Your message dated Tue, 12 Mar 2024 22:19:41 +0000
with message-id <[email protected]>
and subject line Bug#1065759: fixed in libbio-samtools-perl 1.43-5
has caused the Debian Bug report #1065759,
regarding libbio-samtools-perl: FTBFS: lib/Bio/DB/Sam.xs:324:4: error: implicit
declaration of function ‘bam_sort_core’; did you mean ‘bam_format1_core’?
[-Werror=implicit-function-declaration]
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.
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--
1065759: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1065759
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libbio-samtools-perl
Version: 1.43-4
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: [email protected]
https://buildd.debian.org/status/fetch.php?pkg=libbio-samtools-perl&arch=armhf&ver=1.43-4%2Bb2&stamp=1709807129&raw=0
arm-linux-gnueabihf-gcc -I/usr/include/samtools -Ic_bin
-I/usr/lib/arm-linux-gnueabihf/perl/5.38/CORE '-DVERSION="1.43"'
'-DXS_VERSION="1.43"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' '-Wformat=0'
-c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe
-I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2
'-Werror=implicit-function-declaration' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.'
-fstack-protector-strong -fstack-clash-protection -Wformat
'-Werror=format-security' -g -O2 '-Werror=implicit-function-declaration'
'-ffile-prefix-map=/<<PKGBUILDDIR>>=.' -fstack-protector-strong
-fstack-clash-protection -Wformat '-Werror=format-security' -D_LARGEFILE_SOURCE
'-D_FILE_OFFSET_BITS=64' '-D_TIME_BITS=64' -Wdate-time '-D_FORTIFY_SOURCE=2' -o
lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_sort_core’:
lib/Bio/DB/Sam.xs:324:4: error: implicit declaration of function
‘bam_sort_core’; did you mean ‘bam_format1_core’?
[-Werror=implicit-function-declaration]
324 | bam_sort_core(is_by_qname,filename,prefix,max_mem);
| ^~~~~~~~~~~~~
| bam_format1_core
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Header_view1’:
lib/Bio/DB/Sam.xs:916:8: error: implicit declaration of function ‘bam_view1’
[-Werror=implicit-function-declaration]
916 | bam_view1(bamh,alignment);
| ^~~~~~~~~
cc1: some warnings being treated as errors
error building lib/Bio/DB/Sam.o from 'lib/Bio/DB/Sam.c' at
/usr/share/perl/5.38/ExtUtils/CBuilder/Base.pm line 185.
dh_auto_build: error: /usr/bin/perl Build returned exit code 2
Cheers
--
Sebastian Ramacher
--- End Message ---
--- Begin Message ---
Source: libbio-samtools-perl
Source-Version: 1.43-5
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libbio-samtools-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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated libbio-samtools-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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 12 Mar 2024 22:11:21 +0100
Source: libbio-samtools-perl
Architecture: source
Version: 1.43-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Perl Group <[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1065759
Changes:
libbio-samtools-perl (1.43-5) unstable; urgency=medium
.
* Team upload.
.
[ Niko Tyni ]
* Add missing prototypes
Closes: #1065759
.
[ Andreas Tille ]
* Remove trailing whitespace in debian/changelog (routine-update)
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