Your message dated Thu, 31 Oct 2024 22:29:26 +0000
with message-id <e1t6dfs-00gy4x...@fasolo.debian.org>
and subject line Bug#1086359: fixed in libbio-db-hts-perl 3.01-5
has caused the Debian Bug report #1086359,
regarding libbio-db-hts-perl: FTBFS: This module requires HTSlib
(http://htslib.org/)
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.)
--
1086359: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086359
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:libbio-db-hts-perl
Version: 3.01-4
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
/usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now"
This module requires HTSlib (http://htslib.org/)
Install it if you have not done so already.
This script will attempt to locate HTSlib by looking for htslib/hts.h
and libhts.a / libhts.so in:
1. --htslib-includedir and --htslib-libdir command line arguments
2. --htslib command line argument
3. HTSLIB_DIR environment variable
4. --prefix command line argument (which also sets installation location)
5. Alien::HTSlib dependency resolver
6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment
variable)
7. common library locations: /usr /usr/local, /usr/share, /opt/local
If none of the above succeeds but htslib is registered with pkg-config, the
script
will try using pkg-config paths (via ExtUtils::PkgConfig) without checking if
header
and library files exist.
dh_auto_configure: error: /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config
"ld=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro
-Wl,-z,now" returned exit code 1
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: libbio-db-hts-perl
Source-Version: 3.01-5
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
libbio-db-hts-perl, 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 1086...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated libbio-db-hts-perl
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: Thu, 31 Oct 2024 22:38:00 +0100
Source: libbio-db-hts-perl
Architecture: source
Version: 3.01-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1086359
Changes:
libbio-db-hts-perl (3.01-5) unstable; urgency=medium
.
* d/rules: nudge configure steps to find htslib. (Closes: #1086359)
* find_htslib.patch: remove DT_RUNPATH injection.
* d/control: declare myself as uploader.
* d/control: declare compliance to standards version 4.7.0.
* d/*lintian-overrides: freshen section override.
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