[Debian-med-packaging] Bug#1037588: bedtools: ftbfs with GCC-13

[Matthias Klose]

Package: src:bedtools
Version: 2.30.0+dfsg-3
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[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-13/g++-13, but succeeds to build with gcc-12/g++-12. 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/2023/05/22/logs/bedtools_2.30.0+dfsg-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
      |       ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17:
src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note:   by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’
   16 | class BedGraphInterval : public Bed3Interval {
      |       ^~~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18:
src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note:   by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’
   16 | class Bed6Interval : public Bed3Interval {
      |       ^~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19:
src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note:   by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’
   16 | class BedPlusInterval : public Bed3Interval {
      |       ^~~~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20:
src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note:   by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’
   30 |         const Bed12Interval &operator=(const Bed12Interval &other);
      |                              ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21:
src/utils/FileRecordTools/Records/BamRecord.h:25:34: note:   by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’
   25 |         virtual const BamRecord &operator=(const BamRecord &);
      |                                  ^~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22:
src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note:   by ‘VcfRecord::operator=’
   15 | class VcfRecord : public BedPlusInterval {
      |       ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23:
src/utils/FileRecordTools/Records/GffRecord.h:15:7: note:   by ‘GffRecord& GffRecord::operator=(const GffRecord&)’
   15 | class GffRecord : public Bed6Interval {
      |       ^~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24:
src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note:   by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’
   16 | class GffPlusRecord : public GffRecord {
      |       ^~~~~~~~~~~~~
src/utils/FileRecordTools/Records/Record.h:44:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=]
   44 |         virtual const Record & operator=(const Record &);
      |                                ^~~~~~~~
In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25:
src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note:   by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’
   16 | class NoPosPlusRecord : public Record {
      |       ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2