[Debian-med-packaging] Bug#1037856: seqan-raptor: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:31:21 BST 2023
Package: src:seqan-raptor
Version: 2.0.0.0.git.fecfbca+ds-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/seqan-raptor_2.0.0.0.git.fecfbca+ds-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
[...]
int main() {}
Performing C++ SOURCE FILE Test CONCEPTS_FLAG_BUILTIN failed with the following output:
Change Dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_fd778/fast && gmake[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn'
/usr/bin/gmake -f CMakeFiles/cmTC_fd778.dir/build.make CMakeFiles/cmTC_fd778.dir/build
gmake[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn'
Building CXX object CMakeFiles/cmTC_fd778.dir/src.cxx.o
/usr/bin/c++ -DCONCEPTS_FLAG_BUILTIN -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -mpopcnt -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -mpopcnt -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -o CMakeFiles/cmTC_fd778.dir/src.cxx.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn/src.cxx
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn/src.cxx:1:16: error: ‘__cpp_concepts’ was not declared in this scope
1 | static_assert (__cpp_concepts >= 201507); int main() {}
| ^~~~~~~~~~~~~~
gmake[3]: *** [CMakeFiles/cmTC_fd778.dir/build.make:78: CMakeFiles/cmTC_fd778.dir/src.cxx.o] Error 1
gmake[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn'
gmake[2]: *** [Makefile:127: cmTC_fd778/fast] Error 2
gmake[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-gAVnUn'
Source file was:
static_assert (__cpp_concepts >= 201507); int main() {}
Determining if the include file sdsl/version.hpp exists failed with the following output:
Change Dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_5241a/fast && gmake[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva'
/usr/bin/gmake -f CMakeFiles/cmTC_5241a.dir/build.make CMakeFiles/cmTC_5241a.dir/build
gmake[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva'
Building CXX object CMakeFiles/cmTC_5241a.dir/CheckIncludeFile.cxx.o
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -mpopcnt -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -mpopcnt -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -o CMakeFiles/cmTC_5241a.dir/CheckIncludeFile.cxx.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva/CheckIncludeFile.cxx
In file included from /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva/CheckIncludeFile.cxx:1:
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:27:11: error: ‘uint8_t’ does not name a type
27 | constexpr uint8_t sdsl_version_major = SDSL_VERSION_MAJOR;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:12:1: note: ‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
11 | #include <string>
+++ |+#include <cstdint>
12 |
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:29:11: error: ‘uint8_t’ does not name a type
29 | constexpr uint8_t sdsl_version_minor = SDSL_VERSION_MINOR;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:29:11: note: ‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:31:11: error: ‘uint8_t’ does not name a type
31 | constexpr uint8_t sdsl_version_patch = SDSL_VERSION_PATCH;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:31:11: note: ‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:34:49: error: ‘sdsl_version_major’ was not declared in this scope; did you mean ‘sdsl_version’?
34 | std::string const sdsl_version = std::to_string(sdsl_version_major) + "." + std::to_string(sdsl_version_minor) + "." +
| ^~~~~~~~~~~~~~~~~~
| sdsl_version
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:34:92: error: ‘sdsl_version_minor’ was not declared in this scope; did you mean ‘sdsl_version’?
34 | std::string const sdsl_version = std::to_string(sdsl_version_major) + "." + std::to_string(sdsl_version_minor) + "." +
| ^~~~~~~~~~~~~~~~~~
| sdsl_version
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:35:49: error: ‘sdsl_version_patch’ was not declared in this scope; did you mean ‘sdsl_version’?
35 | std::to_string(sdsl_version_patch);
| ^~~~~~~~~~~~~~~~~~
| sdsl_version
gmake[3]: *** [CMakeFiles/cmTC_5241a.dir/build.make:78: CMakeFiles/cmTC_5241a.dir/CheckIncludeFile.cxx.o] Error 1
gmake[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva'
gmake[2]: *** [Makefile:127: cmTC_5241a/fast] Error 2
gmake[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-ktDVva'
dh_auto_configure: error: cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DRAPTOR_NATIVE_BUILD=OFF .. returned exit code 1
make[1]: *** [debian/rules:14: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
More information about the Debian-med-packaging
mailing list