[Debian-med-packaging] Bug#1075071: hts-nim-tools: ftbfs with GCC-14

[Matthias Klose]

Package: src:hts-nim-tools
Version: 0.2.1-1
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/hts-nim-tools_0.2.1-1_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>>/src/copy_number_sampler.nim(10, 8) Hint: duplicate import of 'version'; previous import here: /<<PKGBUILDDIR>>/src/vcf_check.nim(6, 8) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/src/copy_number_sampler.nim(130, 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]
CC: kexpr-c
CC: ../../../../usr/lib/nim/lib/std/private/digitsutils.nim
CC: ../../../../usr/lib/nim/lib/system/assertions.nim
CC: ../../../../usr/lib/nim/lib/system/formatfloat.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/lib/nim/lib/pure/parseutils.nim
CC: ../../../../usr/lib/nim/lib/pure/bitops.nim
CC: ../../../../usr/lib/nim/lib/pure/math.nim
CC: ../../../../usr/lib/nim/lib/pure/algorithm.nim
CC: ../../../../usr/lib/nim/lib/pure/unicode.nim
CC: ../../../../usr/lib/nim/lib/pure/strutils.nim
CC: ../../../../usr/lib/nim/lib/pure/times.nim
CC: ../../../../usr/lib/nim/lib/pure/os.nim
CC: ../../../../usr/share/nimble/hts/hts/private/hts_concat.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.nim
CC: ../../../../usr/lib/nim/lib/pure/hashes.nim
CC: ../../../../usr/lib/nim/lib/pure/collections/tables.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: ../../../../usr/share/nimble/kexpr/kexpr.nim
CC: version.nim
CC: ../../../../usr/share/nimble/lapper/lapper.nim
CC: ../../../../usr/lib/nim/lib/std/sysrand.nim
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c: In function ‘single_match__OOZOOZOOZOOZusrZshareZnimbleZdocoptZdocopt_1666’:
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c:5269:53: error: assignment to ‘tyObject_PatterncolonObjectType___UMJteYlHaV5TEraRE0vAsg *’ from incompatible pointer type ‘tyObject_ArgumentcolonObjectType___DhRoYbiBcyoxV4IeXTvZYQ *’ [-Wincompatible-pointer-types]
 5269 |                                         colontmp__2 = argument__OOZOOZOOZOOZusrZshareZnimbleZdocoptZdocopt_239(T10_, (*pattern).value);
      |                                                     ^
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c: In function ‘single_match__OOZOOZOOZOOZusrZshareZnimbleZdocoptZdocopt_1684’:
/<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c:5426:61: error: assignment to ‘tyObject_PatterncolonObjectType___UMJteYlHaV5TEraRE0vAsg *’ from incompatible pointer type ‘tyObject_CommandcolonObjectType___DxK0NjB3YmW64E9b9bi0erBQ *’ [-Wincompatible-pointer-types]
 5426 |                                                 colontmp__2 = command__OOZOOZOOZOOZusrZshareZnimbleZdocoptZdocopt_269(T18_, T19_);
      |                                                             ^
CC: ../../../../usr/lib/nim/lib/pure/random.nim
CC: hts_nim_tools.nim
Error: execution of an external compiler program 'gcc -c  -w -fmax-errors=3 -g3 -Og   -I/usr/lib/nim/lib -I/<<PKGBUILDDIR>>/src -o /<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c.o /<<PKGBUILDDIR>>/nimcache/@m.. at s..@s.. at s..@susr at sshare@snimble at sdocopt@sdocopt.nim.c' failed with exit code: 1


/<<PKGBUILDDIR>>/nimcache/@mhts_nim_tools.nim.c: In function ‘count__hts95nim95tools_4867’:
/<<PKGBUILDDIR>>/nimcache/@mhts_nim_tools.nim.c:1963:51: error: assignment to ‘int (**)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, NI64 *, NI64 *)’ {aka ‘int (**)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, long int *, long int *)’} from incompatible pointer type ‘tyProc__2SK9ajKLihANR4Vql9aHKvqg’ {aka ‘int (*)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, long int *, long int *)’} [-Wincompatible-pointer-types]
 1963 |                                         read_func = Dl_1392509262_;
      |                                                   ^
/<<PKGBUILDDIR>>/nimcache/@mhts_nim_tools.nim.c:2149:41: error: assignment to ‘int (**)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, NI64 *, NI64 *)’ {aka ‘int (**)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, long int *, long int *)’} from incompatible pointer type ‘tyProc__2SK9ajKLihANR4Vql9aHKvqg’ {aka ‘int (*)(tyObject_BGZF__1CbgyLbhkQrH69bOSZgLbng *, void *, void *, int *, long int *, long int *)’} [-Wincompatible-pointer-types]
 2149 |                                 read_fn = Dl_1392509763_;
      |                                         ^
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2