[Debian-med-packaging] Bug#1075288: mosdepth: ftbfs with GCC-14

[Matthias Klose]

Package: src:mosdepth
Version: 0.3.6+ds-1
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/mosdepth_0.3.6+ds-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html

[...]
/<<PKGBUILDDIR>>/mosdepth.nim(262, 18) template/generic instantiation of `tag` from here
/usr/share/nimble/hts/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/mosdepth.nim(262, 18) template/generic instantiation of `tag` from here
/usr/share/nimble/hts/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/mosdepth.nim(606, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/<<PKGBUILDDIR>>/mosdepth.nim(609, 17) Warning: open; wopen_bgzi is deprecated [Deprecated]
/<<PKGBUILDDIR>>/mosdepth.nim(612, 19) Warning: open; wopen_bgzi is deprecated [Deprecated]
/<<PKGBUILDDIR>>/mosdepth.nim(625, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/<<PKGBUILDDIR>>/mosdepth.nim(879, 13) Warning: implicit conversion to 'cstring' from a non-const location: $args["<BAM-or-CRAM>"]; this will become a compile time error in the future [CStringConv]
/<<PKGBUILDDIR>>/mosdepth.nim(543, 6) Hint: 'to_tuples' is declared but not used [XDeclaredButNotUsed]
/<<PKGBUILDDIR>>/mosdepth.nim(9, 8) Warning: imported and not used: 'strformat' [UnusedImport]
/<<PKGBUILDDIR>>/mosdepth.nim(11, 8) Warning: imported and not used: 'times' [UnusedImport]
CC: ../../../usr/lib/nim/lib/std/private/digitsutils.nim
CC: ../../../usr/lib/nim/lib/system/assertions.nim
CC: ../../../usr/lib/nim/lib/system/dollars.nim
CC: ../../../usr/lib/nim/lib/system/io.nim
CC: ../../../usr/lib/nim/lib/system.nim
CC: ../../../usr/share/nimble/hts/hts/private/hts_concat.nim
CC: ../../../usr/lib/nim/lib/pure/parseutils.nim
CC: ../../../usr/lib/nim/lib/pure/unicode.nim
CC: ../../../usr/lib/nim/lib/pure/math.nim
CC: ../../../usr/lib/nim/lib/pure/algorithm.nim
CC: ../../../usr/lib/nim/lib/pure/strutils.nim
CC: ../../../usr/lib/nim/lib/pure/strformat.nim
CC: ../../../usr/share/nimble/hts/hts/bam.nim
CC: ../../../usr/lib/nim/lib/pure/collections/sequtils.nim
CC: ../../../usr/share/nimble/hts/hts/vcf.nim
CC: ../../../usr/share/nimble/hts/hts/bgzf.nim
CC: ../../../usr/share/nimble/hts/hts/csi.nim
CC: ../../../usr/share/nimble/hts/hts/bgzf/bgzi.nim
CC: ../../../usr/share/nimble/hts/hts.nim
CC: ../../../usr/lib/nim/lib/pure/hashes.nim
CC: ../../../usr/lib/nim/lib/pure/collections/tables.nim
CC: int2str.nim
CC: ../../../usr/lib/nim/lib/pure/times.nim
CC: ../../../usr/lib/nim/lib/pure/os.nim
CC: ../../../usr/lib/nim/lib/pure/collections/sets.nim
CC: ../../../usr/share/nimble/unicodedb/unicodedb/properties_data.nim
CC: ../../../usr/share/nimble/unicodedb/unicodedb/properties.nim
CC: ../../../usr/share/nimble/regex/regex/common.nim
CC: ../../../usr/share/nimble/regex/regex/nodetype.nim
CC: ../../../usr/share/nimble/regex/regex/exptransformation.nim
CC: ../../../usr/share/nimble/regex/regex/nfa.nim
CC: ../../../usr/share/nimble/unicodedb/unicodedb/types_data.nim
CC: ../../../usr/share/nimble/unicodedb/unicodedb/types.nim
CC: ../../../usr/share/nimble/unicodeplus/unicodeplus.nim
CC: ../../../usr/share/nimble/regex/regex/nodematch.nim
CC: ../../../usr/share/nimble/regex/regex/litopt.nim
CC: ../../../usr/share/nimble/regex/regex/nfatype.nim
CC: ../../../usr/share/nimble/regex/regex/nfafindall.nim
CC: ../../../usr/share/nimble/regex/regex/nfamatch.nim
CC: ../../../usr/share/nimble/docopt/docopt/util.nim
CC: ../../../usr/share/nimble/docopt/docopt.nim
CC: depthstat.nim
CC: mosdepth.nim
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c: In function ‘single_match__OOZOOZOOZusrZshareZnimbleZdocoptZdocopt_1666’:
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c:4784:53: error: assignment to ‘tyObject_PatterncolonObjectType___UMJteYlHaV5TEraRE0vAsg *’ from incompatible pointer type ‘tyObject_ArgumentcolonObjectType___DhRoYbiBcyoxV4IeXTvZYQ *’ [-Wincompatible-pointer-types]
 4784 |                                         colontmp__2 = argument__OOZOOZOOZusrZshareZnimbleZdocoptZdocopt_239(T10_, (*pattern).value);
      |                                                     ^
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c: In function ‘single_match__OOZOOZOOZusrZshareZnimbleZdocoptZdocopt_1684’:
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c:4920:61: error: assignment to ‘tyObject_PatterncolonObjectType___UMJteYlHaV5TEraRE0vAsg *’ from incompatible pointer type ‘tyObject_CommandcolonObjectType___DxK0NjB3YmW64E9b9bi0erBQ *’ [-Wincompatible-pointer-types]
 4920 |                                                 colontmp__2 = command__OOZOOZOOZusrZshareZnimbleZdocoptZdocopt_269(T18_, T19_);
      |                                                             ^
Error: execution of an external compiler program 'gcc -c  -w -fmax-errors=3 -g3 -Og -O3 -fno-strict-aliasing -fno-ident   -I/usr/lib/nim/lib -I/<<PKGBUILDDIR>> -o /<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c.o /<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at susr@sshare at snimble@sdocopt at sdocopt.nim.c' failed with exit code: 1


make[1]: *** [debian/rules:14: override_dh_auto_build] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2