Hi all, I have pushed a fix (9aac9cb) to Git, solving the FTBFS. Before doing an upload I would be very happy if an Autotools-savvy person could take another closer look because admittedly I am not really sure about the cause of the problem.
I also had to disable a test (test_usage) that otherwise also seems to (mysteriously?) fail in my building chroot, resulting in: pty_allocate(nonfatal): posix_openpt(): Permission denied at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24. pty_allocate(nonfatal): getpt(): No such file or directory at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24. pty_allocate(nonfatal): openpty(): No such file or directory at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24. pty_allocate(nonfatal): open(/dev/ptmx): Permission denied at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24. Cannot open a pty at test/test.pl line 551. Any comments welcome. Feel free to upload with any modifications if you want. Cheers Sascha > On 16 Oct 2016, at 16:06, Chris Lamb <la...@debian.org> wrote: > > 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>_______________________________________________ > Reproducible-builds mailing list > reproducible-bui...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/reproducible-builds
