[Debian-med-packaging] Bug#1013058: uncalled: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:14:39 BST 2022
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
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/minknow_client.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/args.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/sim_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/debug.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
copying uncalled/pafstats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled
running egg_info
writing uncalled.egg-info/PKG-INFO
writing dependency_links to uncalled.egg-info/dependency_links.txt
writing top-level names to uncalled.egg-info/top_level.txt
reading manifest file 'uncalled.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENCE'
writing manifest file 'uncalled.egg-info/SOURCES.txt'
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled/conf
copying uncalled/conf/defaults.toml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled/conf
copying uncalled/conf/r94_5mers.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled/conf
copying uncalled/conf/r94_5mers_threshs.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_uncalled/build/uncalled/conf
running build_ext
All submodules present
Found libbwa.a
Found libhdf5.a
building '_uncalled' extension
creating build/temp.linux-x86_64-3.10
creating build/temp.linux-x86_64-3.10/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/python3.10 -c src/chunk.cpp -o build/temp.linux-x86_64-3.10/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/python3.10 -c src/client_sim.cpp -o build/temp.linux-x86_64-3.10/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/python3.10 -c src/event_detector.cpp -o build/temp.linux-x86_64-3.10/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/python3.10 -c src/event_profiler.cpp -o build/temp.linux-x86_64-3.10/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/python3.10 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-3.10/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 setup.py build
dh_auto_build: error: pybuild --build -i python{version} -p "3.9 3.10" returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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