[Debian-med-packaging] Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

Thu Oct 20 20:17:03 UTC 2016

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 <lamby at debian.org> wrote:
> 
> Source: samtools
> Version: 1.3.1-2
> Severity: serious
> Justification: fails to build from source
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-builds at 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=lamby at 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 <plessy at 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
>     `. `'`      lamby at debian.org / chris-lamb.co.uk
>       `-
> <samtools.1.3.1-2.unstable.amd64.log.txt.gz>_______________________________________________
> Reproducible-builds mailing list
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