DC-Build-Header: gatb-core 1.4.1+dfsg-3 / 2019-01-09 19:41:07 +0000 DC-Task: type:rebuild-binarch-only source:gatb-core version:1.4.1+dfsg-3 chroot:unstable esttime:1727 logfile:/tmp/gatb-core_1.4.1+dfsg-3_unstable_clang7.log modes:clang7:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang7 gatb-core_1.4.1+dfsg-3' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-1-182.eu-central-1.compute.internal +==============================================================================+ | gatb-core 1.4.1+dfsg-3 (amd64) Wed, 09 Jan 2019 19:41:07 +0000 | +==============================================================================+ Package: gatb-core Version: 1.4.1+dfsg-3 Source Version: 1.4.1+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-cbbb60b0-aa92-45bb-963d-10e9d30867a5' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang7 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=7 + echo 'Install of clang-7' Install of clang-7 + apt-get update Get:1 http://127.0.0.1:9999/debian sid InRelease [238 kB] Get:2 http://127.0.0.1:9999/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:4 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:6 http://127.0.0.1:9999/debian sid/main Translation-en [6275 kB] Fetched 6633 kB in 2s (3386 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-7 libomp-7-dev libobjc-8-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev libclang1-7 libedit2 libgc1c2 libllvm7 libobjc4 libomp5-7 Suggested packages: clang-7-doc libomp-7-doc Recommended packages: llvm-7-dev python The following NEW packages will be installed: clang-7 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev libclang1-7 libedit2 libgc1c2 libllvm7 libobjc-8-dev libobjc4 libomp-7-dev libomp5-7 0 upgraded, 14 newly installed, 0 to remove and 5 not upgraded. Need to get 34.5 MB of archives. After this operation, 185 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libllvm7 amd64 1:7.0.1-4 [13.0 MB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libobjc4 amd64 8.2.0-14 [50.4 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 libobjc-8-dev amd64 8.2.0-14 [225 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libc6-i386 amd64 2.28-4 [2873 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 lib32gcc1 amd64 1:8.2.0-14 [47.9 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lib32stdc++6 amd64 8.2.0-14 [406 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 libclang-common-7-dev amd64 1:7.0.1-4 [3155 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 libclang1-7 amd64 1:7.0.1-4 [5991 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 clang-7 amd64 1:7.0.1-4 [7887 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 libomp5-7 amd64 1:7.0.1-4 [318 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 libomp-7-dev amd64 1:7.0.1-4 [57.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.5 MB in 0s (116 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11802 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm7:amd64. Preparing to unpack .../02-libllvm7_1%3a7.0.1-4_amd64.deb ... Unpacking libllvm7:amd64 (1:7.0.1-4) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../03-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../04-libobjc4_8.2.0-14_amd64.deb ... Unpacking libobjc4:amd64 (8.2.0-14) ... Selecting previously unselected package libobjc-8-dev:amd64. Preparing to unpack .../05-libobjc-8-dev_8.2.0-14_amd64.deb ... Unpacking libobjc-8-dev:amd64 (8.2.0-14) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../06-libc6-i386_2.28-4_amd64.deb ... Unpacking libc6-i386 (2.28-4) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../07-lib32gcc1_1%3a8.2.0-14_amd64.deb ... Unpacking lib32gcc1 (1:8.2.0-14) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../08-lib32stdc++6_8.2.0-14_amd64.deb ... Unpacking lib32stdc++6 (8.2.0-14) ... Selecting previously unselected package libclang-common-7-dev. Preparing to unpack .../09-libclang-common-7-dev_1%3a7.0.1-4_amd64.deb ... Unpacking libclang-common-7-dev (1:7.0.1-4) ... Selecting previously unselected package libclang1-7:amd64. Preparing to unpack .../10-libclang1-7_1%3a7.0.1-4_amd64.deb ... Unpacking libclang1-7:amd64 (1:7.0.1-4) ... Selecting previously unselected package clang-7. Preparing to unpack .../11-clang-7_1%3a7.0.1-4_amd64.deb ... Unpacking clang-7 (1:7.0.1-4) ... Selecting previously unselected package libomp5-7:amd64. Preparing to unpack .../12-libomp5-7_1%3a7.0.1-4_amd64.deb ... Unpacking libomp5-7:amd64 (1:7.0.1-4) ... Selecting previously unselected package libomp-7-dev. Preparing to unpack .../13-libomp-7-dev_1%3a7.0.1-4_amd64.deb ... Unpacking libomp-7-dev (1:7.0.1-4) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libc6-i386 (2.28-4) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libomp5-7:amd64 (1:7.0.1-4) ... Processing triggers for libc-bin (2.28-4) ... Setting up libomp-7-dev (1:7.0.1-4) ... Setting up lib32gcc1 (1:8.2.0-14) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libobjc4:amd64 (8.2.0-14) ... Setting up libobjc-8-dev:amd64 (8.2.0-14) ... Setting up libllvm7:amd64 (1:7.0.1-4) ... Setting up libclang1-7:amd64 (1:7.0.1-4) ... Setting up lib32stdc++6 (8.2.0-14) ... Setting up libclang-common-7-dev (1:7.0.1-4) ... Setting up clang-7 (1:7.0.1-4) ... Processing triggers for libc-bin (2.28-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-7 g++-4.6 + ln -s clang-7 gcc-4.6 + ln -s clang-7 cpp-4.6 + ln -s clang-7 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++-7 g++-4.7 + ln -s clang-7 gcc-4.7 + ln -s clang-7 cpp-4.7 + ln -s clang-7 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++-7 g++-4.8 + ln -s clang-7 gcc-4.8 + ln -s clang-7 cpp-4.8 + ln -s clang-7 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++-7 g++-4.9 + ln -s clang-7 gcc-4.9 + ln -s clang-7 cpp-4.9 + ln -s clang-7 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++-7 g++-5 + ln -s clang-7 gcc-5 + ln -s clang-7 cpp-5 + ln -s clang-7 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++-7 g++-6 + ln -s clang-7 gcc-6 + ln -s clang-7 cpp-6 + ln -s clang-7 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++-7 g++-7 + ln -s clang-7 gcc-7 + ln -s clang-7 cpp-7 + ln -s clang-7 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++-7 g++-8 + ln -s clang-7 gcc-8 + ln -s clang-7 cpp-8 + ln -s clang-7 gcc + echo 'gcc-8 hold' + dpkg --set-selections + echo 'g++-8 hold' + dpkg --set-selections + cd - /build/gatb-core-3MDy3B + 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 I: Finished running '/tmp/clang7'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libmpfr6 libpam-modules libpam-modules-bin libpam-runtime libpam0g 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1519 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libpam0g amd64 1.1.8-4 [124 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules-bin amd64 1.1.8-4 [106 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules amd64 1.1.8-4 [305 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libpam-runtime all 1.1.8-4 [211 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libmpfr6 amd64 4.0.2~rc1-1 [773 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1519 kB in 0s (77.6 MB/s) (Reading database ... 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(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 ... 12592 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.1.8-4_all.deb ... Unpacking libpam-runtime (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam-runtime (1.1.8-4) ... (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 ... 12592 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.0.2~rc1-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.0.2~rc1-1) over (4.0.1-2) ... Setting up libmpfr6:amd64 (4.0.2~rc1-1) ... Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'gatb-core' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gatb-core.git Please use: git clone https://salsa.debian.org/med-team/gatb-core.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2960 kB of source archives. Get:1 http://127.0.0.1:9999/debian sid/main gatb-core 1.4.1+dfsg-3 (dsc) [2312 B] Get:2 http://127.0.0.1:9999/debian sid/main gatb-core 1.4.1+dfsg-3 (tar) [2939 kB] Get:3 http://127.0.0.1:9999/debian sid/main gatb-core 1.4.1+dfsg-3 (diff) [19.4 kB] Fetched 2960 kB in 1s (4051 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/gatb-core-3MDy3B/gatb-core-1.4.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gatb-core-3MDy3B' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-3MngHJ/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-3MngHJ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-3MngHJ/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-3MngHJ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-3MngHJ/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-3MngHJ/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-3MngHJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz Filtered Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz dpkg-deb: building package 'sbuild-build-depends-gatb-core-dummy' in '/<>/resolver-3MngHJ/apt_archive/sbuild-build-depends-gatb-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gatb-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-3MngHJ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-3MngHJ/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-3MngHJ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-3MngHJ/apt_archive ./ Sources [539 B] Get:5 copy:/<>/resolver-3MngHJ/apt_archive ./ Packages [625 B] Fetched 2127 B in 0s (0 B/s) Reading package lists... Reading package lists... Install gatb-core 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 bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.67-dev libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhdf5-103 libhdf5-cpp-103 libhdf5-dev libice6 libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm6.0 libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1 libssl1.1 libsz2 libthai-data libthai0 libtiff5 libtool libuchardet0 libuv1 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 lsb-base m4 man-db po-debconf procps sensible-utils ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff lrzip libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-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 libcppunit-doc libgd-tools krb5-doc krb5-user libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx fonts-liberation ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.67-dev libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhdf5-103 libhdf5-cpp-103 libhdf5-dev libice6 libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm6.0 libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1 libssl1.1 libsz2 libthai-data libthai0 libtiff5 libtool libuchardet0 libuv1 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 lsb-base m4 man-db po-debconf procps sbuild-build-depends-gatb-core-dummy sensible-utils ucf x11-common zlib1g-dev 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 80.7 MB of archives. After this operation, 397 MB of additional disk space will be used. Get:1 copy:/<>/resolver-3MngHJ/apt_archive ./ sbuild-build-depends-gatb-core-dummy 0.invalid.0 [916 B] Get:2 http://127.0.0.1:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 groff-base amd64 1.22.4-2 [917 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-2 [29.5 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 man-db amd64 2.8.5-1 [1274 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lsb-base all 10.2018112800 [28.3 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB] Get:15 http://127.0.0.1:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:16 http://127.0.0.1:9999/debian sid/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:17 http://127.0.0.1:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:18 http://127.0.0.1:9999/debian sid/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:19 http://127.0.0.1:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB] Get:20 http://127.0.0.1:9999/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:21 http://127.0.0.1:9999/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:22 http://127.0.0.1:9999/debian sid/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:23 http://127.0.0.1:9999/debian sid/main amd64 cmake-data all 3.13.2-1 [1476 kB] Get:24 http://127.0.0.1:9999/debian sid/main amd64 libicu63 amd64 63.1-5 [8293 kB] Get:25 http://127.0.0.1:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:26 http://127.0.0.1:9999/debian sid/main amd64 libarchive13 amd64 3.3.3-3 [313 kB] Get:27 http://127.0.0.1:9999/debian sid/main amd64 libkeyutils1 amd64 1.5.9-9.3 [13.0 kB] Get:28 http://127.0.0.1:9999/debian sid/main amd64 libkrb5support0 amd64 1.16.2-1 [63.3 kB] Get:29 http://127.0.0.1:9999/debian sid/main amd64 libk5crypto3 amd64 1.16.2-1 [121 kB] Get:30 http://127.0.0.1:9999/debian sid/main amd64 libkrb5-3 amd64 1.16.2-1 [320 kB] Get:31 http://127.0.0.1:9999/debian sid/main amd64 libgssapi-krb5-2 amd64 1.16.2-1 [158 kB] Get:32 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27~rc8-1 [68.4 kB] Get:33 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-2 amd64 2.1.27~rc8-1 [105 kB] Get:34 http://127.0.0.1:9999/debian sid/main amd64 libldap-common all 2.4.47+dfsg-1 [88.8 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http://127.0.0.1:9999/debian sid/main amd64 cmake amd64 3.13.2-1 [3485 kB] Get:47 http://127.0.0.1:9999/debian sid/main amd64 d-shlibs all 0.83 [17.1 kB] Get:48 http://127.0.0.1:9999/debian sid/main amd64 libtool all 2.4.6-6 [547 kB] Get:49 http://127.0.0.1:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:50 http://127.0.0.1:9999/debian sid/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:51 http://127.0.0.1:9999/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB] Get:52 http://127.0.0.1:9999/debian sid/main amd64 dh-strip-nondeterminism all 1.0.0-1 [12.5 kB] Get:53 http://127.0.0.1:9999/debian sid/main amd64 libelf1 amd64 0.175-2 [160 kB] Get:54 http://127.0.0.1:9999/debian sid/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:55 http://127.0.0.1:9999/debian sid/main amd64 libglib2.0-0 amd64 2.58.2-3 [1257 kB] Get:56 http://127.0.0.1:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:57 http://127.0.0.1:9999/debian sid/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:58 http://127.0.0.1:9999/debian sid/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:59 http://127.0.0.1:9999/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:60 http://127.0.0.1:9999/debian sid/main amd64 debhelper all 12 [1002 kB] Get:61 http://127.0.0.1:9999/debian sid/main amd64 libllvm6.0 amd64 1:6.0.1-9.2 [14.7 MB] Get:62 http://127.0.0.1:9999/debian sid/main amd64 libclang1-6.0 amd64 1:6.0.1-9.2 [6959 kB] Get:63 http://127.0.0.1:9999/debian sid/main amd64 libxapian30 amd64 1.4.9-1 [1101 kB] Get:64 http://127.0.0.1:9999/debian sid/main amd64 doxygen amd64 1.8.13-10 [3985 kB] Get:65 http://127.0.0.1:9999/debian sid/main amd64 libpng16-16 amd64 1.6.36-2 [292 kB] Get:66 http://127.0.0.1:9999/debian sid/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:67 http://127.0.0.1:9999/debian sid/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:68 http://127.0.0.1:9999/debian sid/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:69 http://127.0.0.1:9999/debian sid/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:70 http://127.0.0.1:9999/debian sid/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:71 http://127.0.0.1:9999/debian sid/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:72 http://127.0.0.1:9999/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:73 http://127.0.0.1:9999/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:74 http://127.0.0.1:9999/debian sid/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:75 http://127.0.0.1:9999/debian sid/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:76 http://127.0.0.1:9999/debian sid/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:77 http://127.0.0.1:9999/debian sid/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:78 http://127.0.0.1:9999/debian sid/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:79 http://127.0.0.1:9999/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:80 http://127.0.0.1:9999/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:81 http://127.0.0.1:9999/debian sid/main amd64 libcairo2 amd64 1.16.0-2 [690 kB] Get:82 http://127.0.0.1:9999/debian sid/main amd64 libcdt5 amd64 2.40.1-5+b2 [60.9 kB] Get:83 http://127.0.0.1:9999/debian sid/main amd64 libcgraph6 amd64 2.40.1-5+b2 [84.5 kB] Get:84 http://127.0.0.1:9999/debian sid/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:85 http://127.0.0.1:9999/debian sid/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:86 http://127.0.0.1:9999/debian sid/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:87 http://127.0.0.1:9999/debian sid/main amd64 libtiff5 amd64 4.0.10-3 [257 kB] Get:88 http://127.0.0.1:9999/debian sid/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:89 http://127.0.0.1:9999/debian sid/main amd64 libgd3 amd64 2.2.5-5 [136 kB] Get:90 http://127.0.0.1:9999/debian sid/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get:91 http://127.0.0.1:9999/debian sid/main amd64 libltdl7 amd64 2.4.6-6 [390 kB] Get:92 http://127.0.0.1:9999/debian sid/main amd64 libfribidi0 amd64 1.0.5-3 [63.3 kB] Get:93 http://127.0.0.1:9999/debian sid/main amd64 libthai-data all 0.1.28-1 [170 kB] Get:94 http://127.0.0.1:9999/debian sid/main amd64 libdatrie1 amd64 0.2.12-1 [39.1 kB] Get:95 http://127.0.0.1:9999/debian sid/main amd64 libthai0 amd64 0.1.28-1 [53.9 kB] Get:96 http://127.0.0.1:9999/debian sid/main amd64 libpango-1.0-0 amd64 1.42.4-6 [185 kB] Get:97 http://127.0.0.1:9999/debian sid/main amd64 libgraphite2-3 amd64 1.3.12-1 [80.2 kB] Get:98 http://127.0.0.1:9999/debian sid/main amd64 libharfbuzz0b amd64 2.3.0-1 [1176 kB] Get:99 http://127.0.0.1:9999/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.42.4-6 [67.9 kB] Get:100 http://127.0.0.1:9999/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.42.4-6 [55.5 kB] Get:101 http://127.0.0.1:9999/debian sid/main amd64 libpathplan4 amd64 2.40.1-5+b2 [63.8 kB] Get:102 http://127.0.0.1:9999/debian sid/main amd64 libxdot4 amd64 2.40.1-5+b2 [57.2 kB] Get:103 http://127.0.0.1:9999/debian sid/main amd64 libgvc6 amd64 2.40.1-5+b2 [647 kB] Get:104 http://127.0.0.1:9999/debian sid/main amd64 libgvpr2 amd64 2.40.1-5+b2 [213 kB] Get:105 http://127.0.0.1:9999/debian sid/main amd64 x11-common all 1:7.7+19 [251 kB] Get:106 http://127.0.0.1:9999/debian sid/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:107 http://127.0.0.1:9999/debian sid/main amd64 liblab-gamut1 amd64 2.40.1-5+b2 [221 kB] Get:108 http://127.0.0.1:9999/debian sid/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:109 http://127.0.0.1:9999/debian sid/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:110 http://127.0.0.1:9999/debian sid/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:111 http://127.0.0.1:9999/debian sid/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:112 http://127.0.0.1:9999/debian sid/main amd64 graphviz amd64 2.40.1-5+b2 [595 kB] Get:113 http://127.0.0.1:9999/debian sid/main amd64 hdf5-helpers amd64 1.10.4+repack-8 [35.1 kB] Get:114 http://127.0.0.1:9999/debian sid/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:115 http://127.0.0.1:9999/debian sid/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:116 http://127.0.0.1:9999/debian sid/main amd64 libaec-dev amd64 1.0.2-1 [18.4 kB] Get:117 http://127.0.0.1:9999/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-11 [8386 kB] Get:118 http://127.0.0.1:9999/debian sid/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get:119 http://127.0.0.1:9999/debian sid/main amd64 libcppunit-1.14-0 amd64 1.14.0-3 [140 kB] Get:120 http://127.0.0.1:9999/debian sid/main amd64 libcppunit-dev amd64 1.14.0-3 [196 kB] Get:121 http://127.0.0.1:9999/debian sid/main amd64 libgfortran5 amd64 8.2.0-14 [581 kB] Get:122 http://127.0.0.1:9999/debian sid/main amd64 libhdf5-103 amd64 1.10.4+repack-8 [1324 kB] Get:123 http://127.0.0.1:9999/debian sid/main amd64 libhdf5-cpp-103 amd64 1.10.4+repack-8 [146 kB] Get:124 http://127.0.0.1:9999/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get:125 http://127.0.0.1:9999/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:1.5.2-2+b1 [208 kB] Get:126 http://127.0.0.1:9999/debian sid/main amd64 libjpeg-dev all 1:1.5.2-2 [57.5 kB] Get:127 http://127.0.0.1:9999/debian sid/main amd64 libhdf5-dev amd64 1.10.4+repack-8 [2594 kB] Get:128 http://127.0.0.1:9999/debian sid/main amd64 libjsoncpp-dev amd64 1.7.4-3 [86.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.7 MB in 1s (108 MB/s) Selecting previously unselected package bsdmainutils. 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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 x11-common (1:7.7+19) ... 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 libgfortran5:amd64 (8.2.0-14) ... Setting up hdf5-helpers (1.10.4+repack-8) ... Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up libcdt5 (2.40.1-5+b2) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcgraph6 (2.40.1-5+b2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... 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Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.2 g++-8_8.2.0-14 gcc-8_8.2.0-14 libc6-dev_2.28-4 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 linux-libc-dev_4.19.13-1 Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 clang-7_1:7.0.1-4 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-14 d-shlibs_0.83 dash_0.5.10.2-4 debconf_1.5.69 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 doxygen_1.8.13-10 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2 g++-8_8.2.0-14 gcc_4:8.2.0-2 gcc-8_8.2.0-14 gcc-8-base_8.2.0-14 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 graphviz_2.40.1-5+b2 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hdf5-helpers_1.10.4+repack-8 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8.2.0-14 lib32stdc++6_8.2.0-14 libacl1_2.2.52-3+b1 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-3 libasan5_8.2.0-14 libatomic1_8.2.0-14 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-11 libblkid1_2.33-0.2 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-4 libc-dev-bin_2.28-4 libc6_2.28-4 libc6-dev_2.28-4 libc6-i386_2.28-4 libcairo2_1.16.0-2 libcap-ng0_0.7.9-1+b1 libcc1-0_8.2.0-14 libcdt5_2.40.1-5+b2 libcgraph6_2.40.1-5+b2 libclang-common-7-dev_1:7.0.1-4 libclang1-6.0_1:6.0.1-9.2 libclang1-7_1:7.0.1-4 libcom-err2_1.44.5-1 libcppunit-1.14-0_1.14.0-3 libcppunit-dev_1.14.0-3 libcroco3_0.6.12-3 libcurl4_7.62.0-1 libdatrie1_0.2.12-1 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.246 libdpkg-perl_1.19.2 libedit2_3.1-20181209-1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libfribidi0_1.0.5-3 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.2.0-14 libgcc1_1:8.2.0-14 libgcrypt20_1.8.4-4 libgd3_2.2.5-5 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libgfortran5_8.2.0-14 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2 libgomp1_8.2.0-14 libgpg-error0_1.33-3 libgraphite2-3_1.3.12-1 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libobjc4_8.2.0-14 libomp-7-dev_1:7.0.1-4 libomp5-7_1:7.0.1-4 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpango-1.0-0_1.42.4-6 libpangocairo-1.0-0_1.42.4-6 libpangoft2-1.0-0_1.42.4-6 libpathplan4_2.40.1-5+b2 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libquadmath0_8.2.0-14 librhash0_1.3.7-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.33-0.2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 libsystemd0_240-2 libsz2_1.0.2-1 libtasn1-6_4.13-3 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff5_4.0.10-3 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libtsan0_8.2.0-14 libubsan1_8.2.0-14 libuchardet0_0.0.6-3 libudev1_240-2 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libuv1_1.24.0-1 libwebp6_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxapian30_1.4.9-1 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxdot4_2.40.1-5+b2 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-7+b3 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.13-1 login_1:4.5-1.1 lsb-base_10.2018112800 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mount_2.33-0.2 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 po-debconf_1.0.21 procps_2:3.3.15-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gatb-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 ucf_3.0038+nmu1 util-linux_2.33-0.2 x11-common_1:7.7+19 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 15 10:47:10 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+dfsg-3.dsc dpkg-source: info: extracting gatb-core in /<>/gatb-core-1.4.1+dfsg dpkg-source: info: unpacking gatb-core_1.4.1+dfsg.orig.tar.xz dpkg-source: info: unpacking gatb-core_1.4.1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_hdf5.patch dpkg-source: info: applying fix_hdf5_includes.patch dpkg-source: info: applying dynamic_lib.patch dpkg-source: info: applying fix_install_location.patch dpkg-source: info: applying set_soversion.patch dpkg-source: info: applying dynamic_linking_of_tools.patch dpkg-source: info: applying multiarch.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX 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-cbbb60b0-aa92-45bb-963d-10e9d30867a5 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=gatb-core dh_auto_clean -O--sourcedirectory=gatb-core dh_autoreconf_clean -O--sourcedirectory=gatb-core dh_clean -O--sourcedirectory=gatb-core debian/rules build-arch dh build-arch --sourcedirectory=gatb-core dh_update_autotools_config -a -O--sourcedirectory=gatb-core dh_autoreconf -a -O--sourcedirectory=gatb-core dh_auto_configure -a -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ../gatb-core -- The C compiler identification is Clang 7.0.1 -- The CXX compiler identification is Clang 7.0.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CppUnit: found headers (in /usr/include) but not the static library (/usr/include/../lib/libcppunit.a) -- CppUnit FOUND (/usr/include) -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of __uint128 -- Check size of __uint128 - failed -- Check size of __uint128_t -- Check size of __uint128_t - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") -- HDF5_LIBRARIES="/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_64-linux-gnu/libz.so/usr/lib/x86_64-linux-gnu/libdl.so/usr/lib/x86_64-linux-gnu/libm.so" -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation CMake Warning (dev) at CMakeLists.txt:238 (set): Cannot set "gatb-core-klist": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- ---------- GATB TESTS ---------- -- ---------- GATB TOOLS ---------- DYNAMIC BINARIES for dbgh5 DYNAMIC BINARIES for dbginfo DYNAMIC BINARIES for leon -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") found components: C CMake Warning (dev) at CMakeLists.txt:265 (set): Cannot set "gatb-core-flags": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:266 (set): Cannot set "gatb-core-includes": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:267 (set): Cannot set "gatb-core-libraries": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:268 (set): Cannot set "gatb-core-cmake": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/ cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/json/json.hpp /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json/ make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 0%] Built target thirdparty_copy Scanning dependencies of target gatbcore-dynamic make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build Scanning dependencies of target gatbcore-static make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (&value, sizeof(value), 1, file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 2 warnings generated. [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp 6 warnings generated. [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp 6 warnings generated. [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (&value, sizeof(value), 1, file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp 2 warnings generated. [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 6 warnings generated. [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp 6 warnings generated. [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 6 warnings generated. [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp 6 warnings generated. [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp 6 warnings generated. [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:99:29: warning: implicit conversion from 'double' to 'unsigned int' changes value from 1.1 to 1 [-Wliteral-conversion] _bulgeAltPath_covMult = 1.1; ~ ^~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1822:16: note: in instantiation of member function 'gatb::core::debruijn::impl::Simplifications, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> >, gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >::Simplifications' requested here template class Simplifications; ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:49:86: error: 'iteratorBranching' following the 'template' keyword does not refer to a template GraphIterator > itBranching = this->_graph.Graph::template iteratorBranching(); ~~~~~~~ ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:333:16: note: in instantiation of member function 'gatb::core::debruijn::impl::BranchingTerminatorTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> > >::BranchingTerminatorTemplate' requested here template class BranchingTerminatorTemplate; ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:610:50: note: declared as a non-template here inline GraphIterator > iteratorBranching () const { return getBranchingNodes (); } ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:199:57: error: 'neighborsEdge' following the 'template' keyword does not refer to a template GraphVector neighbors = this->_graph.template neighborsEdge(node.kmer); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:333:16: note: in instantiation of member function 'gatb::core::debruijn::impl::BranchingTerminatorTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> > >::mark' requested here template class BranchingTerminatorTemplate; ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:641:30: note: declared as a non-template here inline GraphVector neighborsEdge ( Node& node, Direction dir=DIR_END) const { return getEdges(node, dir); } ^ 6 warnings and 2 errors generated. make[4]: *** [src/CMakeFiles/gatbcore-dynamic.dir/build.make:313: src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp 6 warnings generated. [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp 7 warnings generated. [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 6 warnings generated. [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 6 warnings generated. [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp 6 warnings generated. [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu 6 warnings generated. [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32: In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:353:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" // remove the "may be uninitialized" message ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:355:44: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:99:29: warning: implicit conversion from 'double' to 'unsigned int' changes value from 1.1 to 1 [-Wliteral-conversion] _bulgeAltPath_covMult = 1.1; ~ ^~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1822:16: note: in instantiation of member function 'gatb::core::debruijn::impl::Simplifications, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> >, gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >::Simplifications' requested here template class Simplifications; ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:40: warning: format specifies type 'long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("bit array of size %lli: \n",_size); ~~~~ ^~~~~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:24: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf(" (%llu) ",ii); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:30: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~ %lu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:33: warning: format specifies type 'long long' but the argument has type '__gnu_cxx::__alloc_traits, unsigned long>::value_type' (aka 'unsigned long') [-Wformat] printf("%llu : %lli, ",ii,_ranks[ii]); ~~~~ ^~~~~~~~~~ %lu /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:49:86: error: 'iteratorBranching' following the 'template' keyword does not refer to a template GraphIterator > itBranching = this->_graph.Graph::template iteratorBranching(); ~~~~~~~ ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:333:16: note: in instantiation of member function 'gatb::core::debruijn::impl::BranchingTerminatorTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> > >::BranchingTerminatorTemplate' requested here template class BranchingTerminatorTemplate; ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:610:50: note: declared as a non-template here inline GraphIterator > iteratorBranching () const { return getBranchingNodes (); } ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:199:57: error: 'neighborsEdge' following the 'template' keyword does not refer to a template GraphVector neighbors = this->_graph.template neighborsEdge(node.kmer); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:333:16: note: in instantiation of member function 'gatb::core::debruijn::impl::BranchingTerminatorTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > >> > >::mark' requested here template class BranchingTerminatorTemplate; ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:641:30: note: declared as a non-template here inline GraphVector neighborsEdge ( Node& node, Direction dir=DIR_END) const { return getEdges(node, dir); } ^ 6 warnings and 2 errors generated. make[4]: *** [src/CMakeFiles/gatbcore-static.dir/build.make:313: src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... 7 warnings generated. 6 warnings generated. make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:192: src/CMakeFiles/gatbcore-dynamic.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... 6 warnings generated. make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:229: src/CMakeFiles/gatbcore-static.dir/all] Error 2 make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[2]: *** [Makefile:155: all] Error 2 make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' dh_auto_build: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:13: override_dh_auto_build-arch] Error 2 make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' make: *** [debian/rules:10: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-01-09T19:42:30Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 84188 Build-Time: 46 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 22 Job: gatb-core_1.4.1+dfsg-3 Machine Architecture: amd64 Package: gatb-core Package-Time: 83 Source-Version: 1.4.1+dfsg-3 Space: 84188 Status: attempted Version: 1.4.1+dfsg-3 -------------------------------------------------------------------------------- Finished at 2019-01-09T19:42:30Z Build needed 00:01:23, 84188k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 83.74103149s DC-Time-Estimation: 83.74103149 versus expected 1727 (r/m: 19.62310398226025 ; m: 83.74103149)