Your message dated Wed, 15 Jan 2025 20:00:58 +0000
with message-id <e1ty9zs-009zjl...@fasolo.debian.org>
and subject line Bug#1066998: fixed in sift 6.2.1-1
has caused the Debian Bug report #1066998,
regarding sift: FTBFS with -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.
(NB: If you are a system administrator and have no idea what this
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--
1066998: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066998
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: sift
Version: 4.0.3b-6
Severity: serious
Tags: ftbfs sid trixie
Justification: fails to build from source
Hi,
sift TBFS with -Werror=implicit-function-declaration which was
recently enabled by default in dpkg 1.22.6 to support the 64-bit time_t
transition. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
make[2]: Entering directory '/build/sift-4.0.3b/src'
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/sift-4.0.3b/src=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wno-unused-result -I/usr/include/blimps -O2 -D__MAKE_PREFIX__=\"/u
sr\" -Wdate-time -D_FORTIFY_SOURCE=2 -c -o
choose_seqs_via_psiblastseedmedian.o choose_seqs_via_psiblastseedmedian.c
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/sift-4.0.3b/src=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wno-unused-result -I/usr/include/blimps -O2 -D__MAKE_PREFIX__=\"/usr\"
-Wdate-time -D_FORTIFY_SOURCE=2 -c -o clump_output_alignedseq.o
clump_output_alignedseq.c
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/sift-4.0.3b/src=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wno-unused-result -I/usr/include/blimps -O2 -D__MAKE_PREFIX__=\"/usr\"
-Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_to_seq.o consensus_to_seq.c
In file included from choose_seqs_via_psiblastseedmedian.c:20:
Matrix_Info.c: In function 'allow_min_and_above':
Matrix_Info.c:916:26: error: implicit declaration of function
'min_aa_in_column' [-Werror=implicit-function-declaration]
916 | min_aa = min_aa_in_column (matrix, pos);
| ^~~~~~~~~~~~~~~~
In file included from clump_output_alignedseq.c:23:
Matrix_Info.c: In function 'allow_min_and_above':
Matrix_Info.c:916:26: error: implicit declaration of function
'min_aa_in_column' [-Werror=implicit-function-declaration]
916 | min_aa = min_aa_in_column (matrix, pos);
| ^~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/sift-4.0.3b/src=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wno-unused-result -I/usr/include/blimps -O2 -D__MAKE_PREFIX__=\"/usr\"
-Wdate-time -D_FORTIFY_SOURCE=2 -c -o info_on_seqs.o info_on_seqs.c
In file included from info_on_seqs.c:10:
Matrix_Info.c: In function 'allow_min_and_above':
Matrix_Info.c:916:26: error: implicit declaration of function
'min_aa_in_column' [-Werror=implicit-function-declaration]
916 | min_aa = min_aa_in_column (matrix, pos);
| ^~~~~~~~~~~~~~~~
cc1: some warnings being treated as errors
make[2]: *** [<builtin>: choose_seqs_via_psiblastseedmedian.o] Error 1
Andreas
--- End Message ---
--- Begin Message ---
Source: sift
Source-Version: 6.2.1-1
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
sift, 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 1066...@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 sift 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: Wed, 15 Jan 2025 20:06:01 +0100
Binary: sift sift-dbgsym
Source: sift
Architecture: amd64 source
Version: 6.2.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1066998
Description:
sift - predicts if a substitution in a protein has a phenotypic effect
Changes:
sift (6.2.1-1) unstable; urgency=medium
.
* Team upload.
.
[ Steffen Moeller ]
* New upstream version. (Closes: #1066998)
* d/u/metadata:
- added RRIDs
- yamllint clean
.
[ Andreas Tille ]
* Fix watch file
* Fix Vcs fields
* Standards-Version: 4.7.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Drop useless get-orig-source target (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Remove trailing whitespace in debian/rules (routine-update)
* No tab in license text (routine-update)
* Trim trailing whitespace.
* Use secure URI in Homepage field.
* Update renamed lintian tag names in lintian overrides.
* Avoid explicitly specifying -Wl,--as-needed linker flag.
Checksums-Sha1:
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Checksums-Sha256:
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sift_6.2.1-1.dsc
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sift_6.2.1-1.debian.tar.xz
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sift_6.2.1-1_amd64.buildinfo
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c914153fd8ed184420734307b29e9e04214f4b72eae8efd2f7982f485be6b09b 281300
sift_6.2.1-1_amd64.deb
Files:
72bb9f299d6d5e8a651b6e7ffcc4709e 1936 non-free/science optional
sift_6.2.1-1.dsc
fb7164cdd17b41c84a4e72b0aef66387 505700 non-free/science optional
sift_6.2.1.orig.tar.xz
86c7180e596fd84cf7105ec27cade776 21016 non-free/science optional
sift_6.2.1-1.debian.tar.xz
87bc9765d97e863cdfa35d2d9172d53c 6009 non-free/science optional
sift_6.2.1-1_amd64.buildinfo
2a4ca40294277b16f05352d53a0dedcc 589220 non-free/debug optional
sift-dbgsym_6.2.1-1_amd64.deb
4de3cc14977d15d08e371151a25b5899 281300 non-free/science optional
sift_6.2.1-1_amd64.deb
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