[Debian-med-packaging] Bug#1105388: jellyfish: FTBFS with make --shuffle=reverse: jellyfish/fastq2sam.cc:12:10: fatal error: jellyfish/fastq2sam_cmdline.hpp: No such file or directory

[Lucas Nussbaum]

Source: jellyfish
Version: 2.3.1-4
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):
> g++ -DHAVE_CONFIG_H -I.  -Wall -Wnon-virtual-dtor -I. -I./include  -Wdate-time -D_FORTIFY_SOURCE=2  -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include  -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc
> jellyfish/fastq2sam.cc:12:10: fatal error: jellyfish/fastq2sam_cmdline.hpp: No such file or directory
>    12 | #include <jellyfish/fastq2sam_cmdline.hpp>
>       |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> compilation terminated.
> make[2]: *** [Makefile:1705: jellyfish/fastq2sam.o] Error 1 shuffle=reverse


The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/jellyfish_2.3.1-4_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