Selecting previously unselected package bsdmainutils. 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Unpacking libssw-java (1.1-9) ... Selecting previously unselected package mhap. Preparing to unpack .../91-mhap_2.1.3+dfsg-2_all.deb ... Unpacking mhap (2.1.3+dfsg-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../92-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libboost1.67-dev:amd64 (1.67.0-17+b1) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up fastjar (2:0.98-6+b1) ... Setting up liblcms2-2:amd64 (2.9-4+b1) ... Setting up libfastutil-java (8.3.1-1) ... 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 libxcb1:amd64 (1.14-2) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up java-common (0.72) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1g-1) ... Setting up libdebhelper-perl (13) ... Setting up libfilesys-df-perl (0.92-6+b5) ... Setting up libsqlite3-0:amd64 (3.31.1-5) ... Setting up x11-common (1:7.7+20) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-3) ... Setting up libssw-java (1.1-9) ... Setting up libkrb5support0:amd64 (1.17-7) ... Setting up libasound2-data (1.2.2-2.1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.9-2) ... Setting up libnspr4:amd64 (2:4.25-1) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:amd64 (0.7-5) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.12.16-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpng16-16:amd64 (1.6.37-2) ... Setting up libmeryl-dev (0~20150903+r2013-7) ... Setting up autopoint (0.19.8.1-10) ... Setting up binfmt-support (2.2.1-1) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.26-3) ... Setting up libk5crypto3:amd64 (1.17-7) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libasound2:amd64 (1.2.2-2.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libx11-6:amd64 (2:1.6.9-2) ... Setting up libkrb5-3:amd64 (1.17-7) ... Setting up libboost-dev:amd64 (1.67.0.2+b1) ... Setting up openssl (1.1.1g-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up jarwrapper (0.72.11) ... Setting up libtool (2.4.6-14) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.7-5) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up m4 (1.4.18-4) ... Setting up libnss3:amd64 (2:3.51-1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libfreetype6:amd64 (2.10.1-2) ... Setting up libguava-java (19.0-1) ... Setting up libgssapi-krb5-2:amd64 (1.17-7) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libavahi-client3:amd64 (0.7-5) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up fontconfig-config (2.13.1-4) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libcups2:amd64 (2.3.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4) ... Setting up po-debconf (1.0.21) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Comodo_AAA_Services_root.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:AddTrust_External_Root.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:ACCVRAIZ1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:AffirmTrust_Premium.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Taiwan_GRCA.pem Adding debian:EC-ACC.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Certigna.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Secure_Global_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:SecureTrust_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Izenpe.com.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem done. Setting up default-jre-headless (2:1.11-72) ... Setting up debhelper (13) ... Setting up jaligner (1.0+dfsg-6) ... Setting up mhap (2.1.3+dfsg-2) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-4) ... 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. done. Setting up openjdk-11-jre-headless:amd64 (11.0.7+10-3) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | 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_10-20200502-1 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 binfmt-support_2.2.1-1 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 ca-certificates-java_20190909 clang-10_1:10.0.0-4 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 default-jre-headless_2:1.11-72 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fastjar_2:0.98-6+b1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 fontconfig-config_2.13.1-4 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 jaligner_1.0+dfsg-6 jarwrapper_0.72.11 java-common_0.72 lib32gcc-s1_10-20200502-1 lib32gcc1_1:10-20200502-1 lib32stdc++6_10-20200502-1 libacl1_2.2.53-8 libapache-pom-java_18-1 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libasound2_1.2.2-2.1 libasound2-data_1.2.2-2.1 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_10-20200502-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libavahi-client3_0.7-5 libavahi-common-data_0.7-5 libavahi-common3_0.7-5 libbinutils_2.34-6 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b1 libboost1.67-dev_1.67.0-17+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcommons-compress-java_1.20-1 libcommons-parent-java_43-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libcups2_2.3.3-1 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.16-2 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfastutil-java_8.3.1-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libfilesys-df-perl_0.92-6+b5 libfontconfig1_2.13.1-4 libfreetype6_2.10.1-2 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libguava-java_19.0-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200502-1 libjpeg62-turbo_1:1.5.2-2+b1 libjsr305-java_0.1~+svn49-11 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 liblcms2-2_2.9-4+b1 libllvm10_1:10.0.0-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmeryl-dev_0~20150903+r2013-7 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnspr4_2:4.25-1 libnss3_2:3.51-1 libobjc-9-dev_9.3.0-11 libobjc4_10-20200502-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libpcsclite1_1.8.26-3 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpng16-16_1.6.37-2 libquadmath0_10-20200502-1 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libssw-java_1.1-9 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200502-1 libubsan1_10-20200502-1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.10+dfsg-5 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libz3-4_4.8.7-4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.3 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mhap_2.1.3+dfsg-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openjdk-11-jre-headless_11.0.7+10-3 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 po-debconf_1.0.21 qt5-qmake_5.12.5+dfsg-10 qt5-qmake-bin_5.12.5+dfsg-10 qtchooser_66-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0038+nmu1 util-linux_2.34-0.1 x11-common_1:7.7+20 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: canu Binary: canu Architecture: any Version: 2.0+dfsg-1 Maintainer: Debian Med Packaging Team Homepage: http://canu.readthedocs.org/en/latest/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/canu Vcs-Git: https://salsa.debian.org/med-team/canu.git Build-Depends: debhelper-compat (= 12), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3) Package-List: canu deb science optional arch=any Checksums-Sha1: 7108de84ccb133607108da7f61eeed1dfca6158d 1254040 canu_2.0+dfsg.orig.tar.xz 3493a153ba4c0283fdc717ed4b51654358b4a7bc 5976 canu_2.0+dfsg-1.debian.tar.xz Checksums-Sha256: 0100031b9e0a88acc18255ab73467f0b01a2a67f3866fb4d3b0be9bc87279a59 1254040 canu_2.0+dfsg.orig.tar.xz 17c82a433c63faf4866ff51de8b2515b4bf63cef12357aafcbfeddc906e92024 5976 canu_2.0+dfsg-1.debian.tar.xz Files: 0edc678cd6a5f954e72d12c116292cdb 1254040 canu_2.0+dfsg.orig.tar.xz 85b22066dfb18aa24a40dc47dee1d6a7 5976 canu_2.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl5+kHYTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0VLED/0c4O9NKRxa6oU7bGHSh9b32TCOiAC7 /2U2DKBRdq7k3Vr9rjMmw9iS8do9NE6nMadHjc6xbKAWNQlU2Ijz65gg0PvgRt8H j9KoCIAoeSD4E8ZKZO4KUZrhS1btkq6+v/AQs0dEh7ufhEQOsKX7m41Ic0G17tdQ OJNGzm8GqwpWes4db+GJlV1O+RomHjgKGzhSwYdxxs65dIoGsVgDCEbyeUSCHm1Y S/BX6Nlw/Vyi125Lr+3lxU+UU+zZcOlL6wmEvONacpCqkgRR5+FCw96kiDnIpxh8 cfAHHvLcm8EgnLeVv6ESr1jnEg0RWiJA9/FEe+GB5v0+b45kDjIv3BIss0cHjgaH 6C4VIf/zoVeU0j0TUG0Dw7hYugBa2csI/ZZLLHxSAYNAaEdXGw08kZ43ytnl2CfT WpntGfZ+D3/gwX+eQ4fNWoqZgTSiu42E4GoQd75ccgkheTSczAUNbYM0VeCbA+re +2fxy/c2wolGdlWFSAhQwAV0tjSBl6BL6gcp91ibAySpSHnVOYjajg4XRZpUvvPX hZkEetPALPA//7gM3HXMTwFFGJqHqIZu5BJBNIKJxGzObaDVL31xv3lL1GQm53Ag 5qTuZBkhdeTRHIBhmyxrfjCIamjhG6ie4QHkNhrTCXQsPdUUskY6879872JNBKQs ULkzmSxy9B7jew== =sDkI -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Mar 27 23:47:02 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./canu_2.0+dfsg-1.dsc dpkg-source: info: extracting canu in /<> dpkg-source: info: unpacking canu_2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking canu_2.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-mhap-at-runtime.patch dpkg-source: info: applying external-mhap.patch dpkg-source: info: applying canu_version.patch 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-19a1575d-86fb-4897-8c0d-565d8f7c2055 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 canu dpkg-buildpackage: info: source version 2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src/ debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf Linux-* rm -f src/canu_version.H make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=src/ dh_clean -O--sourcedirectory=src/ debian/rules build dh build --sourcedirectory=src/ dh_update_autotools_config -O--sourcedirectory=src/ dh_autoreconf -O--sourcedirectory=src/ dh_auto_configure -O--sourcedirectory=src/ debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd src && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/src' Building for 'Linux' '4.19.0-6-cloud-amd64' as 'amd64' into '/<>/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '10.0.0'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security'. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C Building release v2.0 g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C utility/files.C:311:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] symlink(pathToFile, pathToLink); ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ utility/files.C:678:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, FILENAME_MAX, F); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ utility/files.C:684:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, FILENAME_MAX, F); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C 3 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C utility/files-memoryMapped.C:76:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] read(_fd, _data, _length); ^~~~ ~~~~~~~~~~~~~~~~~~~ utility/files-memoryMapped.C:102:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] write(_fd, _data, _length), close(_fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~ 2 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C utility/logging.C:173:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source] snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n", ^ 1 warning generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C In file included from utility/system.C:46: /usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: "The header is deprecated and will be removed." [-W#warnings] #warning "The header is deprecated and will be removed." ^ 1 warning generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C utility/system-stackTrace.C:64:2: warning: LIBBACKTRACE [-W#warnings] #warning LIBBACKTRACE ^ utility/system-stackTrace.C:86:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] WRITE_STRING("\nFailed with '"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/system-stackTrace.C:46:25: note: expanded from macro 'WRITE_STRING' #define WRITE_STRING(S) write(2, S, strlen(S)) ^~~~~ ~~~~~~~~~~~~~~~ utility/system-stackTrace.C:87:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] WRITE_STRING(strsignal(sig_num)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/system-stackTrace.C:46:25: note: expanded from macro 'WRITE_STRING' #define WRITE_STRING(S) write(2, S, strlen(S)) ^~~~~ ~~~~~~~~~~~~~~~ utility/system-stackTrace.C:88:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] WRITE_STRING("'; backtrace (libbacktrace):\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/system-stackTrace.C:46:25: note: expanded from macro 'WRITE_STRING' #define WRITE_STRING(S) write(2, S, strlen(S)) ^~~~~ ~~~~~~~~~~~~~~~ 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C utility/kmers-writer.C:58:2: warning: how to set prefix size for streaming operations? [-W#warnings] #warning how to set prefix size for streaming operations? ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C utility/kmers-exact.C:420:21: warning: format specifies type 'unsigned int' but the argument has type 'uint64' (aka 'unsigned long') [-Wformat] _minValue, _maxValue, value, _valueBits); ^~~~~~~~~ utility/kmers-exact.C:420:32: warning: format specifies type 'unsigned int' but the argument has type 'uint64' (aka 'unsigned long') [-Wformat] _minValue, _maxValue, value, _valueBits); ^~~~~~~~~ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C 2 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C utility/objectStore.C:257:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] args[1] = "download"; ^ utility/objectStore.C:258:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] args[2] = "--overwrite"; ^ utility/objectStore.C:259:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] args[3] = "--no-progress"; ^ utility/objectStore.C:260:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] args[4] = "--output"; ^ 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C correction/computeGlobalScore.C:151:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C stores/sqReadDataWriter.C:109:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("BLOB"); ^ stores/sqReadDataWriter.C:110:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("NAME", _name, _nameLen); ^ stores/sqReadDataWriter.C:115:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only) ^ stores/sqReadDataWriter.C:117:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN) ^ stores/sqReadDataWriter.C:119:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence ^ stores/sqReadDataWriter.C:124:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only) ^ stores/sqReadDataWriter.C:126:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN) ^ stores/sqReadDataWriter.C:128:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence ^ stores/sqReadDataWriter.C:132:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] buffer->closeIFFchunk("BLOB"); ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C 9 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C stores/sqStoreInfo.C:333:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("MAGC", _sqMagic); ^ stores/sqStoreInfo.C:334:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("VERS", _sqVersion); ^ stores/sqStoreInfo.C:336:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("LSIZ", _sqLibrarySize); ^ stores/sqStoreInfo.C:337:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("RSIZ", _sqReadSize); ^ stores/sqStoreInfo.C:338:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("MLB ", _sqMaxLibrariesBits); ^ stores/sqStoreInfo.C:339:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("LNS ", _sqLibraryNameSize); ^ stores/sqStoreInfo.C:340:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("MRB ", _sqMaxReadBits); ^ stores/sqStoreInfo.C:341:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("MRLB", _sqMaxReadLenBits); ^ stores/sqStoreInfo.C:343:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("NLIB", _numLibraries); ^ stores/sqStoreInfo.C:344:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("NREA", _numReads); ^ stores/sqStoreInfo.C:345:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFobject("NBLO", _numBlobs); ^ stores/sqStoreInfo.C:347:20: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFarray("READ", _reads, sqRead_largest); ^ stores/sqStoreInfo.C:348:20: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] B->writeIFFarray("BASE", _bases, sqRead_largest); ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C 13 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C stores/ovOverlap.C:75:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:75:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:76:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:76:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:217:2: warning: NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-W#warnings] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^ 5 warnings generated. stores/ovStoreWriter.C:71:2: warning: not failing if a valid store [-W#warnings] #warning not failing if a valid store ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C stores/ovStoreHistogram.C:360:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:360:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:361:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:361:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C stores/tgTig.C:565:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(LINE, LINEmax, F); LINEnum++; ^~~~~ ~~~~~~~~~~~~~~~~ stores/tgTig.C:690:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(LINE, LINEmax, F); LINEnum++; ^~~~~ ~~~~~~~~~~~~~~~~ stores/tgTig.C:806:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", ^ stores/tgTig.C:826:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", ^ 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); ^ stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenSuggestCircular", lenSuggestCircular); ^ stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenUnassembled", lenUnassembled); ^ stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenBubble", lenBubble); ^ stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenContig", lenContig); ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc 5 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] display("NDalign::processHits()-- ", false); ^ utgcns/libNDalign/NDalign.C:724:15: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] display("NDalign::scanForDeltaBadness()-- ", true); ^ utgcns/libNDalign/NDalign.C:774:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] display("NDalign::realignForward()-- ", displayAlign); ^ utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] display("NDalign::realignBackward()-- ", displayAlign); ^ g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C utgcns/libNDalign/NDalgorithm-forward.C:235:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:235:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:235:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:236:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:236:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:236:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:260:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:260:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:260:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:261:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:261:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:261:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:236:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:236:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:236:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:237:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:237:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:237:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:260:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:260:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:260:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:261:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:261:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:261:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C 4 warnings generated. g++ -o /<>/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C 4 warnings generated. cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/atomic.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/atomic.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/backtrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/backtrace.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/dwarf.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/dwarf.c gfa/gfa.C:123:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] findGFAtokenI(_features, "LN:i:", _length); ^ cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/elf.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/elf.c 1 warning generated. cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/fileline.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/fileline.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/mmap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/mmap.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/mmapio.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/mmapio.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/posix.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/posix.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/print.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/print.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/simple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/simple.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/sort.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/sort.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/state.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/state.c cc -o /<>/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/unknown.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/<>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/libbacktrace/unknown.c g++ -o /<>/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/dumpBlob.C g++ -o /<>/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreBuild.C g++ -o /<>/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreConfig.C stores/ovStoreBuild.C:125:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No overlap store (-O) supplied.\n"); ^ stores/ovStoreBuild.C:128:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No sequence store (-S) supplied.\n"); ^ stores/ovStoreConfig.C:372:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No sequence store (-S) supplied.\n"); ^ stores/ovStoreConfig.C:375:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No input overlap files (-L or last on the command line) supplied.\n"); ^ stores/ovStoreConfig.C:378:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: Can't both -create -describe a config.\n"); ^ stores/ovStoreConfig.C:381:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: Must supply one of -create or -describe.\n"); ^ stores/ovStoreConfig.C:385:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0 ^ 2 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreBucketizer.C g++ -o /<>/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreSorter.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreIndexer.C stores/ovStoreBucketizer.C:139:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No overlap store (-O) supplied.\n"); ^ stores/ovStoreBucketizer.C:142:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No sequence store (-S) supplied.\n"); ^ stores/ovStoreBucketizer.C:145:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No store configuration (-C) supplied.\n"); ^ stores/ovStoreBucketizer.C:148:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); ^ stores/ovStoreSorter.C:167:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No overlap store (-O) supplied.\n"); ^ stores/ovStoreSorter.C:170:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no slice number (-F) supplied.\n"); ^ 4 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreDump.C stores/ovStoreIndexer.C:80:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No overlap store (-O) supplied.\n"); ^ stores/ovStoreIndexer.C:83:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No sequence store (-S) supplied.\n"); ^ stores/ovStoreIndexer.C:86:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No config (-C) supplied.\n"); ^ 2 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/ovStoreStats.C 3 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/sqStoreCreate.C stores/ovStoreDump.C:832:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input seqStore (-S) supplied.\n"); ^ stores/ovStoreDump.C:835:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); ^ stores/ovStoreDump.C:838:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: -prefix is necessary for -binary output.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C 3 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Isequence stores/sqStoreDumpMetaData.C g++ -o /<>/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Isequence sequence/sequence-summarize.C stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); ^ stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); ^ 2 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgStoreCompress.C g++ -o /<>/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgStoreDump.C g++ -o /<>/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgTigSizeAnalysis.C g++ -o /<>/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgStoreLoad.C g++ -o /<>/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgStoreFilter.C stores/tgStoreDump.C:675:2: warning: replace this with genericStatistics [-W#warnings] #warning replace this with genericStatistics ^ stores/tgStoreDump.C:1166:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No sequence store (-S option) supplied.\n"); ^ stores/tgStoreDump.C:1169:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No tig store (-T option) supplied.\n"); ^ stores/tgStoreDump.C:1172:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No tig store version (-T option) supplied.\n"); ^ stores/tgStoreDump.C:1175:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("-coverage needs and output prefix (-o option).\n"); ^ stores/tgStoreDump.C:1178:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No DUMP TYPE supplied.\n"); ^ stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); ^ stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenSuggestCircular", lenSuggestCircular); ^ stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenUnassembled", lenUnassembled); ^ stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenBubble", lenBubble); ^ stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] printSummary(out, "lenContig", lenContig); ^ stores/tgStoreLoad.C:194:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no sequence store (-S) supplied.\n"); ^ stores/tgStoreLoad.C:196:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no tig store (-T) supplied.\n"); ^ stores/tgStoreLoad.C:198:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); ^ 5 warnings generated. 3 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/tgTigDisplay.C g++ -o /<>/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/loadCorrectedReads.C g++ -o /<>/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C stores/loadTrimmedReads.C:180:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no sequence store (-S) supplied.\n"); ^ stores/loadCorrectedReads.C:76:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no sequence store (-S) supplied.\n"); ^ stores/loadCorrectedReads.C:78:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no tig store (-T) supplied.\n"); ^ stores/loadCorrectedReads.C:80:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input tigs supplied on command line and no -L file supplied.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility stores/loadErates.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/meryl.C 3 warnings generated. 6 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylCountArray.C g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylInput.C stores/loadErates.C:214:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No overlap store (-O) supplied.\n"); ^ stores/loadErates.C:217:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No sequence store (-S) supplied.\n"); ^ stores/loadErates.C:220:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); ^ In file included from meryl/meryl.C:46: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ meryl/meryl.C:261:2: warning: HARD CODED NUMBER OF FILES! [-W#warnings] #warning HARD CODED NUMBER OF FILES! ^ In file included from meryl/merylCountArray.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning3: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H warning:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:s58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ generated. In file included from meryl/merylInput.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylOp-count.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylOp-countSimple.C In file included from meryl/merylOp-count.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ In file included from meryl/merylOp-countSimple.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ 6 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylOp-histogram.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylOp-nextMer.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylOp.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/meryl-import.C In file included from meryl/merylOp-histogram.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ In file included from meryl/merylOp-nextMer.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ meryl/merylOp-nextMer.C:98:2: warning: "need to decide whic direction we're going?" [-W#warnings] #warning "need to decide whic direction we're going?" ^ meryl/merylOp-nextMer.C:116:2: warning: "rounding issues in word-frequency!" [-W#warnings] #warning "rounding issues in word-frequency!" ^ In file included from meryl/merylOp.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/merylCountArray.C In file included from meryl/meryl-import.C:31: In file included from meryl/merylCountArray.H:29: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ meryl/meryl-import.C:92:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No input kmer file (-kmers) supplied.\n"); ^ meryl/meryl-import.C:94:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No output database name (-output) supplied.\n"); ^ meryl/meryl-import.C:96:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No kmer size (-k) supplied.\n"); ^ 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Imeryl -I/<>/src -Iutility -Istores meryl/meryl-lookup.C 8 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence.C 7 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-extract.C In file included from meryl/merylCountArray.C:26: In file included from meryl/meryl.H:51: meryl/merylInput.H:51:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_operation) return("meryl-operation"); ^ meryl/merylInput.H:52:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_stream) return("meryl-database"); ^ meryl/merylInput.H:53:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_sequence) return("sequence-file"); ^ meryl/merylInput.H:55:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (_store) return("canu-seqStore"); ^ meryl/merylInput.H:58:11: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] return("invalid-input"); ^ meryl/meryl-lookup.C:285:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No input sequences (-sequence) supplied.\n"); ^ sequence/sequence.C:414:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] meryl/meryl-lookup.C:287:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); ^ err.push_back("No query meryl database (-mers) supplied.\n"); ^ sequence/sequence.C:418meryl/meryl-lookup.C:289:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No report-type (-existence, etc) supplied.\n"); ^ :21: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No input sequence files supplied.\n"); ^ sequence/sequence.C:422:21: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No input sequence files supplied.\n"); ^ sequence/sequence.C:428:21: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); ^ sequence/sequence.C:432:21: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: No input sequence files supplied.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-generate.C 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-mutate.C sequence/sequence-generate.C:92:23: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] ">random%08 " F_U64P "\n", nSeqs); ^ 5 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-sample.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-shiftregister.C 3 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-shiftregister-emit-fast.C sequence/sequence-mutate.C:160:50: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); ^ sequence/sequence-sample.C:272:69: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); ^ sequence/sequence-sample.C:273:69: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name()); ^ sequence/sequence-sample.C:417:73: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); ^ 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-shiftregister-search-fast.C g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-shiftregister-search-slow.C g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-simulate.C sequence/sequence-simulate.C:44:33: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] char *path = findSharedFile("share/sequence", distribName); ^ 3 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Isequence -I/<>/src -Iutility sequence/sequence-summarize.C g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C overlapInCore/overlapInCore-Build_Hash_Index.C:258:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 1024, F); ^~~~~ ~~~~~~~~~~~~~ g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C g++ -o /<>/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C g++ -o /<>/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] FILE *BAT = openOutput(outputPrefix, "ovlbat"); ^ overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] FILE *JOB = openOutput(outputPrefix, "ovljob"); ^ overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] FILE *OPT = openOutput(outputPrefix, "ovlopt"); ^ overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] renameToFinal(outputPrefix, "ovlbat"); ^ overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] renameToFinal(outputPrefix, "ovljob"); ^ overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] renameToFinal(outputPrefix, "ovlopt"); ^ g++ -o /<>/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C 6 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C g++ -o /<>/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C overlapInCore/overlapImport.C:158:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input seqStore (-S) supplied.\n"); ^ overlapInCore/overlapImport.C:161:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no input overlap files supplied.\n"); ^ overlapInCore/overlapImport.C:274:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(S, 1024, in->file()); ^~~~~ ~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:304:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(S, 1024, in->file()); ^~~~~ ~~~~~~~~~~~~~~~~~~~ g++ -o /<>/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C 4 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:131:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&me, sizeof(int32), 1, F); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:132:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&er, sizeof(double), 1, F); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:133:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread( starts, sizeof(int32), MAX_ERRORS, F); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/edalign.C:38:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, lineMax, file); ^~~~~ ~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapPair.C:429:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(bRead, bbgn, bend, blen, "B", bID, ^ overlapInCore/overlapPair.C:430:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] aRead, abgn, aend, alen, "A", aID, ^ overlapInCore/overlapPair.C:437:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(aRead, abgn, aend, alen, "A", aID, ^ overlapInCore/overlapPair.C:438:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] bRead, bbgn, bend, blen, "B", bID, ^ overlapInCore/overlapPair.C:479:2: warning: do we need to check for contained too? [-W#warnings] #warning do we need to check for contained too? ^ overlapInCore/overlapPair.C:506:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(bRead, bbgn, bend, blen, "Bb5", bID, ^ overlapInCore/overlapPair.C:507:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] aRead, abgn, aend, alen, "Ab5", aID, ^ overlapInCore/overlapPair.C:532:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID, ^ overlapInCore/overlapPair.C:533:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] bRead, bbgn, bend, blen, "Ba5", bID, ^ overlapInCore/overlapPair.C:560:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(aRead, abgn, aend, alen, "Aa3", aID, ^ overlapInCore/overlapPair.C:561:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] bRead, bbgn, bend, blen, "Ba3", bID, ^ overlapInCore/overlapPair.C:586:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (extendAlignment(bRead, bbgn, bend, blen, "Bb3", bID, ^ overlapInCore/overlapPair.C:587:56: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] aRead, abgn, aend, alen, "Ab3", aID, ^ 3 warnings generated. 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C g++ -o /<>/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C mhap/mhapConvert.C:162:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:162:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:163:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:163:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ 13 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores correction/filterCorrectionOverlaps.C 4 warnings generated. minimap/mmapConvert.C:142:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:142:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:143:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:143:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ g++ -o /<>/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C 4 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iutgcns utgcns/stashContains.C g++ -o /<>/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores correction/filterCorrectionLayouts.C g++ -o /<>/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iutgcns correction/falconsense.C g++ -o /<>/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iutgcns utgcns/stashContains.C correction/falconsense.C:70:8: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (fgets(L, 1024, R); ^~~~~ ~~~~~~~~~~ correction/falconsense.C:72:8: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(L, 1024, R)) { ^~~~~ ~~~~~~~~~~ correction/falconsense.C:359:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no seqStore input (-S) supplied.\n"); ^ correction/falconsense.C:362:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no corStore input (-C) supplied.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C g++ -o /<>/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C haplotyping/splitHaplotype.C:707:23: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] ">%s\n", s->_names[ii].string()); ^ haplotyping/splitHaplotype.C:771:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("No input sequences supplied with either (-S) or (-R).\n"); ^ haplotyping/splitHaplotype.C:773:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("Only one type of input reads (-S or -R) supported.\n"); ^ haplotyping/splitHaplotype.C:775:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("Not enough haplotypes (-H) supplied.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/trimReads.C 4 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C In file included from overlapBasedTrimming/trimReads.C:31: overlapBasedTrimming/trimStat.H:74:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(N); ^~~~~~ ~ overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] readsIn .generatePlots(outputPrefix, "inputReads", 250); ^ overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); ^ overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); ^ overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); ^ overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); ^ overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); ^ overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); ^ overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] trim5.generatePlots(outputPrefix, "trim5", 25); ^ g++ -o /<>/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] trim3.generatePlots(outputPrefix, "trim3", 25); ^ 4 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/splitReads.C 10 warnings generated. g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C In file included from overlapBasedTrimming/splitReads.C:31: overlapBasedTrimming/trimStat.H:74:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(N); ^~~~~~ ~ g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C g++ -o /<>/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C g++ -o /<>/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C g++ -o /<>/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++11 does not allow conversion from string literal to 'std::vector >::value_type' (aka 'char *') [-Wwritable-strings] err.push_back("ERROR: no sequence store (-S) supplied.\n"); ^ g++ -o /<>/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C 1 warning generated. g++ -o /<>/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/<>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C overlapAlign/computeOverlapAlignment.C:581:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into ^ overlapAlign/computeOverlapAlignment.C:582:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends. ^ overlapAlign/computeOverlapAlignment.C:626:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into ^ overlapAlign/computeOverlapAlignment.C:627:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. ^ overlapAlign/computeOverlapAlignment.C:674:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into ^ overlapAlign/computeOverlapAlignment.C:675:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends. ^ overlapAlign/computeOverlapAlignment.C:719:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into ^ overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. ^ overlapAlign/clearRangeFile.C:29:38: error: addition of default argument on redeclaration makes this constructor a default constructor clearRangeFile::clearRangeFile(char *filename=NULL) { ^ ~~~~ overlapAlign/clearRangeFile.H:36:3: note: previous declaration is here clearRangeFile(char *filename); ^ 1 error generated. make[2]: *** [Makefile:715: /<>/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o] Error 1 make[2]: *** Waiting for unfinished jobs.... 8 warnings generated. make[2]: Leaving directory '/<>/src' dh_auto_build: error: cd src && make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:13: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T04:19:52Z 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: 38892 Build-Time: 34 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: canu_2.0+dfsg-1 Machine Architecture: amd64 Package: canu Package-Time: 69 Source-Version: 2.0+dfsg-1 Space: 38892 Status: attempted Version: 2.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-05-03T04:19:52Z Build needed 00:01:09, 38892k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 70.327657971s DC-Time-Estimation: 70.327657971 versus expected 403 (r/m: 4.73032021294068 ; m: 70.327657971)