DC-Build-Header: rna-star 2.4.0i-1 / 2015-03-26 02:57:32 +0000 DC-Task: source:rna-star version:2.4.0i-1 architecture:any chroot:unstable esttime: logfile:/tmp/rna-star_2.4.0i-1_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang rna-star_2.4.0i-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-10-35.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ rna-star 2.4.0i-1 (amd64) 26 Mar 2015 02:57 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: rna-star Version: 2.4.0i-1 Source Version: 2.4.0i-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/rna-star-q6R_Ok/rna-star-2.4.0i' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/rna-star-q6R_Ok' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-2a3218ca-c692-4830-8e0b-75283781e0b7' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [257 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2015-03-25-1448.37.pdiff [3021 B] Get:6 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [5545 B] Get:7 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [5545 B] Get:8 http://localhost:9999 unstable/main amd64 2015-03-25-1448.37.pdiff [4095 B] Get:9 http://localhost:9999 unstable/main amd64 2015-03-25-2049.47.pdiff [4595 B] Get:10 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Get:11 http://localhost:9999 unstable/main amd64 2015-03-25-2049.47.pdiff [4595 B] Get:12 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Fetched 300 kB in 4s (62.9 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'rna-star' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/rna-star/trunk/ Need to get 267 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main rna-star 2.4.0i-1 (dsc) [2024 B] Get:2 http://localhost:9999/debian/ unstable/main rna-star 2.4.0i-1 (tar) [259 kB] Get:3 http://localhost:9999/debian/ unstable/main rna-star 2.4.0i-1 (diff) [5352 B] Fetched 267 kB in 0s (1150 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/clang ────────── + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.6 + echo 'Install of clang-3.6' Install of clang-3.6 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (12.6 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.6 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.6-doc Recommended packages: llvm-3.6-dev python The following NEW packages will be installed: clang-3.6 libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After this operation, 153 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2+b2 [20.1 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.6 amd64 1:3.6-2 [8137 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.2-10 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.2-10 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.6 amd64 1:3.6-2 [3839 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.6-dev amd64 1:3.6-2 [706 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.6 amd64 1:3.6-2 [25.8 MB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 39.2 MB in 1s (37.9 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11980 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+b2) ... Selecting previously unselected package libllvm3.6:amd64. Preparing to unpack .../libllvm3.6_1%3a3.6-2_amd64.deb ... Unpacking libllvm3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.2-10_amd64.deb ... Unpacking libobjc4:amd64 (4.9.2-10) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.2-10_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.2-10) ... Selecting previously unselected package libclang1-3.6:amd64. Preparing to unpack .../libclang1-3.6_1%3a3.6-2_amd64.deb ... Unpacking libclang1-3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libclang-common-3.6-dev. Preparing to unpack .../libclang-common-3.6-dev_1%3a3.6-2_amd64.deb ... Unpacking libclang-common-3.6-dev (1:3.6-2) ... Selecting previously unselected package clang-3.6. Preparing to unpack .../clang-3.6_1%3a3.6-2_amd64.deb ... Unpacking clang-3.6 (1:3.6-2) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2+b2) ... Setting up libllvm3.6:amd64 (1:3.6-2) ... Setting up libobjc4:amd64 (4.9.2-10) ... Setting up libobjc-4.9-dev:amd64 (4.9.2-10) ... Setting up libclang1-3.6:amd64 (1:3.6-2) ... Setting up libclang-common-3.6-dev (1:3.6-2) ... Setting up clang-3.6 (1:3.6-2) ... Processing triggers for libc-bin (2.19-17) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.6 g++-4.6 + ln -s clang-3.6 gcc-4.6 + ln -s clang-3.6 cpp-4.6 + ln -s clang-3.6 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.6 g++-4.7 + ln -s clang-3.6 gcc-4.7 + ln -s clang-3.6 cpp-4.7 + ln -s clang-3.6 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.6 g++-4.8 + ln -s clang-3.6 gcc-4.8 + ln -s clang-3.6 cpp-4.8 + ln -s clang-3.6 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.6 g++-4.9 + ln -s clang-3.6 gcc-4.9 + ln -s clang-3.6 cpp-4.9 + ln -s clang-3.6 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.6 g++-5 + ln -s clang-3.6 gcc-5 + ln -s clang-3.6 cpp-5 + ln -s clang-3.6 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in 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 + cd - /«BUILDDIR» + 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/clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-N5luew/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/816 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12200 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package `sbuild-build-depends-rna-star-dummy' in `/«BUILDDIR»/resolver-pDrBtC/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install rna-star build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libglib2.0-0 libhts-dev libhts1 libicu52 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf vim-common zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl vim vim-gnome vim-gtk vim-athena vim-nox vim-tiny The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libglib2.0-0 libhts-dev libhts1 libicu52 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common zlib1g-dev 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 16.6 MB/16.6 MB of archives. After this operation, 58.1 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.4.0-1 [27.9 kB] Get:2 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.3-1 [1205 kB] Get:3 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.6 [183 kB] Get:4 http://localhost:9999/debian/ unstable/main man-db amd64 2.7.0.2-5 [1000 kB] Get:5 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.3-2 [31.3 kB] Get:6 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:7 http://localhost:9999/debian/ unstable/main libicu52 amd64 52.1-8 [6780 kB] Get:8 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.2+dfsg1-3 [934 kB] Get:9 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.42.1-1 [2401 kB] Get:10 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:11 http://localhost:9999/debian/ unstable/main libhts1 amd64 1.1-1 [205 kB] Get:12 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:13 http://localhost:9999/debian/ unstable/main vim-common amd64 2:7.4.488-6 [184 kB] Get:14 http://localhost:9999/debian/ unstable/main file amd64 1:5.22+15-2 [60.1 kB] Get:15 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.3-2 [121 kB] Get:16 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.3-2 [1240 kB] Get:17 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:18 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:19 http://localhost:9999/debian/ unstable/main debhelper all 9.20150101 [813 kB] Get:20 http://localhost:9999/debian/ unstable/main libhts-dev amd64 1.1-1 [250 kB] Get:21 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Preconfiguring packages ... Fetched 16.6 MB in 0s (21.5 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.0-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ... Unpacking groff-base (1.22.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ... Unpacking bsdmainutils (9.0.6) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.0.2-5_amd64.deb ... Unpacking man-db (2.7.0.2-5) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.3-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.3-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2) ... Selecting previously unselected package libicu52:amd64. Preparing to unpack .../libicu52_52.1-8_amd64.deb ... Unpacking libicu52:amd64 (52.1-8) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.2+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.2+dfsg1-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.42.1-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.42.1-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3+b1) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../libhts1_1.1-1_amd64.deb ... Unpacking libhts1:amd64 (1.1-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ... Selecting previously unselected package vim-common. Preparing to unpack .../vim-common_2%3a7.4.488-6_amd64.deb ... Unpacking vim-common (2:7.4.488-6) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ... Unpacking file (1:5.22+15-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.3-2_amd64.deb ... Unpacking gettext-base (0.19.3-2) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.3-2_amd64.deb ... Unpacking gettext (0.19.3-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ... Unpacking po-debconf (1.0.16+nmu3) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20150101_all.deb ... Unpacking debhelper (9.20150101) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../libhts-dev_1.1-1_amd64.deb ... Unpacking libhts-dev:amd64 (1.1-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package sbuild-build-depends-rna-star-dummy. Preparing to unpack .../sbuild-build-depends-rna-star-dummy.deb ... Unpacking sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.4.0-1) ... Setting up groff-base (1.22.3-1) ... Setting up bsdmainutils (9.0.6) ... 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 man-db (2.7.0.2-5) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.19.3-2) ... Setting up libmagic1:amd64 (1:5.22+15-2) ... Setting up libicu52:amd64 (52.1-8) ... Setting up libxml2:amd64 (2.9.2+dfsg1-3) ... Setting up libglib2.0-0:amd64 (2.42.1-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up libhts1:amd64 (1.1-1) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up vim-common (2:7.4.488-6) ... Setting up file (1:5.22+15-2) ... Setting up gettext-base (0.19.3-2) ... Setting up gettext (0.19.3-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20150101) ... Setting up libhts-dev:amd64 (1.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-17) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-17 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt7-1 Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.7 apt-utils_1.0.9.7 base-files_8 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7+b2 clang-3.6_1:3.6-2 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 less_458-3 libacl1_2.2.52-2 libapt-inst1.5_1.0.9.7 libapt-pkg4.12_1.0.9.7 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libblkid1_2.25.2-5 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7+b2 libc-bin_2.19-17 libc-dev-bin_2.19-17 libc6_2.19-17 libc6-dev_2.19-17 libcap2_1:2.24-7 libcap2-bin_1:2.24-7 libcilkrts5_4.9.2-10 libclang-common-3.6-dev_1:3.6-2 libclang1-3.6_1:3.6-2 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.1 libdpkg-perl_1.17.24 libedit2_3.1-20140620-2 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.42.1-1 libgmp10_2:6.0.0+dfsg-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libhts-dev_1.1-1 libhts1_1.1-1 libicu52_52.1-8 libisl10_0.12.2-2 libitm1_4.9.2-10 libkmod2_20-1 libllvm3.6_1:3.6-2 liblsan0_4.9.2-10 liblzma5_5.1.1alpha+20120614-2+b3 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.3-1 libmpfr4_3.1.2-3 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libobjc-4.9-dev_4.9.2-10 libobjc4_4.9.2-10 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libprocps3_2:3.3.9-9 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-12 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-5 libxml2_2.9.2+dfsg1-3 linux-libc-dev_3.16.7-ckt7-1 login_1:4.2-3 lsb-base_4.1+Debian13+nmu1 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-5 multiarch-support_2.19-17 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 nvi_1.81.6-11+b1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-2 perl-base_5.20.2-2 perl-modules_5.20.2-2 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.12-1 systemd_215-12 systemd-sysv_215-12 sysv-rc_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2+b1 tzdata_2015b-1 udev_215-12 util-linux_2.25.2-5 vim-common_2:7.4.488-6 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jan 30 16:30:54 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./rna-star_2.4.0i-1.dsc dpkg-source: info: extracting rna-star in rna-star-2.4.0i dpkg-source: info: unpacking rna-star_2.4.0i.orig.tar.xz dpkg-source: info: unpacking rna-star_2.4.0i-1.debian.tar.xz dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying compilationstuff.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-2a3218ca-c692-4830-8e0b-75283781e0b7 SCHROOT_UID=1001 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package rna-star dpkg-buildpackage: source version 2.4.0i-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build rna-star-2.4.0i dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/«PKGBUILDDIR»' cd source && /usr/bin/make clean make[2]: Entering directory '/«PKGBUILDDIR»/source' rm -f *.o STAR STARstatic Depend.list make[2]: Leaving directory '/«PKGBUILDDIR»/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/«PKGBUILDDIR»' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro" make[2]: Entering directory '/«PKGBUILDDIR»/source' Makefile:66: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo ReadAlign_multMapSelect.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SuffixArrayFuns.cpp ReadAlign_storeAligns.cpp Stats.cpp Transcript.cpp sjSplitAlign.cpp OutSJ.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp Parameters.cpp sjdbLoadFromStream.cpp ReadAlign_oneRead.cpp Parameters_closeReadsFiles.cpp genomeGenerate.cpp BAMfunctions.cpp ReadAlign_outputAlignments.cpp ReadAlign.cpp stitchWindowAligns.cpp blocksOverlap.cpp sjdbPrepare.cpp Transcriptome.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp alignSmithWaterman.cpp outputSJ.cpp ReadAlign_mapOneRead.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_maxMappableLength2strands.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp serviceFuns.cpp ThreadControl.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp TimeFunctions.cpp Genome.cpp ReadAlignChunk_mapChunk.cpp streamFuns.cpp Transcriptome_geneCounts.cpp extendAlign.cpp ReadAlignChunk_processChunks.cpp Transcript_alignScore.cpp ReadAlign_stitchPieces.cpp GlobalVariables.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputTranscriptSJ.cpp Parameters_openReadsFiles.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp STAR.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp InOutStreams.cpp stringSubstituteAll.cpp Quantifications.cpp ErrorWarning.cpp Transcriptome_geneCountsAddAlign.cpp stitchGapIndel.cpp ReadAlign_outputTranscriptCIGARp.cpp sysRemoveDir.cpp SequenceFuns.cpp bam_cat.c ReadAlign_multMapSelect.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SuffixArrayFuns.cpp ReadAlign_storeAligns.cpp Stats.cpp Transcript.cpp sjSplitAlign.cpp OutSJ.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp Parameters.cpp sjdbLoadFromStream.cpp ReadAlign_oneRead.cpp Parameters_closeReadsFiles.cpp genomeGenerate.cpp BAMfunctions.cpp ReadAlign_outputAlignments.cpp ReadAlign.cpp stitchWindowAligns.cpp blocksOverlap.cpp sjdbPrepare.cpp Transcriptome.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp alignSmithWaterman.cpp outputSJ.cpp ReadAlign_mapOneRead.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_maxMappableLength2strands.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp serviceFuns.cpp ThreadControl.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp TimeFunctions.cpp Genome.cpp ReadAlignChunk_mapChunk.cpp streamFuns.cpp Transcriptome_geneCounts.cpp extendAlign.cpp ReadAlignChunk_processChunks.cpp Transcript_alignScore.cpp ReadAlign_stitchPieces.cpp GlobalVariables.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputTranscriptSJ.cpp Parameters_openReadsFiles.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp STAR.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp InOutStreams.cpp stringSubstituteAll.cpp Quantifications.cpp ErrorWarning.cpp Transcriptome_geneCountsAddAlign.cpp stitchGapIndel.cpp ReadAlign_outputTranscriptCIGARp.cpp sysRemoveDir.cpp SequenceFuns.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:08 UTC 2015 :/«PKGBUILDDIR»/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -MM ReadAlign_multMapSelect.cpp PackedArray.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SuffixArrayFuns.cpp ReadAlign_storeAligns.cpp Stats.cpp Transcript.cpp sjSplitAlign.cpp OutSJ.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp ReadAlign_chimericDetection.cpp signalFromBAM.cpp Parameters.cpp sjdbLoadFromStream.cpp ReadAlign_oneRead.cpp Parameters_closeReadsFiles.cpp genomeGenerate.cpp BAMfunctions.cpp ReadAlign_outputAlignments.cpp ReadAlign.cpp stitchWindowAligns.cpp blocksOverlap.cpp sjdbPrepare.cpp Transcriptome.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp alignSmithWaterman.cpp outputSJ.cpp ReadAlign_mapOneRead.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_maxMappableLength2strands.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp serviceFuns.cpp ThreadControl.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp TimeFunctions.cpp Genome.cpp ReadAlignChunk_mapChunk.cpp streamFuns.cpp Transcriptome_geneCounts.cpp extendAlign.cpp ReadAlignChunk_processChunks.cpp Transcript_alignScore.cpp ReadAlign_stitchPieces.cpp GlobalVariables.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputTranscriptSJ.cpp Parameters_openReadsFiles.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp STAR.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp InOutStreams.cpp stringSubstituteAll.cpp Quantifications.cpp ErrorWarning.cpp Transcriptome_geneCountsAddAlign.cpp stitchGapIndel.cpp ReadAlign_outputTranscriptCIGARp.cpp sysRemoveDir.cpp SequenceFuns.cpp bam_cat.c parametersDefault.xxd >> Depend.list clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: parametersDefault.xxd: 'linker' input unused g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' PackedArray.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' SuffixArrayFuns.cpp SuffixArrayFuns.cpp:15:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int64 ii; ^~~~~~~~~ SuffixArrayFuns.cpp:172:9: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int64 ii; ^~~~~~~~~ 2 warnings generated. g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' STAR.cpp STAR.cpp:306:23: warning: implicit conversion from 'double' to 'unsigned int' changes value from 0.1 to 0 [-Wliteral-conversion] sleep(0.1); ~~~~~ ^~~ 1 warning generated. g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Parameters.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' InOutStreams.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' SequenceFuns.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Genome.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Stats.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Transcript.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Transcript_alignScore.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_storeAligns.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_stitchPieces.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_multMapSelect.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_mapOneRead.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' readLoad.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlignChunk.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlignChunk_processChunks.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlignChunk_mapChunk.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' OutSJ.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' outputSJ.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' blocksOverlap.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ThreadControl.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' sysRemoveDir.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_maxMappableLength2strands.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' binarySearch2.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_outputAlignments.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_outputTranscriptSAM.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_outputTranscriptSJ.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_assignAlignToWindow.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_oneRead.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_stitchWindowSeeds.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_chimericDetection.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' stitchWindowAligns.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' extendAlign.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' stitchAlignToTranscript.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' alignSmithWaterman.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' genomeGenerate.cpp genomeGenerate.cpp:451:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(sysCom.str().c_str()); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' TimeFunctions.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ErrorWarning.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' loadGTF.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' streamFuns.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' stringSubstituteAll.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Transcriptome.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Transcriptome_quantAlign.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' ReadAlign_quantTranscriptome.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Quantifications.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' Transcriptome_geneCountsAddAlign.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' sjdbLoadFromFiles.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' sjdbLoadFromStream.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' sjdbPrepare.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' sjdbBuildIndex.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' mapThreadsSpawn.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' BAMoutput.cpp g++ -c -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILATION_TIME_PLACE="Thu Mar 26 02:58:14 UTC 2015 :/«PKGBUILDDIR»/source"' BAMfunctions.cpp BAMfunctions.cpp:22:11: error: cannot initialize a variable of type 'char *' with an rvalue of type 'const char *' char *attrStart=strstr(bamAux,attrName); ^ ~~~~~~~~~~~~~~~~~~~~~~~ 1 error generated. make[2]: *** [BAMfunctions.o] Error 1 Makefile:38: recipe for target 'BAMfunctions.o' failed make[2]: Leaving directory '/«PKGBUILDDIR»/source' make[1]: *** [override_dh_auto_build] Error 2 debian/rules:17: recipe for target 'override_dh_auto_build' failed make[1]: Leaving directory '/«PKGBUILDDIR»' make: *** [build-arch] Error 2 debian/rules:14: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150326-0259 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 16740 Build-Time: 74 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 10 Job: rna-star_2.4.0i-1 Machine Architecture: amd64 Package: rna-star Package-Time: 109 Source-Version: 2.4.0i-1 Space: 16740 Status: attempted Version: 2.4.0i-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150326-0259 Build needed 00:01:49, 16740k disc space DC-Status: Failed 109.93403311s DC-Time-Estimation: 109.93403311 versus expected 1 (r/m: 108.93403311 ; m: 1.0)