[Debian-med-packaging] Bug#1112655: nim-hts: FTBFS: tests/cigartest.nim(20, 11) Error: type mismatch

[Santiago Vila]

Package: src:nim-hts
Version: 0.3.25+ds-2
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Note: All the following packages also FTBFS, if you happen to have a fix for any of them
maybe you can also fix some of the others:

src:hts-nim-tools
src:mosdepth
src:nim-hts
src:nim-lapper
src:nim-regex

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202508/

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 add an affects on src:nim-hts, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
# remnants from testing
rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi
rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai tests/all tests/htstest tests/bgzftest tests/bamtest
rm -rf tests/nimcache
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars debian/files
	rm -fr -- debian/nim-hts-dev/ debian/tmp/ debian/nim-hts-examples/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
# Regenerate repacked files
cat tests/sa.sam | samtools view -Sb - > tests/sa.bam
samtools index tests/sa.bam tests/sa.bam.bai
cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam
samtools index tests/HG02002.bam tests/HG02002.bam.bai
tabix tests/test.vcf.gz
bcftools index tests/test.bcf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/nim-hts-dev.debhelper.log debian/nim-hts-examples.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
nim c --nimcache:/<<PKGBUILDDIR>>/tests/nimcache tests/all.nim
Hint: used config file '/etc/nim/nim.cfg' [Conf]
Hint: used config file '/etc/nim/config.nims' [Conf]
Hint: used config file '/<<PKGBUILDDIR>>/tests/nim.cfg' [Conf]
.......................................................................................................................................
/<<PKGBUILDDIR>>/src/hts/bam/flag.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(1, 17) [DuplicateModuleImport]
.
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /<<PKGBUILDDIR>>/src/hts/bam/flag.nim(1, 18) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(2, 8) Hint: duplicate import of 'strutils'; previous import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(4, 8) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/src/hts/bam.nim(262, 52) Warning: implicit conversion to 'cstring' from a non-const location: region; this will become a compile time error in the future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/bam.nim(373, 28) Warning: implicit conversion to 'cstring' from a non-const location: mode; this will become a compile time error in the future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/bam.nim(409, 35) Warning: implicit conversion to 'cstring' from a non-const location: spl[0]; this will become a compile time error in the future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/bam.nim(409, 43) Warning: implicit conversion to 'cstring' from a non-const location: spl[1]; this will become a compile time error in the future [CStringConv]
..
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(3, 1) Hint: duplicate import of 'strformat'; previous import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(3, 8) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/tests/cigartest.nim(4, 1) template/generic instantiation of `suite` from here
/<<PKGBUILDDIR>>/tests/cigartest.nim(18, 3) template/generic instantiation of `test` from here
/<<PKGBUILDDIR>>/tests/cigartest.nim(20, 11) Error: type mismatch
Expression: GC_ref(els)
  [1] els: seq[CigarElement]

Expected one of (first mismatch at [position]):
[1] proc GC_ref[T](x: ref T)

make[1]: *** [debian/rules:20: override_dh_auto_test] Error 1
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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