[Debian-med-packaging] Bug#1089272: snippy: FTBFS with make 4.4.1

[Santiago Vila]

Package: src:snippy
Version: 4.6.0+dfsg-4
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_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd test && /usr/bin/make
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
mkdir -p S1
wgsim -S 1 \
	 -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
	 example.fna S1/R1.fq S1/R1.fq > S1/dwgsim.tab
[wgsim] seed = 1
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
Makefile:35: warning: pattern recipe did not update peer target 'S1/R2.fq'.
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq
[21:16:23] This is snippy 4.6.0
[21:16:23] Written by Torsten Seemann
[21:16:23] Obtained from https://github.com/tseemann/snippy
[21:16:23] Detected operating system: linux
[21:16:23] Enabling bundled linux tools.
[21:16:23] Found bwa - /usr/bin/bwa
[21:16:23] Found bcftools - /usr/bin/bcftools
[21:16:23] Found samtools - /usr/bin/samtools
[21:16:23] Found java - /usr/bin/java
[21:16:23] Found snpEff - /usr/bin/snpEff
[21:16:23] Found samclip - /usr/bin/samclip
[21:16:23] Found seqtk - /usr/bin/seqtk
[21:16:23] Found parallel - /usr/bin/parallel
[21:16:23] Found freebayes - /usr/bin/freebayes
[21:16:23] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[21:16:23] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[21:16:23] Found vcfstreamsort - /usr/bin/vcfstreamsort
[21:16:23] Found vcfuniq - /usr/bin/vcfuniq
[21:16:23] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[21:16:23] Found gzip - /usr/bin/gzip
[21:16:23] Found vt - /usr/bin/vt
[21:16:23] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab
[21:16:23] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report
[21:16:23] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[21:16:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.20
[21:16:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7
[21:16:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[21:16:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[21:16:23] Using reference: /<<PKGBUILDDIR>>/test/example.fna
[21:16:23] Treating reference as 'fasta' format.
[21:16:23] Will use 2 CPU cores.
[21:16:23] Can not read sequence file: S1/R2.fq
make[2]: *** [Makefile:32: S1/snps.tab] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: *** [debian/rules:10: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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