DC-Build-Header: rna-star 2.5.2b+dfsg-1 / 2016-08-29 17:03:35 +0000 DC-Task: type:rebuild-binarch-only source:rna-star version:2.5.2b+dfsg-1 chroot:unstable esttime:95 logfile:/tmp/rna-star_2.5.2b+dfsg-1_unstable_clang3.8.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang rna-star_2.5.2b+dfsg-1' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-3-154.eu-central-1.compute.internal +==============================================================================+ | rna-star 2.5.2b+dfsg-1 (amd64) Mon, 29 Aug 2016 17:03:35 +0000 | +==============================================================================+ Package: rna-star Version: 2.5.2b+dfsg-1 Source Version: 2.5.2b+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-8f8e3375-cdfa-4c4e-a312-66191597ec5b' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.8 + echo 'Install of clang-3.8' Install of clang-3.8 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [209 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en [5451 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0319.00.pdiff [16.7 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0319.00.pdiff [13.2 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Fetched 5755 kB in 3s (1912 kB/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges + apt-get install --yes --no-install-recommends --force-yes clang-3.8 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.8-doc Recommended packages: llvm-3.8-dev python The following NEW packages will be installed: clang-3.8 libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. Need to get 38.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20150325-1+b1 [85.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.8 amd64 1:3.8.1-9 [10.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 6.2.0-1 [110 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.2.0-1 [394 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.8 amd64 1:3.8.1-9 [4188 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.8-dev amd64 1:3.8.1-9 [1477 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.8 amd64 1:3.8.1-9 [21.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.3 MB in 1s (19.7 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 ... 9446 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../1-libedit2_3.1-20150325-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20150325-1+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../2-libffi6_3.2.1-4_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-4) ... Selecting previously unselected package libllvm3.8:amd64. Preparing to unpack .../3-libllvm3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libllvm3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../4-libobjc4_6.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (6.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../5-libobjc-6-dev_6.2.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.2.0-1) ... Selecting previously unselected package libclang1-3.8:amd64. Preparing to unpack .../6-libclang1-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libclang1-3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libclang-common-3.8-dev. Preparing to unpack .../7-libclang-common-3.8-dev_1%3a3.8.1-9_amd64.deb ... Unpacking libclang-common-3.8-dev (1:3.8.1-9) ... Selecting previously unselected package clang-3.8. Preparing to unpack .../8-clang-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking clang-3.8 (1:3.8.1-9) ... Setting up libobjc4:amd64 (6.2.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up libobjc-6-dev:amd64 (6.2.0-1) ... Setting up libffi6:amd64 (3.2.1-4) ... Setting up libedit2:amd64 (3.1-20150325-1+b1) ... Setting up libllvm3.8:amd64 (1:3.8.1-9) ... Setting up libclang-common-3.8-dev (1:3.8.1-9) ... Setting up libclang1-3.8:amd64 (1:3.8.1-9) ... Setting up clang-3.8 (1:3.8.1-9) ... Processing triggers for libc-bin (2.23-5) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. W: No sandbox user '_apt' on the system, can not drop privileges + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.8 g++-4.6 + ln -s clang-3.8 gcc-4.6 + ln -s clang-3.8 cpp-4.6 + ln -s clang-3.8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.8 g++-4.7 + ln -s clang-3.8 gcc-4.7 + ln -s clang-3.8 cpp-4.7 + ln -s clang-3.8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.8 g++-4.8 + ln -s clang-3.8 gcc-4.8 + ln -s clang-3.8 cpp-4.8 + ln -s clang-3.8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.8 g++-4.9 + ln -s clang-3.8 gcc-4.9 + ln -s clang-3.8 cpp-4.9 + ln -s clang-3.8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.8 g++-5 + ln -s clang-3.8 gcc-5 + ln -s clang-3.8 cpp-5 + ln -s clang-3.8 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.8 g++-6 + ln -s clang-3.8 gcc-6 + ln -s clang-3.8 cpp-6 + ln -s clang-3.8 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + cd - /build/rna-star-5r8Q2A + 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. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1158 kB of archives. After this operation, 60.4 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 linux-libc-dev amd64 4.7.2-1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1158 kB in 0s (69.7 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 ... 9769 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.7.2-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.7.2-1) over (4.6.4-1) ... Setting up linux-libc-dev:amd64 (4.7.2-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | 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 697 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.2b+dfsg-1 (dsc) [2137 B] Get:2 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.2b+dfsg-1 (tar) [321 kB] Get:3 http://127.0.0.1:9999/debian unstable/main rna-star 2.5.2b+dfsg-1 (diff) [374 kB] Fetched 697 kB in 0s (4359 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-5r8Q2A/rna-star-2.5.2b+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-5r8Q2A' 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-jylLTZ/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-jylLTZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jylLTZ/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-jylLTZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jylLTZ/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-jylLTZ/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 774 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-jylLTZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 774 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 9775 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) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 ppc64el mips64el s390x) +------------------------------------------------------------------------------+ | 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-OOmnt0/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-rna-star-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-OOmnt0/apt_archive ./ InRelease Get:2 copy:/<>/resolver-OOmnt0/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-OOmnt0/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-OOmnt0/apt_archive ./ Sources [364 B] Get:5 copy:/<>/resolver-OOmnt0/apt_archive ./ Packages [460 B] Fetched 1781 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu57 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf vim-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl vim | vim-gnome | 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 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu57 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common zlib1g-dev 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 25.1 MB of archives. After this operation, 80.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-OOmnt0/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [800 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-8 [1162 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.5-1 [1003 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 vim-common amd64 2:7.4.1829-1 [229 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.50.1-1 [278 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libhts1 amd64 1.3.1-2 [256 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.3.1-2 [315 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.1 MB in 0s (69.4 MB/s) Selecting previously unselected package groff-base. (Reading database ... 9775 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.10_amd64.deb ... Unpacking bsdmainutils (9.0.10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libssl1.0.2:amd64. Preparing to unpack .../04-libssl1.0.2_1.0.2h-1_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2h-1) ... Selecting previously unselected package vim-common. Preparing to unpack .../05-vim-common_2%3a7.4.1829-1_amd64.deb ... Unpacking vim-common (2:7.4.1829-1) ... Selecting previously unselected package libmagic-mgc. 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Setting up libnghttp2-14:amd64 (1.13.0-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:amd64 (2.48.1-3) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ... Setting up gettext-base (0.19.8.1-1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:amd64 (57.1-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Setting up libtasn1-6:amd64 (4.9-4) ... Setting up libmagic-mgc (1:5.28-4) ... Setting up libmagic1:amd64 (1:5.28-4) ... Setting up libhogweed4:amd64 (3.2-1) ... Setting up libcroco3:amd64 (0.6.11-1) ... Setting up libssl1.0.2:amd64 (1.0.2h-1) ... Setting up libssh2-1:amd64 (1.7.0-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libp11-kit0:amd64 (0.23.2-5) ... Setting up vim-common (2:7.4.1829-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.10) ... 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 (0.19.8.1-1) ... Setting up libidn11:amd64 (1.33-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up gettext (0.19.8.1-1) ... Setting up libgnutls30:amd64 (3.5.3-3) ... Setting up autoconf (2.69-10) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Setting up file (1:5.28-4) ... Setting up libkrb5support0:amd64 (1.14.3+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ... Setting up automake (1:1.15-4) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libk5crypto3:amd64 (1.14.3+dfsg-1) ... Setting up po-debconf (1.0.19) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Setting up libcurl3-gnutls:amd64 (7.50.1-1) ... Setting up libhts1:amd64 (1.3.1-2) ... Setting up libhts-dev:amd64 (1.3.1-2) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160814) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.023-2) ... Processing triggers for libc-bin (2.23-5) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.27-6 dpkg-dev_1.18.10 g++-6_6.2.0-1 gcc-6_6.2.0-1 libc6-dev_2.23-5 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 linux-libc-dev_4.7.2-1 Package versions: adduser_3.115 apt_1.3~rc2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6 base-passwd_3.5.40 bash_4.3-15 binutils_2.27-6 bsdmainutils_9.0.10 bsdutils_1:2.28.1-1 build-essential_12.2 bzip2_1.0.6-8 clang-3.8_1:3.8.1-9 coreutils_8.25-2 cpp_4:6.1.1-1 cpp-6_6.2.0-1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debian-archive-keyring_2014.3 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 eatmydata_105-3 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1 g++-6_6.2.0-1 gcc_4:6.1.1-1 gcc-6_6.2.0-1 gcc-6-base_6.2.0-1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gpgv_2.1.14-5 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init-system-helpers_1.42 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapt-pkg5.0_1.3~rc2 libarchive-zip-perl_1.59-1 libasan3_6.2.0-1 libatomic1_6.2.0-1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libblkid1_2.28.1-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcap-ng0_0.7.7-3 libcc1-0_6.2.0-1 libcilkrts5_6.2.0-1 libclang-common-3.8-dev_1:3.8.1-9 libclang1-3.8_1:3.8.1-9 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdebconfclient0_0.215 libdpkg-perl_1.18.10 libeatmydata1_105-3 libedit2_3.1-20150325-1+b1 libfakeroot_1.21-1 libfdisk1_2.28.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-1 libgcc1_1:6.2.0-1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-3 libgomp1_6.2.0-1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-1 libhogweed4_3.2-1 libhts-dev_1.3.1-2 libhts1_1.3.1-2 libicu57_57.1-3 libidn11_1.33-1 libisl15_0.17.1-1 libitm1_6.2.0-1 libk5crypto3_1.14.3+dfsg-1 libkeyutils1_1.5.9-9 libkrb5-3_1.14.3+dfsg-1 libkrb5support0_1.14.3+dfsg-1 libldap-2.4-2_2.4.42+dfsg-2+b2 libllvm3.8_1:3.8.1-9 liblsan0_6.2.0-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libmpx2_6.2.0-1 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnghttp2-14_1.13.0-1 libobjc-6-dev_6.2.0-1 libobjc4_6.2.0-1 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libquadmath0_6.2.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.1-1 libss2_1.43.1-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2h-1 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 libsystemd0_231-5 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libtsan0_6.2.0-1 libubsan0_6.2.0-1 libudev1_231-5 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-5 libuuid1_2.28.1-1 libxml2_2.9.4+dfsg1-1+b1 linux-libc-dev_4.7.2-1 login_1:4.2-3.1 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 mount_2.28.1-1 multiarch-support_2.23-5 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 util-linux_2.28.1-1 vim-common_2:7.4.1829-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Aug 23 12:50:04 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.5.2b+dfsg-1.dsc dpkg-source: info: extracting rna-star in /<>/rna-star-2.5.2b+dfsg dpkg-source: info: unpacking rna-star_2.5.2b+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.5.2b+dfsg-1.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 disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-8f8e3375-cdfa-4c4e-a312-66191597ec5b 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 2.5.2b+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build rna-star-2.5.2b+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.5.2b+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.5.2b+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.5.2b+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.5.2b+dfsg' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.5.2b+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.5.2b+dfsg=. -fPIE -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-2.5.2b+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-fPIE -pie -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/rna-star-2.5.2b+dfsg/source' Makefile:89: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.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 Quantifications.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 sysRemoveDir.cpp ReadAlign_storeAligns.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 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 Quantifications.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 sysRemoveDir.cpp ReadAlign_storeAligns.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-2.5.2b+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.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 Quantifications.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 sysRemoveDir.cpp ReadAlign_storeAligns.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 clang: warning: parametersDefault.xxd: 'linker' input unused 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. In file included from genomeScanFastaFiles.cpp:1: In file included from ./genomeScanFastaFiles.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjdbBuildIndex.cpp:1: In file included from ./sjdbBuildIndex.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_mapOneRead.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_outputTranscriptSAM.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from PackedArray.cpp:1: In file included from ./PackedArray.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_createExtendWindowsWithAlign.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from readLoad.cpp:1: In file included from ./readLoad.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from binarySearch2.cpp:1: In file included from ./binarySearch2.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjdbInsertJunctions.cpp:1: In file included from ./sjdbInsertJunctions.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Stats.cpp:1: In file included from ./Stats.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjdbPrepare.cpp:1: In file included from ./sjdbPrepare.h:4: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_stitchPieces.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from STAR.cpp:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from BAMbinSortByCoordinate.cpp:1: In file included from ./BAMbinSortByCoordinate.h:3: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Transcriptome_quantAlign.cpp:1: In file included from ./Transcriptome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_outputAlignments.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_alignBAM.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_stitchWindowSeeds.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from extendAlign.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_outputTranscriptCIGARp.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ErrorWarning.cpp:4: In file included from ./ErrorWarning.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Parameters_openReadsFiles.cpp:1: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Quantifications.cpp:1: In file included from ./Quantifications.h:3: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjdbLoadFromStream.cpp:1: In file included from ./sjdbLoadFromStream.h:5: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlignChunk.cpp:1: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from stitchAlignToTranscript.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from stitchGapIndel.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from genomeSAindex.cpp:1: In file included from ./genomeSAindex.h:3: In file included from ./PackedArray.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from signalFromBAM.cpp:1: In file included from ./signalFromBAM.h:6: In file included from ./Stats.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from genomeGenerate.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from outputSJ.cpp:1: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Parameters_closeReadsFiles.cpp:1: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from stitchWindowAligns.cpp:1: In file included from ./stitchWindowAligns.h:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Parameters.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjSplitAlign.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Transcriptome.cpp:1: In file included from ./Transcriptome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_chimericDetection.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from BAMfunctions.cpp:1: In file included from ./BAMfunctions.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_maxMappableLength2strands.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlignChunk_mapChunk.cpp:1: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from serviceFuns.cpp:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ThreadControl.cpp:1: In file included from ./ThreadControl.h:4: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Genome_insertSequences.cpp:4: In file included from ./Genome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Genome.cpp:1: In file included from ./Genome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from BAMbinSortUnmapped.cpp:1: In file included from ./BAMbinSortUnmapped.h:3: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from insertSeqSA.cpp:5: In file included from ./insertSeqSA.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from streamFuns.cpp:1: In file included from ./streamFuns.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlignChunk_processChunks.cpp:1: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from BAMoutput.cpp:1: In file included from ./BAMoutput.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from genomeParametersWrite.cpp:1: In file included from ./genomeParametersWrite.h:3: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_multMapSelect.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Transcript_alignScore.cpp:1: In file included from ./Transcript.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_outputTranscriptSJ.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from mapThreadsSpawn.cpp:1: In file included from ./mapThreadsSpawn.h:3: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from loadGTF.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_assignAlignToWindow.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from GlobalVariables.cpp:1: In file included from ./GlobalVariables.h:4: In file included from ./ThreadControl.h:4: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Transcriptome_geneCountsAddAlign.cpp:1: In file included from ./Transcriptome.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_storeAligns.cpp:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from bamRemoveDuplicates.cpp:2: In file included from ./bamRemoveDuplicates.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from InOutStreams.cpp:1: In file included from ./InOutStreams.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from ReadAlign_oneRead.cpp:1: In file included from ./ReadAlign.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from Transcript.cpp:1: In file included from ./Transcript.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from SuffixArrayFuns.cpp:1: In file included from ./SuffixArrayFuns.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from alignSmithWaterman.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from SequenceFuns.cpp:1: In file included from ./SequenceFuns.h:12: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from OutSJ.cpp:1: In file included from ./OutSJ.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from sjdbLoadFromFiles.cpp:1: In file included from ./sjdbLoadFromFiles.h:5: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. In file included from blocksOverlap.cpp:1: In file included from ./blocksOverlap.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-2.5.2b+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-2.5.2b+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 2016-08-29T17:04:14Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 3 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 9 Job: rna-star_2.5.2b+dfsg-1 Machine Architecture: amd64 Package: rna-star Package-Time: 39 Source-Version: 2.5.2b+dfsg-1 Space: 0 Status: failed Version: 2.5.2b+dfsg-1 -------------------------------------------------------------------------------- Finished at 2016-08-29T17:04:14Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 40.322366421s DC-Time-Estimation: 40.322366421 versus expected 95 (r/m: 1.3560125169271748 ; m: 40.322366421)