DC-Build-Header: rna-star 2.7.3a+dfsg-1 / 2020-02-25 16:43:13 +0000 DC-Task: type:rebuild-binarch-only source:rna-star version:2.7.3a+dfsg-1 chroot:unstable esttime:155 logfile:/tmp/rna-star_2.7.3a+dfsg-1_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang8 rna-star_2.7.3a+dfsg-1' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-13-114.eu-central-1.compute.internal +==============================================================================+ | rna-star 2.7.3a+dfsg-1 (amd64) Tue, 25 Feb 2020 16:43:13 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.3a+dfsg-1 Source Version: 2.7.3a+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-80b22636-55bd-472d-9f97-277e8f05d997' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [142 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-0823.32.pdiff [11.0 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-1420.34.pdiff [30.2 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-2014.03.pdiff [16.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0213.11.pdiff [23.2 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:9 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-1413.15.pdiff [16.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-0823.32.pdiff [15.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-1420.34.pdiff [27.5 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-2014.03.pdiff [21.6 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0213.11.pdiff [35.0 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-1413.15.pdiff [18.4 kB] Get:9 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-1413.15.pdiff [16.3 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-1413.15.pdiff [18.4 kB] Get:16 http://127.0.0.1:12990/debian sid/main Translation-en [6195 kB] Fetched 6638 kB in 2s (3783 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libgcc-9-dev libllvm8 libmpx2 libobjc-8-dev libobjc4 libomp5-8 libstdc++-8-dev libstdc++-9-dev Suggested packages: clang-8-doc gcc-9-locales g++-9-multilib gcc-9-doc gcc-9-multilib libomp-8-doc libstdc++-8-doc libstdc++-9-doc Recommended packages: llvm-8-dev python3 The following NEW packages will be installed: clang-8 gcc-8-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libllvm8 libmpx2 libobjc-8-dev libobjc-9-dev libobjc4 libomp-8-dev libomp5-8 libstdc++-8-dev The following packages will be upgraded: cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev 7 upgraded, 20 newly installed, 0 to remove and 3 not upgraded. Need to get 74.9 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.2.1-30 [389 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 gcc-9 amd64 9.2.1-30 [10.0 MB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.2.1-30 [2349 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 cpp-9 amd64 9.2.1-30 [9711 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 gcc-9-base amd64 9.2.1-30 [196 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libllvm8 amd64 1:8.0.1-7 [13.8 MB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gcc-8-base amd64 8.3.0-29 [194 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmpx2 amd64 8.3.0-29 [11.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libgcc-8-dev amd64 8.3.0-29 [2297 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-8-dev amd64 8.3.0-29 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200222-1 [41.6 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-8-dev amd64 8.3.0-29 [227 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.29-10 [2918 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200222-1 [49.4 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200222-1 [1104 B] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200222-1 [510 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-8-dev amd64 1:8.0.1-7 [2989 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libclang1-8 amd64 1:8.0.1-7 [6244 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 clang-8 amd64 1:8.0.1-7 [8010 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.2.1-30 [219 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libomp5-8 amd64 1:8.0.1-7 [331 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp-8-dev amd64 1:8.0.1-7 [62.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.9 MB in 1s (100 MB/s) (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 ... 12119 files and directories currently installed.) Preparing to unpack .../00-libasan5_9.2.1-30_amd64.deb ... Unpacking libasan5:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../01-g++-9_9.2.1-30_amd64.deb ... Unpacking g++-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../02-gcc-9_9.2.1-30_amd64.deb ... Unpacking gcc-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../03-libstdc++-9-dev_9.2.1-30_amd64.deb ... 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W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 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++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 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++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 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++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 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++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 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++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 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++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 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++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-8 g++-9 + ln -s clang-8 gcc-9 + ln -s clang-8 cpp-9 + ln -s clang-8 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-8 g++-10 + ln -s clang-8 gcc-10 + ln -s clang-8 cpp-10 + ln -s clang-8 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/rna-star-pRE9Oz + 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/clang8'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/rna-star-pRE9Oz/resolver-9mP5dV' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bash libgmp10 zlib1g 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1722 kB of archives. After this operation, 4096 B of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 bash amd64 5.0-6 [1379 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libgmp10 amd64 2:6.2.0+dfsg-4 [253 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1722 kB in 0s (69.2 MB/s) (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 ... 13887 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-6_amd64.deb ... Unpacking bash (5.0-6) over (5.0-5) ... Setting up bash (5.0-6) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 13887 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.0+dfsg-4) over (2:6.2.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.2.0+dfsg-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 ... 13887 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-2) over (1:1.2.11.dfsg-1.2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'rna-star' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rna-star.git Please use: git clone https://salsa.debian.org/med-team/rna-star.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 779 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main rna-star 2.7.3a+dfsg-1 (dsc) [1797 B] Get:2 http://127.0.0.1:12990/debian sid/main rna-star 2.7.3a+dfsg-1 (tar) [402 kB] Get:3 http://127.0.0.1:12990/debian sid/main rna-star 2.7.3a+dfsg-1 (diff) [375 kB] Fetched 779 kB in 0s (8601 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-pRE9Oz/rna-star-2.7.3a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-pRE9Oz' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12), libhts-dev, vim-common, xxd, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 12), libhts-dev, vim-common, xxd, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [393 B] Get:5 copy:/<>/apt_archive ./ Packages [475 B] Fetched 1825 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils vim-common xxd zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl vim | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils vim-common xxd zlib1g-dev 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 28.9 MB of archives. After this operation, 89.0 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 xxd amd64 2:8.1.2269-1+b1 [141 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 vim-common all 2:8.1.2269-1 [224 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-13 [513 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] 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Get:35 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 12.9 [994 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6 [266 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.49+dfsg-1 [91.9 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-1 [226 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libdeflate0 amd64 1.5-3 [55.8 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libhts3 amd64 1.10.2-3 [370 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libhts-dev amd64 1.10.2-3 [4846 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.9 MB in 0s (98.6 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 13887 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package xxd. 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Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up xxd (2:8.1.2269-1+b1) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up vim-common (2:8.1.2269-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-10) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up liblzma-dev:amd64 (5.2.4-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-13) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.10.2-3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.9) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 ppc64el mips64el) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-8_1:8.0.1-7 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.2.1-30 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-base_9.2.1-30 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200222-1 lib32gcc1_1:10-20200222-1 lib32stdc++6_10-20200222-1 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-30 libatomic1_10-20200222-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-3 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-dev_2.29-10 libc6-i386_2.29-10 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200222-1 libclang-common-8-dev_1:8.0.1-7 libclang1-8_1:8.0.1-7 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-3 libctf0_2.34-3 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-s1_10-20200222-1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libitm1_10-20200222-1 libk5crypto3_1.17-6 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.49+dfsg-1 libldap-common_2.4.49+dfsg-1 libllvm8_1:8.0.1-7 liblsan0_10-20200222-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libobjc-8-dev_8.3.0-29 libobjc-9-dev_9.2.1-30 libobjc4_10-20200222-1 libomp-8-dev_1:8.0.1-7 libomp5-8_1:8.0.1-7 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpsl5_0.20.2-2 libquadmath0_10-20200222-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-3 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 util-linux_2.34-0.1 vim-common_2:8.1.2269-1 xxd_2:8.1.2269-1+b1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 ppc64el mips64el Version: 2.7.3a+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12), libhts-dev, vim-common, xxd, zlib1g-dev Package-List: rna-star deb science optional arch=amd64,arm64,ppc64el,mips64el Checksums-Sha1: 266317b4505263953cc5b6da1760723a090d0cc3 401788 rna-star_2.7.3a+dfsg.orig.tar.xz 61784784e1e6e8eb8bf9b6baa1afafc74bd7fb3f 375088 rna-star_2.7.3a+dfsg-1.debian.tar.xz Checksums-Sha256: 31ce1c59dfcb7786630dadb31900aa28bfff4add297bb81e0a3ca2222299eb2f 401788 rna-star_2.7.3a+dfsg.orig.tar.xz 5f854617a609320fac1e6fc22b6058b93793137c431103285c473d33e09b9955 375088 rna-star_2.7.3a+dfsg-1.debian.tar.xz Files: f9c87b95a89dec35d24076b29c0486eb 401788 rna-star_2.7.3a+dfsg.orig.tar.xz 04fb9388faea163c5fed0c3704a627aa 375088 rna-star_2.7.3a+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAl2eYc4ACgkQUfhKj+zK fgk6bQf/UIosw6T1+a3OCMZwdOCmOf6OC7xyTHV+tJsNHx2ou5nHkL/et43Ljsbo QPETTCG/TVdYDDUllMqe5usFrkVYEMcUia/XL/DZE/hVK4KsU6Nq9Uq1CE3Yp9JK a4mmENahs/c2REz49m+2Lv6ikC/hlQ8d1/0vfvCO3Fx3wEiaBVLG2mwUvHT80tsS gEhbRNOJSRCkf+CeGCDQpF9NQyniMJDY6Gu+rXPf3spTCN4GQ70CpF8uxfhA/uj5 fi+vLr+BEp6o27eAAGxpUbrjLq7K3PsiucokF3mgs/lvcdJD0BhbS195XHylRYFU CJuGpMo6M2D3RiJSrHmgjsU+EWC+Ng== =bOkL -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 9 22:40:14 2019 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.3a+dfsg-1.dsc dpkg-source: info: extracting rna-star in /<> dpkg-source: info: unpacking rna-star_2.7.3a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.3a+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-80b22636-55bd-472d-9f97-277e8f05d997 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.3a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedirectory=source -- CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" cd source && make -j4 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/source' xxd -i parametersDefault > parametersDefault.xxd echo sjdbPrepare.cpp SoloFeature_collapseUMI.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp SoloBarcode.cpp ChimericAlign.cpp blocksOverlap.cpp SoloReadBarcode.cpp Transcriptome.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp Transcript_generateCigarP.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp SoloReadFeature_record.cpp ReadAlign_calcCIGAR.cpp Genome_genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp SoloFeature_statsOutput.cpp ReadAlign_chimericDetectionOld.cpp SoloFeature_countCBgeneUMI.cpp stitchWindowAligns.cpp SoloRead_record.cpp binarySearch2.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp SoloFeature_addBAMtags.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp BAMbinSortUnmapped.cpp Quantifications.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_chimericDetectionOldOutput.cpp SoloFeature_countVelocyto.cpp SoloReadFeature.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp ChimericDetection_chimericDetectionMult.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp ReadAlign_mappedFilter.cpp ChimericDetection.cpp ParametersChimeric_initialize.cpp ReadAlign_storeAligns.cpp sjAlignSplit.cpp SharedMemory.cpp mapThreadsSpawn.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_oneRead.cpp Transcript.cpp SoloReadBarcode_getCBandUMI.cpp Transcript_variationOutput.cpp genomeScanFastaFiles.cpp ParametersSolo.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp Parameters.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp ReadAlign_mapOneRead.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp SoloFeature_cellFiltering.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Variation.cpp ReadAlign_outputTranscriptSAM.cpp ChimericAlign_chimericJunctionOutput.cpp readLoad.cpp ReadAlign_CIGAR.cpp ReadAlign_outputVariation.cpp sjdbInsertJunctions.cpp Solo.cpp genomeParametersWrite.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp SoloReadFeature_inputRecords.cpp ChimericSegment.cpp Transcriptome_classifyAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature_sumThreads.cpp bamSortByCoordinate.cpp SoloFeature.cpp STAR.cpp SoloBarcode_extractBarcode.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp ReadAlignChunk.cpp bam_cat.c sjdbPrepare.cpp SoloFeature_collapseUMI.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp SoloBarcode.cpp ChimericAlign.cpp blocksOverlap.cpp SoloReadBarcode.cpp Transcriptome.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp Transcript_generateCigarP.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp SoloReadFeature_record.cpp ReadAlign_calcCIGAR.cpp Genome_genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp SoloFeature_statsOutput.cpp ReadAlign_chimericDetectionOld.cpp SoloFeature_countCBgeneUMI.cpp stitchWindowAligns.cpp SoloRead_record.cpp binarySearch2.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp SoloFeature_addBAMtags.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp BAMbinSortUnmapped.cpp Quantifications.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_chimericDetectionOldOutput.cpp SoloFeature_countVelocyto.cpp SoloReadFeature.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp ChimericDetection_chimericDetectionMult.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp ReadAlign_mappedFilter.cpp ChimericDetection.cpp ParametersChimeric_initialize.cpp ReadAlign_storeAligns.cpp sjAlignSplit.cpp SharedMemory.cpp mapThreadsSpawn.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_oneRead.cpp Transcript.cpp SoloReadBarcode_getCBandUMI.cpp Transcript_variationOutput.cpp genomeScanFastaFiles.cpp ParametersSolo.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp Parameters.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp ReadAlign_mapOneRead.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp SoloFeature_cellFiltering.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Variation.cpp ReadAlign_outputTranscriptSAM.cpp ChimericAlign_chimericJunctionOutput.cpp readLoad.cpp ReadAlign_CIGAR.cpp ReadAlign_outputVariation.cpp sjdbInsertJunctions.cpp Solo.cpp genomeParametersWrite.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp SoloReadFeature_inputRecords.cpp ChimericSegment.cpp Transcriptome_classifyAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature_sumThreads.cpp bamSortByCoordinate.cpp SoloFeature.cpp STAR.cpp SoloBarcode_extractBarcode.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp ReadAlignChunk.cpp bam_cat.c 'rm' -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM sjdbPrepare.cpp SoloFeature_collapseUMI.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp SoloBarcode.cpp ChimericAlign.cpp blocksOverlap.cpp SoloReadBarcode.cpp Transcriptome.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp Transcript_generateCigarP.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp SoloReadFeature_record.cpp ReadAlign_calcCIGAR.cpp Genome_genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp SoloFeature_statsOutput.cpp ReadAlign_chimericDetectionOld.cpp SoloFeature_countCBgeneUMI.cpp stitchWindowAligns.cpp SoloRead_record.cpp binarySearch2.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp SoloFeature_addBAMtags.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp BAMbinSortUnmapped.cpp Quantifications.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_chimericDetectionOldOutput.cpp SoloFeature_countVelocyto.cpp SoloReadFeature.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp ChimericDetection_chimericDetectionMult.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp ReadAlign_mappedFilter.cpp ChimericDetection.cpp ParametersChimeric_initialize.cpp ReadAlign_storeAligns.cpp sjAlignSplit.cpp SharedMemory.cpp mapThreadsSpawn.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_oneRead.cpp Transcript.cpp SoloReadBarcode_getCBandUMI.cpp Transcript_variationOutput.cpp genomeScanFastaFiles.cpp ParametersSolo.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp Parameters.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp ReadAlign_mapOneRead.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp SoloFeature_cellFiltering.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Variation.cpp ReadAlign_outputTranscriptSAM.cpp ChimericAlign_chimericJunctionOutput.cpp readLoad.cpp ReadAlign_CIGAR.cpp ReadAlign_outputVariation.cpp sjdbInsertJunctions.cpp Solo.cpp genomeParametersWrite.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp SoloReadFeature_inputRecords.cpp ChimericSegment.cpp Transcriptome_classifyAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature_sumThreads.cpp bamSortByCoordinate.cpp SoloFeature.cpp STAR.cpp SoloBarcode_extractBarcode.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp ReadAlignChunk.cpp bam_cat.c parametersDefault.xxd >> Depend.list clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: parametersDefault.xxd: 'linker' input unused [-Wunused-command-line-argument] g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode.cpp bamSortByCoordinate.cpp:67:31: warning: implicit conversion from 'double' to 'unsigned int' changes value from 0.1 to 0 [-Wliteral-conversion] sleep(0.1); ~~~~~ ^~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp 1 warning generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp STAR.cpp:343:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(P.inOut->outBAMfileUnsorted); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:347:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(P.inOut->outQuantBAMfile); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp SuffixArrayFuns.cpp:18:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int64 ii; ^~~~~~~~~ SuffixArrayFuns.cpp:234:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int64 ii; ^~~~~~~~~ SuffixArrayFuns.cpp:359:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register uint saind=0; ^~~~~~~~~ SuffixArrayFuns.cpp:362:9: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register uint128 g1=*( (uint128*) (gSeq+SAstr) ); ^~~~~~~~~ SuffixArrayFuns.cpp:365:13: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char g2=(char) g1; ^~~~~~~~~ SuffixArrayFuns.cpp:379:9: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); ^~~~~~~~~ SuffixArrayFuns.cpp:382:13: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char g2=(char) (g1>>(8*(15-ii))); ^~~~~~~~~ 7 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp 2 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp In file included from OutSJ.cpp:1: ./OutSJ.h:50:13: warning: private field 'mapGen' is not used [-Wunused-private-field] Genome &mapGen; ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp 1 warning generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' alignSmithWaterman.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' loadGTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] bam_cat.c:80:12: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if (h) bam_hdr_write(fp, h); ^~~~~~~~~~~~~ ~~~~~ bam_cat.c:96:31: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if (h == 0 && i == 0) bam_hdr_write(fp, old); ^~~~~~~~~~~~~ ~~~~~~~ bam_cat.c:99:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(fp); ^~~~~~~~~~ ~~ bam_cat.c:111:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_raw_write(fp, ebuf, len); ^~~~~~~~~~~~~~ ~~~~~~~~~~~~~ bam_cat.c:115:26: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if(j!=0) bgzf_raw_write(fp, ebuf, es); ^~~~~~~~~~~~~~ ~~~~~~~~~~~~ bam_cat.c:118:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_raw_write(fp, buf, len); ^~~~~~~~~~~~~~ ~~~~~~~~~~~~ bam_cat.c:131:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_raw_write(fp, ebuf, es); ^~~~~~~~~~~~~~ ~~~~~~~~~~~~ 8 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp Parameters_readSAMheader.cpp:26:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(com1.c_str()); ^~~~~~ ~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp 1 warning generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMfunctions.cpp:12:25: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] for (int i = 0; i < c->n_cigar; ++i) { ~ ^ ~~~~~~~~~~ BAMfunctions.cpp:59:16: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~ ^ ~~~~~~~~~ BAMfunctions.cpp:85:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,(char*) &rlen,sizeof(rlen)); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:86:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,(char*) &slen,sizeof(slen)); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:76:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,"BAM\001",4); ^~~~~~~~~~ ~~~~~~~~~~~~~~ BAMfunctions.cpp:78:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,(char*) &hlen,sizeof(hlen)); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:79:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,samh.c_str(),hlen); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(fp,(char*) &nchr,sizeof(nchr)); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(fp); ^~~~~~~~~~ ~~ BAMoutput.cpp:59:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp:72:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp In file included from BAMoutput.cpp:1: ./BAMoutput.h:28:12: warning: private field 'binGlen' is not used [-Wunused-private-field] uint64 binGlen;//bin genomic length ^ 3 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp BAMbinSortByCoordinate.cpp:73:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfBin, bam0, size0); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(bgzfBin); ^~~~~~~~~~ ~~~~~~~ 2 warnings generated. g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp:152:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamS); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:125:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bam_hdr_write(bgzfOut, bamHeader); ^~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamLength); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(bgzfOut); ^~~~~~~~~~ ~~~~~~~ 4 warnings generated. BAMbinSortUnmapped.cpp:62:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_write(bgzfBin, bam0, size0); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bgzf_flush(bgzfBin); ^~~~~~~~~~ ~~~~~~~ 2 warnings generated. g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Bstatic -lhts -Bdynamic -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp:61:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(("ls -lL " + rfName + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. /usr/bin/ld: /usr/lib/llvm-8/bin/../lib/LLVMgold.so: error loading plugin: /usr/lib/llvm-8/bin/../lib/LLVMgold.so: cannot open shared object file: No such file or directory clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [Makefile:110: STAR] Error 1 make[2]: Leaving directory '/<>/source' dh_auto_build: error: cd source && make -j4 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" returned exit code 2 make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:15: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-25T16:44:18Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 50864 Build-Time: 43 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 5 Job: rna-star_2.7.3a+dfsg-1 Machine Architecture: amd64 Package: rna-star Package-Time: 65 Source-Version: 2.7.3a+dfsg-1 Space: 50864 Status: attempted Version: 2.7.3a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-02-25T16:44:18Z Build needed 00:01:05, 50864k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 66.075405658s DC-Time-Estimation: 66.075405658 versus expected 155 (r/m: 1.3458047431788045 ; m: 66.075405658)