Your message dated Fri, 19 Dec 2025 20:24:06 +0000
with message-id <[email protected]>
and subject line Bug#1105678: fixed in raxml 8.2.13+dfsg-3
has caused the Debian Bug report #1105678,
regarding raxml: FTBFS with make --shuffle=reverse: ld: cannot find multiple.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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--
1105678: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105678
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: raxml
Version: 8.2.13+dfsg-2
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 -o raxmlHPC-PTHREADS axml.o optimizeModel.o multiple.o searchAlgo.o
> topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o
> rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o
> newviewGenericSpecial.o makenewzGenericSpecial.o classify.o
> fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o
> ancestralStates.o mem_alloc.o eigen.o -lm -pthread -Wl,-z,relro -Wl,-z,now
> /usr/bin/ld: cannot find multiple.o: No such file or directory
> /usr/bin/ld: cannot find searchAlgo.o: No such file or directory
> /usr/bin/ld: cannot find topologies.o: No such file or directory
> /usr/bin/ld: cannot find parsePartitions.o: No such file or directory
> /usr/bin/ld: cannot find treeIO.o: No such file or directory
> /usr/bin/ld: cannot find rapidBootstrap.o: No such file or directory
> /usr/bin/ld: cannot find evaluatePartialGenericSpecial.o: No such file or
> directory
> /usr/bin/ld: cannot find evaluateGenericSpecial.o: No such file or directory
> /usr/bin/ld: cannot find classify.o: No such file or directory
> /usr/bin/ld: cannot find fastDNAparsimony.o: No such file or directory
> /usr/bin/ld: cannot find fastSearch.o: No such file or directory
> /usr/bin/ld: cannot find leaveDropping.o: No such file or directory
> /usr/bin/ld: cannot find rmqs.o: No such file or directory
> /usr/bin/ld: cannot find rogueEPA.o: No such file or directory
> /usr/bin/ld: cannot find ancestralStates.o: No such file or directory
> /usr/bin/ld: cannot find mem_alloc.o: No such file or directory
> /usr/bin/ld: cannot find eigen.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/raxml_8.2.13+dfsg-2_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: raxml
Source-Version: 8.2.13+dfsg-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
raxml, 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 raxml 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, 19 Dec 2025 20:36:27 +0100
Source: raxml
Architecture: source
Version: 8.2.13+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1105678
Changes:
raxml (8.2.13+dfsg-3) unstable; urgency=medium
.
* d/control: fix standards version declaration.
* d/copyright: drop the old FSF mail address.
* d/watch: convert to v5 Github template.
* d/control: drop redundant Rules-Requires-Root: no.
* stabilize-makefiles.patch: new.
This patche makes the "all" target more robust to unordered
invocations by dropping the dependency on the "clean" target.
(Closes: #1105678)
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