Your message dated Tue, 25 Oct 2016 07:40:00 +0000
with message-id <e1bywl2-0000ai...@franck.debian.org>
and subject line Bug#840974: fixed in samtools 1.3.1-3
has caused the Debian Bug report #840974,
regarding samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is
not defined; is a m4 file missing?
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
840974: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=840974
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: samtools
Source-Version: 1.3.1-3
We believe that the bug you reported is fixed in the latest version of
samtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 840...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sascha Steinbiss <sa...@debian.org> (supplier of updated samtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 24 Oct 2016 16:33:30 +0200
Source: samtools
Binary: samtools samtools-test
Architecture: source
Version: 1.3.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <sa...@debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Closes: 840974
Changes:
samtools (1.3.1-3) unstable; urgency=medium
.
* Team upload.
* Refresh existing patches.
* Fix FTBFS by including upstream patches.
Closes: #840974
Checksums-Sha1:
d209e362f1874e8438eb5f04f5ca56e3359b7d25 2186 samtools_1.3.1-3.dsc
fe0dd319bdbb8313ad4da76fd42edfce1d3b984a 16680 samtools_1.3.1-3.debian.tar.xz
Checksums-Sha256:
e6d4a192e86536f12d6fcf0d640c9d777c40c893e89d613f3563ffe9ca9ade48 2186
samtools_1.3.1-3.dsc
3d2bdaca861314f478b4ab8a6d9825014a52e64d6bb095998b2c47740f2de156 16680
samtools_1.3.1-3.debian.tar.xz
Files:
544b0b049e2491a65419858adac4e609 2186 science optional samtools_1.3.1-3.dsc
b2be2e04aac1c46ebd9c0162623e6c91 16680 science optional
samtools_1.3.1-3.debian.tar.xz
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