[Debian-med-packaging] Bug#1105366: genomethreader: FTBFS with make --shuffle=reverse: src/libgenomethreader/gthversionfunc.c:3:10: fatal error: gth_config.h: No such file or directory

[Lucas Nussbaum]

Source: genomethreader
Version: 1.7.3+dfsg-10
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):
> cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj  -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch  -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 
> src/libgenomethreader/gthversionfunc.c:3:10: fatal error: gth_config.h: No such file or directory
>     3 | #include "gth_config.h"
>       |          ^~~~~~~~~~~~~~
> compilation terminated.
> make[2]: *** [Makefile:324: obj/src/libgenomethreader/gthversionfunc.o] Error 1 shuffle=reverse


The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/genomethreader_1.7.3+dfsg-10_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