DC-Build-Header: stacks 1.42-1 / 2016-08-29 16:47:03 +0000 DC-Task: type:rebuild-binarch-only source:stacks version:1.42-1 chroot:unstable esttime:305 logfile:/tmp/stacks_1.42-1_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 stacks_1.42-1' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-8-35.eu-central-1.compute.internal +==============================================================================+ | stacks 1.42-1 (amd64) Mon, 29 Aug 2016 16:47:04 +0000 | +==============================================================================+ Package: stacks Version: 1.42-1 Source Version: 1.42-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-a5841dc2-e111-4814-bf98-c6d830f97fe0' 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 2s (1959 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 10s (3773 kB/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/stacks-7KEz09 + 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 (70.4 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: 'stacks' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/stacks.git Please use: git clone https://anonscm.debian.org/git/debian-med/stacks.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 908 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main stacks 1.42-1 (dsc) [2042 B] Get:2 http://127.0.0.1:9999/debian unstable/main stacks 1.42-1 (tar) [898 kB] Get:3 http://127.0.0.1:9999/debian unstable/main stacks 1.42-1 (diff) [8100 B] Fetched 908 kB in 0s (5006 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/stacks-7KEz09/stacks-1.42' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-7KEz09' 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-AJUBt0/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-AJUBt0/apt_archive ./ InRelease Get:2 copy:/<>/resolver-AJUBt0/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-AJUBt0/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-AJUBt0/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-AJUBt0/apt_archive ./ Packages [433 B] Fetched 1739 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 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-AJUBt0/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 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 any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools Filtered Build-Depends: debhelper (>= 9), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<>/resolver-RLoNUk/apt_archive/sbuild-build-depends-stacks-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-stacks-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-RLoNUk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-RLoNUk/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-RLoNUk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-RLoNUk/apt_archive ./ Sources [383 B] Get:5 copy:/<>/resolver-RLoNUk/apt_archive ./ Packages [472 B] Fetched 1812 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 stacks 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 libbam-dev libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu57 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common samtools 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 python-doc python-tk python2.7-doc binfmt-support readline-doc 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 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 libbam-dev libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu57 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common samtools sbuild-build-depends-stacks-dummy zlib1g-dev 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 29.9 MB of archives. After this operation, 99.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-RLoNUk/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [816 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 libpython2.7-minimal amd64 2.7.12-2 [387 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-minimal amd64 2.7.12-2 [1348 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 python-minimal amd64 2.7.11-2 [40.3 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.0-1 [82.0 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 6.3-8 [57.7 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libreadline6 amd64 6.3-8+b4 [142 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.14.1-1 [559 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.12-2 [1875 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 python2.7 amd64 2.7.12-2 [277 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpython-stdlib amd64 2.7.11-2 [19.8 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 python amd64 2.7.11-2 [153 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libbam-dev amd64 0.1.19-2 [123 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.50.1-1 [278 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libhts1 amd64 1.3.1-2 [256 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 samtools amd64 1.3.1-2 [251 kB] Get:66 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 29.9 MB in 4s (6294 kB/s) Selecting previously unselected package groff-base. 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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 libbam-dev (0.1.19-2) ... Setting up libsqlite3-0:amd64 (3.14.1-1) ... 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 libreadline6:amd64 (6.3-8+b4) ... 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 libpython2.7-stdlib:amd64 (2.7.12-2) ... 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 python2.7 (2.7.12-2) ... Setting up libpython-stdlib:amd64 (2.7.11-2) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up python (2.7.11-2) ... 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 samtools (1.3.1-2) ... Setting up dh-strip-nondeterminism (0.023-2) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160814) ... Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ... 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 libbam-dev_0.1.19-2 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 libexpat1_2.2.0-1 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 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 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-2 libpython2.7-stdlib_2.7.12-2 libquadmath0_6.2.0-1 libreadline6_6.3-8+b4 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 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.14.1-1 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 mime-support_3.60 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 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-2 python2.7-minimal_2.7.12-2 readline-common_6.3-8 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-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 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 Sat Aug 13 08:58:35 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./stacks_1.42-1.dsc dpkg-source: info: extracting stacks in /<> dpkg-source: info: unpacking stacks_1.42.orig.tar.gz dpkg-source: info: unpacking stacks_1.42-1.debian.tar.xz dpkg-source: info: applying constants.php.patch dpkg-source: info: applying email-settings.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-a5841dc2-e111-4814-bf98-c6d830f97fe0 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 1.42-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build stacks-1.42 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --with python2 dh_testdir -a dh_update_autotools_config -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib configure: WARNING: unrecognized options: --disable-maintainer-mode, --with-bam-include-path, --with-bam-lib-path checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether g++ supports C++11 features by default... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for gcc option to support OpenMP... unsupported checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode, --with-bam-include-path, --with-bam-lib-path make[1]: Leaving directory '/<>' dh_auto_build -a make -j1 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in htslib make[3]: Entering directory '/<>/htslib' echo '/* Empty config.h generated by Makefile */' > config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.1"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) ^ ./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2' __KS_INLINED(__read) ^ ./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[3]: Leaving directory '/<>/htslib' Making all in . make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-cmb.o `test -f 'src/cmb.cc' || echo './'`src/cmb.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks-ustacks.o src/ustacks-stacks.o src/ustacks-mstack.o src/ustacks-mst.o src/ustacks-cmb.o src/ustacks-DNASeq.o src/ustacks-DNANSeq.o src/ustacks-models.o src/ustacks-utils.o src/ustacks-kmers.o src/ustacks-aln_utils.o src/ustacks-input.o -lz -lgomp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-pstacks.o `test -f 'src/pstacks.cc' || echo './'`src/pstacks.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc g++ -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wl,-z,relro -Wl,-z,now -o pstacks src/pstacks-pstacks.o src/pstacks-stacks.o src/pstacks-mstack.o src/pstacks-DNANSeq.o src/pstacks-DNASeq.o src/pstacks-models.o src/pstacks-utils.o src/pstacks-input.o ./htslib/libhts.a -lz -lgomp /usr/bin/ld: ./htslib/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_kill@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:1234: recipe for target 'pstacks' failed make[3]: *** [pstacks] Error 1 make[3]: Leaving directory '/<>' Makefile:3417: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/<>' Makefile:892: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: make -j1 returned exit code 2 debian/rules:12: 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 2016-08-29T16:50:53Z 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: 43 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 57 Job: stacks_1.42-1 Machine Architecture: amd64 Package: stacks Package-Time: 229 Source-Version: 1.42-1 Space: 0 Status: failed Version: 1.42-1 -------------------------------------------------------------------------------- Finished at 2016-08-29T16:50:53Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 230.44609282s