Source: libslow5lib Version: 0.7.0+dfsg-2 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: [email protected] Usertags: qa-doublebuild
Hi, This package fails to do build a binary-only build (not source) after a successful build (dpkg-buildpackage ; dpkg-buildpackage -b). This is probably a clear violation of Debian Policy section 4.9 (clean target), but this is filed as severity:minor for now, because a discussion on debian-devel showed that we might want to revisit the requirement of a working 'clean' target. More information about this class of issues, included common problems and solutions, is available at https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild Relevant part of the build log: > cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env > -us -uc -rfakeroot -b > ---------------------------------------------------------------------------------------------------------------------------------- > > dpkg-buildpackage: info: source package libslow5lib > dpkg-buildpackage: info: source version 0.7.0+dfsg-2 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Nilesh Patra <[email protected]> > dpkg-source --before-build . > dpkg-buildpackage: info: host architecture amd64 > debian/rules clean > dh clean --with python3 --buildsystem=cmake > dh_auto_clean -O--buildsystem=cmake > dh_autoreconf_clean -O--buildsystem=cmake > dh_clean -O--buildsystem=cmake > debian/rules binary > dh binary --with python3 --buildsystem=cmake > dh_update_autotools_config -O--buildsystem=cmake > dh_autoreconf -O--buildsystem=cmake > debian/rules override_dh_auto_configure > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_configure -- \ > -DSLOW5_USE_ZSTD="ON" > 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 > -DSLOW5_USE_ZSTD=ON .. > -- The C compiler identification is GNU 13.2.0 > -- The CXX compiler identification is GNU 13.2.0 > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working C compiler: /usr/bin/cc - skipped > -- Detecting C compile features > -- Detecting C compile features - done > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ - skipped > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Configuring done (0.4s) > -- Generating done (0.0s) > CMake Warning: > Manually-specified variables were not used by the project: > > CMAKE_EXPORT_NO_PACKAGE_REGISTRY > CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY > CMAKE_FIND_USE_PACKAGE_REGISTRY > CMAKE_INSTALL_LOCALSTATEDIR > CMAKE_INSTALL_RUNSTATEDIR > CMAKE_INSTALL_SYSCONFDIR > FETCHCONTENT_FULLY_DISCONNECTED > > > -- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > dh_auto_configure --buildsystem=pybuild > I: pybuild base:291: dh_auto_configure --buildsystem=cmake > --builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_slow5/build -- > -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.11 > -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.11 > -DPython_EXECUTABLE=/usr/bin/python3.11 > -DPython_LIBRARY=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > -DPython_INCLUDE_DIR=/usr/include/python3.11 > -DPython3_EXECUTABLE=/usr/bin/python3.11 > -DPython3_LIBRARY=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > -DPython3_INCLUDE_DIR=/usr/include/python3.11 > cd .pybuild/cpython3_3.11_slow5/build && 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 > -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.11 > -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.11 > -DPython_EXECUTABLE=/usr/bin/python3.11 > -DPython_LIBRARY=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > > -DPython_INCLUDE_DIR=/usr/include/python3.11 > -DPython3_EXECUTABLE=/usr/bin/python3.11 > -DPython3_LIBRARY=/usr/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.so > -DPython3_INCLUDE_DIR=/usr/include/python3.11 ../../.. > -- The C compiler identification is GNU 13.2.0 > -- The CXX compiler identification is GNU 13.2.0 > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working C compiler: /usr/bin/cc - skipped > -- Detecting C compile features > -- Detecting C compile features - done > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ - skipped > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Configuring done (0.5s) > -- Generating done (0.0s) > CMake Warning: > Manually-specified variables were not used by the project: > > CMAKE_EXPORT_NO_PACKAGE_REGISTRY > CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY > CMAKE_FIND_USE_PACKAGE_REGISTRY > CMAKE_INSTALL_LOCALSTATEDIR > CMAKE_INSTALL_RUNSTATEDIR > CMAKE_INSTALL_SYSCONFDIR > FETCHCONTENT_FULLY_DISCONNECTED > PYTHON_EXECUTABLE > PYTHON_INCLUDE_DIR > PYTHON_LIBRARY > Python3_EXECUTABLE > Python3_INCLUDE_DIR > Python3_LIBRARY > Python_EXECUTABLE > Python_INCLUDE_DIR > Python_LIBRARY > > > -- Build files have been written to: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_slow5/build > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > debian/rules override_dh_auto_build > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_build > cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install > --strip-program=true" VERBOSE=1 > make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > /usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > --check-build-system CMakeFiles/Makefile.cmake 0 > /usr/bin/cmake -E cmake_progress_start > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks > make -f CMakeFiles/Makefile2 all > make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f CMakeFiles/slow5_static.dir/build.make > CMakeFiles/slow5_static.dir/depend > make -f CMakeFiles/slow5.dir/build.make CMakeFiles/slow5.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>> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/slow5.dir/DependInfo.cmake > "--color=" > 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>> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/slow5_static.dir/DependInfo.cmake > "--color=" > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f CMakeFiles/slow5.dir/build.make CMakeFiles/slow5.dir/build > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f CMakeFiles/slow5_static.dir/build.make > CMakeFiles/slow5_static.dir/build > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > [ 10%] Building C object CMakeFiles/slow5.dir/src/slow5.c.o > /usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g > -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5.c.o -MF > CMakeFiles/slow5.dir/src/slow5.c.o.d -o CMakeFiles/slow5.dir/src/slow5.c.o -c > /<<PKGBUILDDIR>>/src/slow5.c > [ 20%] Building C object CMakeFiles/slow5.dir/src/slow5_press.c.o > [ 40%] Building C object CMakeFiles/slow5_static.dir/src/slow5.c.o > [ 40%] Building C object CMakeFiles/slow5.dir/src/slow5_misc.c.o > [ 50%] Building C object CMakeFiles/slow5.dir/src/slow5_idx.c.o > /usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g > -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_press.c.o -MF > CMakeFiles/slow5.dir/src/slow5_press.c.o.d -o > CMakeFiles/slow5.dir/src/slow5_press.c.o -c /<<PKGBUILDDIR>>/src/slow5_press.c > /usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5.c.o -MF > CMakeFiles/slow5_static.dir/src/slow5.c.o.d -o > CMakeFiles/slow5_static.dir/src/slow5.c.o -c /<<PKGBUILDDIR>>/src/slow5.c > /usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g > -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_idx.c.o -MF > CMakeFiles/slow5.dir/src/slow5_idx.c.o.d -o > CMakeFiles/slow5.dir/src/slow5_idx.c.o -c /<<PKGBUILDDIR>>/src/slow5_idx.c > [ 60%] Building C object CMakeFiles/slow5_static.dir/src/slow5_misc.c.o > /usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g > -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_misc.c.o -MF > CMakeFiles/slow5.dir/src/slow5_misc.c.o.d -o > CMakeFiles/slow5.dir/src/slow5_misc.c.o -c /<<PKGBUILDDIR>>/src/slow5_misc.c > /usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -MF > CMakeFiles/slow5_static.dir/src/slow5_misc.c.o.d -o > CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -c > /<<PKGBUILDDIR>>/src/slow5_misc.c > [ 70%] Building C object CMakeFiles/slow5_static.dir/src/slow5_idx.c.o > /usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -MF > CMakeFiles/slow5_static.dir/src/slow5_idx.c.o.d -o > CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -c > /<<PKGBUILDDIR>>/src/slow5_idx.c > [ 80%] Building C object CMakeFiles/slow5_static.dir/src/slow5_press.c.o > /usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 > -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_press.c.o -MF > CMakeFiles/slow5_static.dir/src/slow5_press.c.o.d -o > CMakeFiles/slow5_static.dir/src/slow5_press.c.o -c > /<<PKGBUILDDIR>>/src/slow5_press.c > In file included from /<<PKGBUILDDIR>>/src/slow5_idx.c:5: > /<<PKGBUILDDIR>>/src/slow5_idx.h:7:10: fatal error: slow5/slow5.h: No such > file or directory > 7 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > make[4]: *** [CMakeFiles/slow5.dir/build.make:93: > CMakeFiles/slow5.dir/src/slow5_idx.c.o] Error 1 > make[4]: *** Waiting for unfinished jobs.... > /<<PKGBUILDDIR>>/src/slow5.c:40:10: fatal error: slow5/slow5.h: No such file > or directory > 40 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > make[4]: *** [CMakeFiles/slow5_static.dir/build.make:79: > CMakeFiles/slow5_static.dir/src/slow5.c.o] Error 1 > make[4]: *** Waiting for unfinished jobs.... > /<<PKGBUILDDIR>>/src/slow5.c:40:10: fatal error: slow5/slow5.h: No such file > or directory > 40 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > make[4]: *** [CMakeFiles/slow5.dir/build.make:79: > CMakeFiles/slow5.dir/src/slow5.c.o] Error 1 > /<<PKGBUILDDIR>>/src/slow5_press.c:7:10: fatal error: slow5/slow5.h: No such > file or directory > 7 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > In file included from /<<PKGBUILDDIR>>/src/slow5_idx.c:5: > /<<PKGBUILDDIR>>/src/slow5_idx.h:7:10: fatal error: slow5/slow5.h: No such > file or directory > 7 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > /<<PKGBUILDDIR>>/src/slow5_misc.c:15:10: fatal error: slow5/slow5_error.h: No > such file or directory > 15 | #include <slow5/slow5_error.h> > | ^~~~~~~~~~~~~~~~~~~~~ > compilation terminated. > make[4]: *** [CMakeFiles/slow5_static.dir/build.make:93: > CMakeFiles/slow5_static.dir/src/slow5_idx.c.o] Error 1 > make[4]: *** [CMakeFiles/slow5.dir/build.make:121: > CMakeFiles/slow5.dir/src/slow5_press.c.o] Error 1 > make[4]: *** [CMakeFiles/slow5.dir/build.make:107: > CMakeFiles/slow5.dir/src/slow5_misc.c.o] Error 1 > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > /<<PKGBUILDDIR>>/src/slow5_press.c:7:10: fatal error: slow5/slow5.h: No such > file or directory > 7 | #include <slow5/slow5.h> > | ^~~~~~~~~~~~~~~ > compilation terminated. > make[3]: *** [CMakeFiles/Makefile2:114: CMakeFiles/slow5.dir/all] Error 2 > make[3]: *** Waiting for unfinished jobs.... > make[4]: *** [CMakeFiles/slow5_static.dir/build.make:121: > CMakeFiles/slow5_static.dir/src/slow5_press.c.o] Error 1 > /<<PKGBUILDDIR>>/src/slow5_misc.c:15:10: fatal error: slow5/slow5_error.h: No > such file or directory > 15 | #include <slow5/slow5_error.h> > | ^~~~~~~~~~~~~~~~~~~~~ > compilation terminated. > make[4]: *** [CMakeFiles/slow5_static.dir/build.make:107: > CMakeFiles/slow5_static.dir/src/slow5_misc.c.o] Error 1 > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[3]: *** [CMakeFiles/Makefile2:88: CMakeFiles/slow5_static.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:23: override_dh_auto_build] Error 25 > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > make: *** [debian/rules:15: binary] Error 2 > dpkg-buildpackage: error: debian/rules binary subprocess returned exit status > 2 > > E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage > --sanitize-env -us -uc -rfakeroot -b' failed to run. The full build log is available from: http://qa-logs.debian.net/2023/08/16/libslow5lib_0.7.0+dfsg-2_unstable.log If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
