[Debian-med-packaging] Bug#1013058: uncalled: ftbfs with GCC-12

Mon Jul 25 11:39:24 BST 2022

close -1

Can't repro.
Builds fine as seem on salsa CI as well, closing.

	https://salsa.debian.org/med-team/uncalled/-/jobs/3035453

On Thu, 16 Jun 2022 12:14:39 +0000 Matthias Klose <doko at debian.org> wrote:
> Package: src:uncalled
> Version: 2.2+ds1-1
> Severity: normal
> Tags: sid bookworm
> User: debian-gcc at lists.debian.org
> Usertags: ftbfs-gcc-12
> 
> [This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
> severity of this report will be raised before the bookworm release.
> 
> The full build log can be found at:
> http://qa-logs.debian.net/2022/06/09/gcc12/uncalled_2.2+ds1-1_unstable_gcc12.log
> The last lines of the build log are at the end of this report.
> 
> To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
> 
> GCC 11 defaults to the GNU++17 standard.  If your package installs
> header files in /usr/include, please don't work around C++17 issues
> by choosing a lower C++ standard for the package build, but fix these
> issues to build with the C++17 standard.
> 
> [...]
> creating build/temp.linux-x86_64-3.9/src
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.9 -c src/chunk.cpp -o build/temp.linux-x86_64-3.9/src/chunk.o -std=c++11 -O3
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.9 -c src/client_sim.cpp -o build/temp.linux-x86_64-3.9/src/client_sim.o -std=c++11 -O3
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.9 -c src/event_detector.cpp -o build/temp.linux-x86_64-3.9/src/event_detector.o -std=c++11 -O3
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.9 -c src/event_profiler.cpp -o build/temp.linux-x86_64-3.9/src/event_profiler.o -std=c++11 -O3
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.9 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-3.9/src/fast5_reader.o -std=c++11 -O3
> In file included from src/read_buffer.hpp:30,
>                  from src/fast5_reader.hpp:31,
>                  from src/fast5_reader.cpp:26:
> /usr/include/fast5/hdf5_tools.hpp: In member function ‘void hdf5_tools::detail::Reader<Dest_Type>::operator()(hid_t, const std::string&, Data_Type&, Args&& ...) const’:
> /usr/include/fast5/hdf5_tools.hpp:1369:70: error: no match for ‘operator[]’ (operand types are ‘__gnu_cxx::__alloc_traits<std::allocator<std::array<char, 1> >, std::array<char, 1> >::value_type’ {aka ‘std::array<char, 1>’} and ‘int’)
>  1369 |             reinterpret_cast<std::string &>(out).assign(&char_buff[0][0], reader_base.dspace_size);
>       |                                                                      ^
> /usr/include/fast5/hdf5_tools.hpp: In static member function ‘static void hdf5_tools::File::copy_attribute(const hdf5_tools::File&, const hdf5_tools::File&, const std::string&, const std::string&)’:
> /usr/include/fast5/hdf5_tools.hpp:2301:33: error: no match for ‘operator[]’ (operand types are ‘__gnu_cxx::__alloc_traits<std::allocator<std::array<char, 1> >, std::array<char, 1> >::value_type’ {aka ‘std::array<char, 1>’} and ‘int’)
>  2301 |                         tmp_v[i][0] = tmp[i];
>       |                                 ^
> error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
> E: pybuild pybuild:369: build: plugin distutils failed with: exit code=1: /usr/bin/python3.9 setup.py build 
> I: pybuild base:239: /usr/bin/python3 setup.py build 
> running build

-- 
Best,
Nilesh
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