Your message dated Fri, 24 Oct 2025 18:21:52 +0000
with message-id <[email protected]>
and subject line Bug#1105578: fixed in soapdenovo2 242+dfsg-5
has caused the Debian Bug report #1105578,
regarding soapdenovo2: FTBFS with make --shuffle=reverse: ld: cannot find
sparsePregraph/*.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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--
1105578: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105578
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: soapdenovo2
Version: 242+dfsg-4
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):
> g++ sparsePregraph/*.o standardPregraph/*.o -L./sparsePregraph/inc
> -L./standardPregraph/inc -L/lib64 -L/usr/lib64 -pthread -lz -lm -lbam -lrt
> -Wl,--hash-style=both -o SOAPdenovo-127mer `dpkg-buildflags --get LDFLAGS`
> /usr/bin/ld: cannot find sparsePregraph/*.o: No such file or directory
> /usr/bin/ld: cannot find standardPregraph/*.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/soapdenovo2_242+dfsg-4_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: soapdenovo2
Source-Version: 242+dfsg-5
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
soapdenovo2, 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 soapdenovo2 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: Fri, 24 Oct 2025 19:53:20 +0200
Source: soapdenovo2
Architecture: source
Version: 242+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097909 1105578
Changes:
soapdenovo2 (242+dfsg-5) unstable; urgency=medium
.
* Team upload.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097909)
* fix-deps.patch: new: stabilise make rules ordering. (Closes: #1105578)
* reproducible patch: normalise Last-Update timestamp.
* d/watch: bump to watch file version 5.
* d/u/metadata: locate upstream repository.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
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