[Debian-med-packaging] Bug#1105234: allelecount: FTBFS with make --shuffle=reverse: ld: cannot find ./src/bam_access.o: No such file or directory

[Lucas Nussbaum]

Source: allelecount
Version: 4.3.0-3
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 -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