Source: samtools Version: 1.3.1-2 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
Dear Maintainer, samtools fails to build from source in unstable/amd64: […] ************************************************************************************** ** Starting build ** ************************************************************************************** Package: samtools Version: 1.3.1-2 Build architecture: amd64 Date: Sun, 16 Oct 2016 16:05:23 +0200 Hostname: 80cae65f0728 Uname: Linux 80cae65f0728 4.7.0-1-amd64 #1 SMP Debian 4.7.5-1 (2016-09-26) x86_64 GNU/Linux /etc/timezone: Europe/Belgrade ************************************************************************************** ** Installing build dependencies ** ************************************************************************************** dh_testdir dh_testroot dh_prep dh_testdir dh_testroot dh_install dh_installdocs dh_installchangelogs dh_compress dh_fixperms dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'samtools-build-deps' in '../samtools-build-deps_1.3.1-2_all.deb'. The package has been created. Attention, the package has been created in the current directory, not in ".." as indicated by the message above! Selecting previously unselected package samtools-build-deps. (Reading database ... 23458 files and directories currently installed.) Preparing to unpack samtools-build-deps_1.3.1-2_all.deb ... Unpacking samtools-build-deps (1.3.1-2) ... Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following additional packages will be installed: autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev libtinfo-dev tabix zlib1g-dev Suggested packages: ncurses-doc The following NEW packages will be installed: autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev libtinfo-dev tabix zlib1g-dev 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 2175 kB of archives. After this operation, 12.3 MB of additional disk space will be used. Get:1 http://httpredir.debian.org/debian sid/main amd64 bash-completion all 1:2.1-4.3 [178 kB] Get:2 http://httpredir.debian.org/debian sid/main amd64 libtinfo-dev amd64 6.0+20160917-1 [77.3 kB] Get:3 http://httpredir.debian.org/debian sid/main amd64 libncurses5-dev amd64 6.0+20160917-1 [173 kB] Get:4 http://httpredir.debian.org/debian sid/main amd64 libhts1 amd64 1.3.1-3 [256 kB] Get:5 http://httpredir.debian.org/debian sid/main amd64 libhts-dev amd64 1.3.1-3 [315 kB] Get:6 http://httpredir.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Get:7 http://httpredir.debian.org/debian sid/main amd64 autoconf-archive all 20160916-1 [716 kB] Get:8 http://httpredir.debian.org/debian sid/main amd64 tabix amd64 1.3.1-3 [254 kB] Fetched 2175 kB in 0s (3409 kB/s) Selecting previously unselected package bash-completion. (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 ... 23462 files and directories currently installed.) Preparing to unpack .../0-bash-completion_1%3a2.1-4.3_all.deb ... Unpacking bash-completion (1:2.1-4.3) ... Selecting previously unselected package libtinfo-dev:amd64. Preparing to unpack .../1-libtinfo-dev_6.0+20160917-1_amd64.deb ... Unpacking libtinfo-dev:amd64 (6.0+20160917-1) ... Selecting previously unselected package libncurses5-dev:amd64. Preparing to unpack .../2-libncurses5-dev_6.0+20160917-1_amd64.deb ... Unpacking libncurses5-dev:amd64 (6.0+20160917-1) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../3-libhts1_1.3.1-3_amd64.deb ... Unpacking libhts1:amd64 (1.3.1-3) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../4-libhts-dev_1.3.1-3_amd64.deb ... Unpacking libhts-dev:amd64 (1.3.1-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../5-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../6-autoconf-archive_20160916-1_all.deb ... Unpacking autoconf-archive (20160916-1) ... Selecting previously unselected package tabix. Preparing to unpack .../7-tabix_1.3.1-3_amd64.deb ... Unpacking tabix (1.3.1-3) ... Setting up libhts1:amd64 (1.3.1-3) ... Setting up libhts-dev:amd64 (1.3.1-3) ... Setting up bash-completion (1:2.1-4.3) ... Setting up libtinfo-dev:amd64 (6.0+20160917-1) ... Setting up libncurses5-dev:amd64 (6.0+20160917-1) ... Setting up autoconf-archive (20160916-1) ... Processing triggers for libc-bin (2.24-3) ... Processing triggers for man-db (2.7.5-1) ... Setting up tabix (1.3.1-3) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up samtools-build-deps (1.3.1-2) ... ************************************************************************************** ** Environment ** ************************************************************************************** PATH=/home/lamby/git/projects/dotfiles/dotfiles/..//bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin HOSTNAME=80cae65f0728 TERM=xterm PAGER=more DISPLAY=:0 DOCKER_IMAGE=lamby-debian-sid DEB_BUILD_OPTIONS=parallel=9 PIP_DOWNLOAD_CACHE=/home/lamby/.cache/pip HOME=/home/lamby LOGNAME=lamby SHLVL=1 PWD=/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1 OLDPWD=/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools GPG_TTY=/dev/console QUILT_PATCHES=debian/patches QUILT_NO_DIFF_INDEX=1 QUILT_REFRESH_ARGS=-p ab --no-timestamps --no-index DEBEMAIL=la...@debian.org DEBFULLNAME=Chris Lamb EDITOR=vim LESS=-cgiFx4M GPG_KEY=1E953E27D4311E58 BLASTER=A220 I5 D1 H5 P330 T6 _=/usr/bin/env ************************************************************************************** ** Building samtools 1.3.1-2 on amd64 ** ************************************************************************************** dpkg-buildpackage -rfakeroot -D -us -uc -b dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.3.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Charles Plessy <ple...@debian.org> dpkg-source --before-build samtools-1.3.1 dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' touch config.mk dh_auto_clean -- make -j9 distclean make[2]: Entering directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS make[2]: Leaving directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' make[1]: Leaving directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' dh_clean -O--parallel rm -f debian/debhelper-build-stamp rm -f debian/samtools.substvars rm -f debian/samtools.*.debhelper rm -rf debian/samtools/ rm -f debian/samtools-test.substvars rm -f debian/samtools-test.*.debhelper rm -rf debian/samtools-test/ rm -rf debian/.debhelper/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp debian/rules build dh build --parallel dh_testdir -O--parallel dh_update_autotools_config -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' touch config.mk aclocal --force -I /usr/share/aclocal/ -I debian/ configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing? /usr/share/aclocal/ax_require_defined.m4:35: AX_REQUIRE_DEFINED is expanded from... /usr/share/aclocal/ax_with_curses.m4:197: _FIND_CURSES_FLAGS is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... /usr/share/aclocal/ax_with_curses.m4:250: AX_WITH_CURSES is expanded from... configure.ac:69: the top level autom4te: /usr/bin/m4 failed with exit status: 1 aclocal: error: echo failed with exit status: 1 debian/rules:13: recipe for target 'override_dh_auto_configure' failed make[1]: *** [override_dh_auto_configure] Error 1 make[1]: Leaving directory '/home/lamby/temp/cdt.20161016160520.GxW32gLmlE.db.samtools/samtools-1.3.1' debian/rules:6: recipe for target 'build' failed make: *** [build] Error 2 […] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
samtools.1.3.1-2.unstable.amd64.log.txt.gz
Description: Binary data