[Debian-med-packaging] Bug#1049769: libslow5lib: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 09:26:38 BST 2023
Source: libslow5lib
Version: 0.7.0+dfsg-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
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 <nilesh at debian.org>
> 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.
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