[Debian-med-packaging] Bug#1105678: raxml: FTBFS with make --shuffle=reverse: ld: cannot find multiple.o: No such file or directory

[Lucas Nussbaum]

Source: raxml
Version: 8.2.13+dfsg-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
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