[Debian-med-packaging] Bug#789488: seqprep: FTBFS everywhere except on amd64/linux

[Andreas Beckmann]

Package: seqprep
Version: 1.1-1
Severity: serious
Justification: fails to build from source

Hi,

seqprep fails to build everywhere:
https://buildd.debian.org/status/package.php?p=seqprep&suite=unstable

either (e.g. arm64) with

 fakeroot debian/rules binary-arch
dh binary-arch
   dh_testroot -a
   dh_prep -a
   dh_auto_install -a
	make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/«PKGBUILDDIR»'
cp SeqPrep /sbuild-nonexistent/bin
cp: cannot create regular file '/sbuild-nonexistent/bin': No such file or directory
make[1]: [install] Error 1 (ignored)
Makefile:16: recipe for target 'install' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
   debian/rules override_dh_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_install
sed -i 's#../SeqPrep#/usr/bin/seqprep#' /«PKGBUILDDIR»/debian/seqprep-data/usr/share/doc/seqprep/examples/RUNTEST.sh
sed: can't read /«PKGBUILDDIR»/debian/seqprep-data/usr/share/doc/seqprep/examples/RUNTEST.sh: No such file or directory
make[1]: *** [override_dh_install] Error 2
debian/rules:28: recipe for target 'override_dh_install' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
make: *** [binary-arch] Error 2
debian/rules:5: recipe for target 'binary-arch' failed
dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2

why is the install error ignored? this should fail earlier ...
why is it going to touch $HOME?


or with testsuite output mismatch (e.g. i386):

   debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
# This checks that the tests run and produce byte-identical results.
cd Test && mkdir -p out info && \
    bash -xc 'gzcat(){ zcat "$@" ; } ; . RUNTEST.sh'
+ . RUNTEST.sh
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_merged_1.fastq.gz -2 ./out/pe_bad_contam_merged_2.fastq.gz -s ./out/pe_bad_contam_merged_s.fastq.gz -E ./info/alignments_merged.txt.gz
Processing reads... \
Pairs Processed:	100000
Pairs Merged:	14306
Pairs With Adapters:	4091
Pairs Discarded:	2228
CPU Time Used (Minutes):	0.346382
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_trimmed_1.fastq.gz -2 ./out/pe_bad_contam_trimmed_2.fastq.gz -E ./info/alignments_trimmed.txt.gz
Processing reads... \
Pairs Processed:	100000
Pairs Merged:	0
Pairs With Adapters:	4091
Pairs Discarded:	2228
CPU Time Used (Minutes):	0.342337
++ prog=gzcat
++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ python seqlens.py
++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ python seqlens.py
++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz
++ python seqlens.py
++ zcat ./out/pe_bad_contam_merged_1.fastq.gz
++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz
++ python seqlens.py
++ zcat ./out/pe_bad_contam_merged_2.fastq.gz
++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz
++ zcat ./out/pe_bad_contam_merged_s.fastq.gz
++ python seqlens.py
[ `cat Test/info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ]
make[1]: *** [override_dh_auto_test] Error 1
debian/rules:19: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
debian/rules:5: recipe for target 'build-arch' failed


Andreas