[Debian-med-packaging] Bug#1089249: allelecount: FTBFS with make 4.4.1

[Santiago Vila]

Package: src:allelecount
Version: 4.3.0-2
User: debian-qa at lists.debian.org
Usertags: make-4.4
Severity: important
Tags: ftbfs

Dear Maintainer,

This package fails to build from source with Make 4.4.1, most likely because of
changes in $(shell) environment handling: environment variables exported from
Makefiles are now made available to commands invoked using $(shell), which
can cause issues with recursive definitions in particular. See
https://salsa.debian.org/debian/make/-/blob/master/debian/NEWS for a complete
list of backward-incompatible changes since Make 4.3.

Below you will find how the builds end, hopefully the most relevant
part from the build log. A full build log is available here:

https://people.debian.org/~sanvila/make-4.4/build-logs/

Make 4.4.1 is currently available in experimental and will hopefully
soon be uploaded to unstable, at which time this bug will become
release-critical.

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Please reach out to the Make maintainer, Stephen Kitt <skitt at debian.org> if
you need help fixing this.

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  debian/rules binary
dh binary
    dh_update_autotools_config
    dh_autoreconf
    debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure --sourcedirectory=c
dh_auto_configure --sourcedirectory=perl
	cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now"
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for alleleCount
Writing MYMETA.yml and MYMETA.json
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
    debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=c
	cd c && make -j2 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/c'
rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
mkdir -p ./bin
mkdir -p ./htslib_tmp
#Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic -c src/bam_access.c  -o src/bam_access.o
ln -fs /libhts.a ./htslib_tmp/libhts.a
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
make[2]: *** [<builtin>: tests/bam_access_tests] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/c'
dh_auto_build: error: cd c && make -j2 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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