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. -------------------------------------------------------------------------------- [...] 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 --------------------------------------------------------------------------------
