Your message dated Thu, 05 Mar 2026 21:49:43 +0000
with message-id <[email protected]>
and subject line Bug#1105234: fixed in allelecount 4.3.0-4
has caused the Debian Bug report #1105234,
regarding allelecount: FTBFS with make --shuffle=reverse: ld: cannot find
./src/bam_access.o: No such file or directory
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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--
1105234: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105234
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: allelecount
Version: 4.3.0-3
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-shuffle
Hi,
GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/
This package fails to build with make --shuffle=reverse.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.
More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle
Relevant part (hopefully):
> gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2
> -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/
> -I/ -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2
> -llzma -lm -ldl -L/usr/local//lib -Wdate-time -D_FORTIFY_SOURCE=2
> -Wl,-z,relro -Wl,-z,now tests/bam_access_tests.c -o tests/bam_access_tests
> tests/bam_access_tests.c: In function
> ‘test_bam_access_get_position_base_counts’:
> tests/bam_access_tests.c:45:13: warning: variable ‘res’ set but not used
> [-Wunused-but-set-variable]
> 45 | int res =
> bam_access_get_position_base_counts(chr,pos,stats,0,NULL);
> | ^~~
> /usr/bin/ld: cannot find ./src/bam_access.o: No such file or directory
> collect2: error: ld returned 1 exit status
The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/allelecount_4.3.0-3_unstable_reverse.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
--- End Message ---
--- Begin Message ---
Source: allelecount
Source-Version: 4.3.0-4
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
allelecount, 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.
Étienne Mollier <[email protected]> (supplier of updated allelecount 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: SHA512
Format: 1.8
Date: Thu, 05 Mar 2026 22:25:20 +0100
Source: allelecount
Architecture: source
Version: 4.3.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1105234
Changes:
allelecount (4.3.0-4) unstable; urgency=medium
.
* stabilise-makefiles.patch: new: fix --shuffle. (Closes: #1105234)
* hardening.patch: normalize Last-Update time stamp.
* d/watch: bump to Github uscan template version 5.
* perl-fixups.patch: new: fix heading, typos and style in manuals.
* d/control: add myself to uploaders.
* d/control: drop redundant Priority: optional.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.3.
* d/lintian-overrides: delete: unused override.
Checksums-Sha1:
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0867a1fbd68c7123999717f1a2868d6cf8161ed6 17472
allelecount_4.3.0-4.debian.tar.xz
Checksums-Sha256:
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072dc464e963c0e65bfdf5dd3bb53071214fc7a98858549b52af8218b547a6ef 17472
allelecount_4.3.0-4.debian.tar.xz
Files:
9d2331b60b05b9d09c1a6727e67ba348 2570 science optional allelecount_4.3.0-4.dsc
9a06fbc370b360713ea37cd76507ad43 17472 science optional
allelecount_4.3.0-4.debian.tar.xz
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