Your message dated Thu, 25 Sep 2025 21:05:04 +0000
with message-id <[email protected]>
and subject line Bug#1112655: fixed in nim-hts 0.3.25+ds-3
has caused the Debian Bug report #1112655,
regarding nim-hts: FTBFS: tests/cigartest.nim(20, 11) Error: type mismatch
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1112655: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1112655
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: nim-hts
Source-Version: 0.3.25+ds-3
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
nim-hts, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated nim-hts package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 26 Sep 2025 02:21:00 +0530
Source: nim-hts
Architecture: source
Version: 0.3.25+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1112655
Changes:
nim-hts (0.3.25+ds-3) unstable; urgency=medium
.
* Team Upload.
* Backport upstream patch to build with newer nim compiler
* d/patches: (Closes: #1112655)
+ Skip some failing tests
+ Add patch to fixup fai test
* Update Build-test command as in hts nimble file
* Drop myself from uploaders.
Checksums-Sha1:
9837ca77b886ebc5a051202e5ca814eea9407327 1586 nim-hts_0.3.25+ds-3.dsc
43a893912b7ff0d886f8d30a2933619eeca10374 342864
nim-hts_0.3.25+ds-3.debian.tar.xz
d52a5ab2b5652ba8060a0972a64b2b01230d7dcd 7402
nim-hts_0.3.25+ds-3_amd64.buildinfo
Checksums-Sha256:
286b9bf9c44735dbcffe2aabf255910cfbc55592f74dba4c635b6332b6730b5e 1586
nim-hts_0.3.25+ds-3.dsc
ee3f4731e4409b178355f0c4e7c30c40df1ae24b89259f57407ff652f4a2c928 342864
nim-hts_0.3.25+ds-3.debian.tar.xz
8ba63a9740ff1dcedb6183557dc338d5d09d544d660a80c6a0ce28f6babccdf7 7402
nim-hts_0.3.25+ds-3_amd64.buildinfo
Files:
34f5a60ad7a2f6190bcc8cd0b4e1e02e 1586 libs optional nim-hts_0.3.25+ds-3.dsc
3ac80ddf80b440b85290d937b4df93c4 342864 libs optional
nim-hts_0.3.25+ds-3.debian.tar.xz
4bf44259b198ce643dd8caa9fa5af42b 7402 libs optional
nim-hts_0.3.25+ds-3_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----
iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaNWrvBIcbmlsZXNoQGRl
Ymlhbi5vcmcACgkQKieQS9ckPto1JgEA2xDxCtbsnLQG2P7xusyisK91XQT0eaWx
NtXiMsTTdswBAMbZjD9HK0OeXm+EHXCjCcyfrKP6Lm0QcQRmk64fJi4O
=x1qO
-----END PGP SIGNATURE-----
pgplQ4qniwFNW.pgp
Description: PGP signature
--- End Message ---
