[Debian-med-packaging] Bug#1096281: aegean: ftbfs with GCC-15

[Matthias Klose]

Package: src:aegean
Version: 0.16.0+dfsg-4
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15

[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/aegean_0.16.0+dfsg-4_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html

[...]
dh_auto_build -- prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp 64bit=yes errorcheck=no
	make -j8 "INSTALL=install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
[print inc/core/AgnVersion.h]
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:31: SyntaxWarning: invalid escape sequence '\S'
  sha1match = re.search('commit (\S+)', logout)
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:37: SyntaxWarning: invalid escape sequence '\s'
  yearmatch = re.search('Date:\s+.+(\d{4}) ', logout)
[compile AgnAttributeFilterStream]
[compile AgnCliquePair]
[compile AgnCompareReportHTML]
[compile AgnCompareReportText]
[compile AgnFilterStream]
[compile AgnComparison]
[compile AgnGaevalVisitor]
[compile AgnGeneStream]
src/core/AgnCompareReportText.c: In function ‘compare_report_text_comp_class_summary’:
src/core/AgnCompareReportText.c:287:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  287 |   strncpy(header + 4, label, strlen(label));
      |   ^
src/core/AgnCompareReportText.c:287:30: note: length computed here
  287 |   strncpy(header + 4, label, strlen(label));
      |                              ^~~~~~~~~~~~~
[compile AgnInferCDSVisitor]
src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’:
src/core/AgnCompareReportText.c:589:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  589 |   strncpy(buffer + 14, units, strlen(units));
      |   ^
src/core/AgnCompareReportText.c:589:31: note: length computed here
  589 |   strncpy(buffer + 14, units, strlen(units));
      |                               ^~~~~~~~~~~~~
src/core/AgnCompareReportText.c:599:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  599 |   strncpy(buffer + 15, units, strlen(units));
      |   ^
src/core/AgnCompareReportText.c:599:31: note: length computed here
  599 |   strncpy(buffer + 15, units, strlen(units));
      |                               ^~~~~~~~~~~~~
[compile AgnInferExonsVisitor]
[compile AgnInferParentStream]
[compile AgnLocus]
[compile AgnLocusFilterStream]
[compile AgnLocusMapVisitor]
[compile AgnLocusRefineStream]
[compile AgnLocusStream]
[compile AgnMrnaRepVisitor]
[compile AgnPseudogeneFixVisitor]
[compile AgnRemoveChildrenVisitor]
src/core/AgnRemoveChildrenVisitor.c:47:16: error: conflicting types for ‘agn_remove_children_visitor_new’; have ‘GtNodeVisitor *(GtLogger *)’
   47 | GtNodeVisitor *agn_remove_children_visitor_new(GtLogger *logger)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/AgnRemoveChildrenVisitor.c:10:
inc/core/AgnRemoveChildrenVisitor.h:33:16: note: previous declaration of ‘agn_remove_children_visitor_new’ with type ‘GtNodeVisitor *(void)’
   33 | GtNodeVisitor *agn_remove_children_visitor_new();
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/AgnPseudogeneFixVisitor.c:49:16: error: conflicting types for ‘agn_pseudogene_fix_visitor_new’; have ‘GtNodeVisitor *(GtLogger *)’
   49 | GtNodeVisitor *agn_pseudogene_fix_visitor_new(GtLogger *logger)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/AgnPseudogeneFixVisitor.c:12:
inc/core/AgnPseudogeneFixVisitor.h:34:16: note: previous declaration of ‘agn_pseudogene_fix_visitor_new’ with type ‘GtNodeVisitor *(void)’
   34 | GtNodeVisitor *agn_pseudogene_fix_visitor_new();
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [Makefile:107: obj/AgnRemoveChildrenVisitor.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [Makefile:107: obj/AgnPseudogeneFixVisitor.o] Error 1
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no returned exit code 2
make[1]: *** [debian/rules:21: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2