[Debian-med-packaging] Bug#1037599: bustools: ftbfs with GCC-13

[Matthias Klose]

Package: src:bustools
Version: 0.42.0+dfsg-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/bustools_0.42.0+dfsg-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

[...]
[ 64%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_predict.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_predict.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_predict.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_predict.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_predict.cpp
[ 68%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_project.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_project.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_project.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_project.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_project.cpp
[ 72%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_sort.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_sort.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_sort.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_sort.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_sort.cpp
[ 76%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_text.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_text.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_text.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_text.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_text.cpp
[ 80%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_umicorrect.cpp
[ 84%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o -MF CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o.d -o CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_whitelist.cpp
[ 88%] Building C object src/CMakeFiles/bustools_core.dir/roaring.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cc  -I/<<PKGBUILDDIR>>/src -I/usr/include/eigen3 -I/usr/include/LBFGSpp -std=c99 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools_core.dir/roaring.c.o -MF CMakeFiles/bustools_core.dir/roaring.c.o.d -o CMakeFiles/bustools_core.dir/roaring.c.o -c /<<PKGBUILDDIR>>/src/roaring.c
[ 92%] Linking CXX static library libbustools_core.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bustools_core.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bustools_core.dir/link.txt --verbose=1
/usr/bin/ar qc libbustools_core.a CMakeFiles/bustools_core.dir/BUSData.cpp.o CMakeFiles/bustools_core.dir/Common.cpp.o CMakeFiles/bustools_core.dir/bustools_capture.cpp.o CMakeFiles/bustools_core.dir/bustools_clusterhist.cpp.o CMakeFiles/bustools_core.dir/bustools_collapse.cpp.o CMakeFiles/bustools_core.dir/bustools_compress.cpp.o CMakeFiles/bustools_core.dir/bustools_correct.cpp.o CMakeFiles/bustools_core.dir/bustools_count.cpp.o CMakeFiles/bustools_core.dir/bustools_decompress.cpp.o CMakeFiles/bustools_core.dir/bustools_extract.cpp.o CMakeFiles/bustools_core.dir/bustools_inspect.cpp.o CMakeFiles/bustools_core.dir/bustools_linker.cpp.o CMakeFiles/bustools_core.dir/bustools_main.cpp.o CMakeFiles/bustools_core.dir/bustools_mash.cpp.o CMakeFiles/bustools_core.dir/bustools_merge.cpp.o CMakeFiles/bustools_core.dir/bustools_predict.cpp.o CMakeFiles/bustools_core.dir/bustools_project.cpp.o CMakeFiles/bustools_core.dir/bustools_sort.cpp.o CMakeFiles/bustools_core.dir/bustools_text.cpp.o CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o CMakeFiles/bustools_core.dir/roaring.c.o
/usr/bin/ar: CMakeFiles/bustools_core.dir/BUSData.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib libbustools_core.a
/usr/bin/ranlib: libbustools_core.a(BUSData.cpp.o): plugin needed to handle lto object
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 92%] Built target bustools_core
make  -f src/CMakeFiles/bustools.dir/build.make src/CMakeFiles/bustools.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/bustools.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f src/CMakeFiles/bustools.dir/build.make src/CMakeFiles/bustools.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 96%] Building CXX object src/CMakeFiles/bustools.dir/bustools_main.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/usr/include/eigen3 -I/usr/include/LBFGSpp -I/<<PKGBUILDDIR>>/src -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -g -flto -MD -MT src/CMakeFiles/bustools.dir/bustools_main.cpp.o -MF CMakeFiles/bustools.dir/bustools_main.cpp.o.d -o CMakeFiles/bustools.dir/bustools_main.cpp.o -c /<<PKGBUILDDIR>>/src/bustools_main.cpp
[100%] Linking CXX executable bustools
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bustools.dir/link.txt --verbose=1
/usr/bin/c++ -std=c++11 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -flto -rdynamic CMakeFiles/bustools.dir/bustools_main.cpp.o -o bustools  libbustools_core.a -lpthread -lz -lrt 
lto-wrapper: warning: using serial compilation of 2 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
/usr/bin/ld: /tmp/ccmPUvEz.ltrans1.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/bustools_main.cpp:2842: undefined reference to `bustools_sort(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2860: undefined reference to `bustools_merge_different_index(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2879: undefined reference to `bustools_mash(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2924: undefined reference to `bustools_fromtext(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2906: undefined reference to `bustools_text(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2944: undefined reference to `bustools_split_correct(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2969: undefined reference to `bustools_count_mult(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2992: undefined reference to `bustools_predict(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2948: undefined reference to `bustools_correct(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3008: undefined reference to `bustools_umicorrect(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:2973: undefined reference to `bustools_count(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3026: undefined reference to `bustools_capture(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3044: undefined reference to `bustools_whitelist(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3062: undefined reference to `bustools_project(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3080: undefined reference to `bustools_inspect(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3098: undefined reference to `bustools_linker(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3116: undefined reference to `bustools_collapse(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3133: undefined reference to `bustools_clusterhist(Bustools_opt&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3151: undefined reference to `bustools_extract(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3173: undefined reference to `bustools_compress(Bustools_opt const&)'
/usr/bin/ld: /<<PKGBUILDDIR>>/src/bustools_main.cpp:3196: undefined reference to `bustools_decompress(Bustools_opt const&)'
collect2: error: ld returned 1 exit status
make[4]: *** [src/CMakeFiles/bustools.dir/build.make:102: src/bustools] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:129: src/CMakeFiles/bustools.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2