[Debichem-devel] Bug#1037873: toppic: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:31:56 BST 2023
Package: src:toppic
Version: 1.5.3+dfsg1-1
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/toppic_1.5.3+dfsg1-1_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
[...]
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[ 47%] Building CXX object CMakeFiles/topmg.dir/src/stat/mcmc/mcmc_mass_table_util.cpp.o
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[ 47%] Building CXX object CMakeFiles/topdiff.dir/src/prsm/simple_prsm_str.cpp.o
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CMakeFiles/toppic.dir/src/stat/tdgf/comp_prob_value_array.cpp.o CMakeFiles/toppic.dir/src/stat/tdgf/comp_pvalue_array.cpp.o CMakeFiles/toppic.dir/src/stat/tdgf/comp_pvalue_lookup_table.cpp.o CMakeFiles/toppic.dir/src/stat/tdgf/evalue_processor.cpp.o CMakeFiles/toppic.dir/src/stat/tdgf/prob_peak.cpp.o CMakeFiles/toppic.dir/src/stat/tdgf/tdgf_mng.cpp.o CMakeFiles/toppic.dir/src/stat/local/local_mng.cpp.o CMakeFiles/toppic.dir/src/stat/local/local_processor.cpp.o CMakeFiles/toppic.dir/src/stat/local/local_proteoform.cpp.o CMakeFiles/toppic.dir/src/stat/local/local_util.cpp.o CMakeFiles/toppic.dir/src/visual/anno_cleavage.cpp.o CMakeFiles/toppic.dir/src/visual/anno_file_list.cpp.o CMakeFiles/toppic.dir/src/visual/anno_mass_shift.cpp.o CMakeFiles/toppic.dir/src/visual/anno_proteoform.cpp.o CMakeFiles/toppic.dir/src/visual/anno_prsm.cpp.o CMakeFiles/toppic.dir/src/visual/anno_ptm.cpp.o CMakeFiles/toppic.dir/src/visual/anno_ptm_position.cpp.o CMakeFiles/toppic.dir/src/visual/anno_residue.cpp.o CMakeFiles/toppic.dir/src/visual/anno_xml_util.cpp.o CMakeFiles/toppic.dir/src/visual/json_transformer.cpp.o CMakeFiles/toppic.dir/src/visual/xml_generator.cpp.o -o /<<PKGBUILDDIR>>/bin/toppic -lxerces-c -lboost_program_options -lboost_filesystem -lboost_system -lboost_serialization -lboost_thread -lpthread -lz -lhts
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