DC-Build-Header: rna-star 2.5.3a+dfsg-3 / 2017-08-20 18:54:21 +0000 DC-Task: type:rebuild-binarch-only source:rna-star version:2.5.3a+dfsg-3 chroot:unstable esttime:88 logfile:/tmp/rna-star_2.5.3a+dfsg-3_unstable_clang5.0.log modes:clang50:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang50 rna-star_2.5.3a+dfsg-3' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-45-118.eu-central-1.compute.internal +==============================================================================+ | rna-star 2.5.3a+dfsg-3 (amd64) Sun, 20 Aug 2017 18:54:22 +0000 | +==============================================================================+ Package: rna-star Version: 2.5.3a+dfsg-3 Source Version: 2.5.3a+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-e22d75dc-595a-4aec-8dfd-bb5fe71f1ece' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang50 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=5.0 + echo 'Install of clang-5.0' Install of clang-5.0 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5785 kB] Fetched 5785 kB in 1s (3818 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-5.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libasan3 libbsd0 libclang-common-5.0-dev libclang1-5.0 libedit2 libgcc-6-dev libjsoncpp1 libllvm5.0 libncurses5 libobjc-6-dev libobjc4 libstdc++-6-dev Suggested packages: gnustep gnustep-devel clang-5.0-doc libomp-dev libstdc++-6-doc Recommended packages: llvm-5.0-dev python libgpm2 The following NEW packages will be installed: clang-5.0 libasan3 libbsd0 libclang-common-5.0-dev libclang1-5.0 libedit2 libgcc-6-dev libjsoncpp1 libllvm5.0 libncurses5 libobjc-6-dev libobjc4 libstdc++-6-dev 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 88.4 MB of archives. After this operation, 376 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.6-1 [90.3 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20170715-2 [93.8 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm5.0 amd64 1:5.0~+rc2-1 [13.5 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-5.0 amd64 1:5.0~+rc2-1 [6729 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libasan3 amd64 6.4.0-3 [311 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libgcc-6-dev amd64 6.4.0-3 [2296 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libstdc++-6-dev amd64 6.4.0-3 [1421 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.2.0-1 [51.0 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-3 [197 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-5.0-dev amd64 1:5.0~+rc2-1 [1989 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 clang-5.0 amd64 1:5.0~+rc2-1 [61.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.4 MB in 0s (98.3 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 ... 9822 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.6-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../01-libncurses5_6.0+20170715-2_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20170715-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm5.0:amd64. Preparing to unpack .../03-libllvm5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libllvm5.0:amd64 (1:5.0~+rc2-1) ... Selecting previously unselected package libclang1-5.0:amd64. Preparing to unpack .../04-libclang1-5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libclang1-5.0:amd64 (1:5.0~+rc2-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../05-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libasan3:amd64. Preparing to unpack .../06-libasan3_6.4.0-3_amd64.deb ... Unpacking libasan3:amd64 (6.4.0-3) ... Selecting previously unselected package libgcc-6-dev:amd64. Preparing to unpack .../07-libgcc-6-dev_6.4.0-3_amd64.deb ... Unpacking libgcc-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libstdc++-6-dev:amd64. Preparing to unpack .../08-libstdc++-6-dev_6.4.0-3_amd64.deb ... Unpacking libstdc++-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_7.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (7.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../10-libobjc-6-dev_6.4.0-3_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-3) ... Selecting previously unselected package libclang-common-5.0-dev. Preparing to unpack .../11-libclang-common-5.0-dev_1%3a5.0~+rc2-1_amd64.deb ... Unpacking libclang-common-5.0-dev (1:5.0~+rc2-1) ... Selecting previously unselected package clang-5.0. Preparing to unpack .../12-clang-5.0_1%3a5.0~+rc2-1_amd64.deb ... Unpacking clang-5.0 (1:5.0~+rc2-1) ... Setting up libncurses5:amd64 (6.0+20170715-2) ... Setting up libobjc4:amd64 (7.2.0-1) ... Setting up libasan3:amd64 (6.4.0-3) ... Setting up libgcc-6-dev:amd64 (6.4.0-3) ... Setting up libstdc++-6-dev:amd64 (6.4.0-3) ... Setting up libbsd0:amd64 (0.8.6-1) ... Processing triggers for libc-bin (2.24-14) ... Setting up libobjc-6-dev:amd64 (6.4.0-3) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm5.0:amd64 (1:5.0~+rc2-1) ... Setting up libclang1-5.0:amd64 (1:5.0~+rc2-1) ... Setting up libclang-common-5.0-dev (1:5.0~+rc2-1) ... Setting up clang-5.0 (1:5.0~+rc2-1) ... Processing triggers for libc-bin (2.24-14) ... 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' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-5.0 g++-4.6 + ln -s clang-5.0 gcc-4.6 + ln -s clang-5.0 cpp-4.6 + ln -s clang-5.0 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++-5.0 g++-4.7 + ln -s clang-5.0 gcc-4.7 + ln -s clang-5.0 cpp-4.7 + ln -s clang-5.0 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++-5.0 g++-4.8 + ln -s clang-5.0 gcc-4.8 + ln -s clang-5.0 cpp-4.8 + ln -s clang-5.0 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++-5.0 g++-4.9 + ln -s clang-5.0 gcc-4.9 + ln -s clang-5.0 cpp-4.9 + ln -s clang-5.0 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++-5.0 g++-5 + ln -s clang-5.0 gcc-5 + ln -s clang-5.0 cpp-5 + ln -s clang-5.0 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-5.0 g++-6 + ln -s clang-5.0 gcc-6 + ln -s clang-5.0 cpp-6 + ln -s clang-5.0 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++-5.0 g++-7 + ln -s clang-5.0 gcc-7 + ln -s clang-5.0 cpp-7 + ln -s clang-5.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections + echo 'g++-7 hold' + dpkg --set-selections + cd - /build/rna-star-sSKnGH + 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/clang50'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'rna-star' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/rna-star.git Please use: git clone https://anonscm.debian.org/git/debian-med/rna-star.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 712 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.3a+dfsg-3 (dsc) [1812 B] Get:2 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.3a+dfsg-3 (tar) [335 kB] Get:3 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.3a+dfsg-3 (diff) [374 kB] Fetched 712 kB in 0s (1392 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-sSKnGH/rna-star-2.5.3a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-sSKnGH' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-zmjycD/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-zmjycD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zmjycD/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-zmjycD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zmjycD/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-zmjycD/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-zmjycD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11331 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 ppc64el mips64el) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-zmjycD/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-rna-star-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-zmjycD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zmjycD/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-zmjycD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zmjycD/apt_archive ./ Sources [511 B] Get:5 copy:/<>/resolver-zmjycD/apt_archive ./ Packages [591 B] Fetched 2065 B in 0s (0 B/s) Reading package lists... 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 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 libtimedate-perl libtool libxml2 m4 man-db po-debconf tabix 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 less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl vim | vim-gtk | 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 file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 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 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy tabix vim-common xxd zlib1g-dev 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 24.3 MB of archives. After this operation, 79.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zmjycD/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [808 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.2-1 [28.3 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-4 [1349 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 xxd amd64 2:8.0.0946-1 [136 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 vim-common all 2:8.0.0946-1 [178 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.31-1 [223 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.31-1 [112 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.31-1 [64.2 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15.1-2 [62.2 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15.1-2 [120 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15.1-2 [312 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15.1-2 [155 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.45+dfsg-1 [87.0 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1 [223 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.038-1 [11.1 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.53.4-3 [2796 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.7.2 [975 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.18.0-2 [43.4 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.55.0-1 [294 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libhts2 amd64 1.5-1 [293 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 liblzma-dev amd64 5.2.2-1.3 [292 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 tabix amd64 1.5-1 [317 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.5-1 [396 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.3 MB in 0s (62.1 MB/s) Selecting previously unselected package groff-base. (Reading database ... 11331 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.2-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../04-libssl1.1_1.1.0f-4_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0f-4) ... Selecting previously unselected package xxd. Preparing to unpack .../05-xxd_2%3a8.0.0946-1_amd64.deb ... Unpacking xxd (2:8.0.0946-1) ... Selecting previously unselected package vim-common. 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Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Selecting previously unselected package libldap-common. Preparing to unpack .../18-libldap-common_2.4.45+dfsg-1_all.deb ... Unpacking libldap-common (2.4.45+dfsg-1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../19-libldap-2.4-2_2.4.45+dfsg-1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.45+dfsg-1) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../20-libicu57_57.1-6_amd64.deb ... Unpacking libicu57:amd64 (57.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../21-libxml2_2.9.4+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../22-libsigsegv2_2.11-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.11-1) ... Selecting previously unselected package m4. Preparing to unpack .../23-m4_1.4.18-1_amd64.deb ... 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Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libmagic-mgc (1:5.31-1) ... Setting up libmagic1:amd64 (1:5.31-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Processing triggers for libc-bin (2.24-14) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1) ... Setting up libssl1.1:amd64 (1.1.0f-4) ... Setting up vim-common (2:8.0.0946-1) ... Setting up liblzma-dev:amd64 (5.2.2-1.3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... 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 (0.19.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.31-1) ... Setting up libkrb5support0:amd64 (1.15.1-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libk5crypto3:amd64 (1.15.1-2) ... Setting up po-debconf (1.0.20) ... Setting up libkrb5-3:amd64 (1.15.1-2) ... Setting up libgssapi-krb5-2:amd64 (1.15.1-2) ... Setting up libcurl3-gnutls:amd64 (7.55.0-1) ... Setting up tabix (1.5-1) ... Setting up libhts2:amd64 (1.5-1) ... Setting up libhts-dev:amd64 (1.5-1) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.7.2) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-14) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.29-4 dpkg-dev_1.18.24 g++-7_7.2.0-1 gcc-7_7.2.0-1 libc6-dev_2.24-14 libstdc++-6-dev_6.4.0-3 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 linux-libc-dev_4.12.6-1 Package versions: adduser_3.116 apt_1.5~beta2 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.29-4 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-4 build-essential_12.3 bzip2_1.0.6-8.1 clang-5.0_1:5.0~+rc2-1 coreutils_8.26-3 cpp_4:7.1.0-2 cpp-7_7.2.0-1 dash_0.5.8-2.5 debconf_1.5.63 debfoster_2.7-2.1+b1 debhelper_10.7.2 debian-archive-keyring_2017.5 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 eatmydata_105-5 fakeroot_1.22-1 fdisk_2.29.2-4 file_1:5.31-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-2 g++-7_7.2.0-1 gcc_4:7.1.0-2 gcc-6-base_6.4.0-3 gcc-7_7.2.0-1 gcc-7-base_7.2.0-1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.23-2 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hostname_3.18+b1 init-system-helpers_1.49 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta2 libarchive-zip-perl_1.59-1 libasan3_6.4.0-3 libasan4_7.2.0-1 libatomic1_7.2.0-1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b2 libblkid1_2.29.2-4 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3+b1 libcc1-0_7.2.0-1 libcilkrts5_7.2.0-1 libclang-common-5.0-dev_1:5.0~+rc2-1 libclang1-5.0_1:5.0~+rc2-1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcurl3-gnutls_7.55.0-1 libdb5.3_5.3.28-13 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libfakeroot_1.22-1 libfdisk1_2.29.2-4 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-3 libgcc-7-dev_7.2.0-1 libgcc1_1:7.2.0-1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-3 libgomp1_7.2.0-1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1+b1 libhts-dev_1.5-1 libhts2_1.5-1 libicu57_57.1-6 libidn2-0_2.0.2-3 libisl15_0.18-1 libitm1_7.2.0-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libllvm5.0_1:5.0~+rc2-1 liblsan0_7.2.0-1 liblz4-1_0.0~r131-2+b1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmount1_2.29.2-4 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.2.0-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1+b1 libnghttp2-14_1.24.0-1 libobjc-6-dev_6.4.0-3 libobjc4_7.2.0-1 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.26_5.26.0-5 libpipeline1_1.4.2-1 libpsl5_0.18.0-2 libquadmath0_7.2.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-4 libss2_1.43.5-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-4 libstdc++-6-dev_6.4.0-3 libstdc++-7-dev_7.2.0-1 libstdc++6_7.2.0-1 libsystemd0_234-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libtsan0_7.2.0-1 libubsan0_7.2.0-1 libudev1_234-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-4 libxml2_2.9.4+dfsg1-3 linux-libc-dev_4.12.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-4 multiarch-support_2.24-14 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.26.0-5 perl-base_5.26.0-5 perl-modules-5.26_5.26.0-5 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 sysvinit-utils_2.88dsf-59.9 tabix_1.5-1 tar_1.29b-2 util-linux_2.29.2-4 vim-common_2:8.0.0946-1 xxd_2:8.0.0946-1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Aug 10 14:10:26 2017 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.5.3a+dfsg-3.dsc dpkg-source: info: extracting rna-star in /<>/rna-star-2.5.3a+dfsg dpkg-source: info: unpacking rna-star_2.5.3a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.5.3a+dfsg-3.debian.tar.xz 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=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-e22d75dc-595a-4aec-8dfd-bb5fe71f1ece SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.5.3a+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build rna-star-2.5.3a+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.5.3a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.5.3a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.5.3a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.5.3a+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.5.3a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.5.3a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.5.3a+dfsg=. -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 '/<>/rna-star-2.5.3a+dfsg/source' Makefile:89: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp extendAlign.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_storeAligns.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp bam_cat.c ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp extendAlign.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_storeAligns.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.5.3a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp Chain.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp extendAlign.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_storeAligns.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.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] In file included from ReadAlign_quantTranscriptome.cpp:1: In file included from ./Transcriptome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^~~~~~~ 1 error generated. Makefile:86: recipe for target 'Depend.list' failed make[2]: *** [Depend.list] Error 1 make[2]: Leaving directory '/<>/rna-star-2.5.3a+dfsg/source' debian/rules:18: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/rna-star-2.5.3a+dfsg' debian/rules:15: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-08-20T18:54:51Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 2276 Build-Time: 1 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 7 Job: rna-star_2.5.3a+dfsg-3 Machine Architecture: amd64 Package: rna-star Package-Time: 29 Source-Version: 2.5.3a+dfsg-3 Space: 2276 Status: attempted Version: 2.5.3a+dfsg-3 -------------------------------------------------------------------------------- Finished at 2017-08-20T18:54:51Z Build needed 00:00:29, 2276k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 29.919211026s DC-Time-Estimation: 29.919211026 versus expected 88 (r/m: 1.9412540298448178 ; m: 29.919211026)