[Debichem-devel] Bug#976491: openstructure: FTBFS on arm64: E: Build killed with signal TERM after 150 minutes of inactivity

[Lucas Nussbaum]

Source: openstructure
Version: 2.2.0-1
Severity: serious
Justification: FTBFS on arm64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201205 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on arm64 (I don't know if it also fails on amd64).

Relevant part (hopefully):
> [ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_star_parser.cc
> [ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_mmcif_reader.cc
> [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_mmcif_info.cc
> [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_io_img.cc
> [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -fPIC -o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -c /<<PKGBUILDDIR>>/modules/io/tests/test_exceptions.cc
> [ 94%] Linking CXX executable ../../../tests/ost_io_tests
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1
> /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -g -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests   -L/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/lib  -Wl,-rpath,/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_io.so.2.2.0 ../../../stage/lib/libost_mol_alg.so.2.2.0 ../../../stage/lib/libost_conop.so.2.2.0 ../../../stage/lib/libost_db.so.2.2.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so -lpthread /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.2.0 ../../../stage/lib/libost_seq.so.2.2.0 ../../../stage/lib/libost_mol.so.2.2.0 ../../../stage/lib/libost_img_alg.so.2.2.0 ../../../stage/lib/libost_img.so.2.2.0 ../../../stage/lib/libost_info.so.2.2.0 ../../../stage/lib/libost_base.so.2.2.0 ../../../stage/lib/libost_geom.so.2.2.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.1 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.1 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.1 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so 
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
> [ 94%] Built target ost_io_tests
> E: Build killed with signal TERM after 150 minutes of inactivity

The full build log is available from:
   http://qa-logs.debian.net/2020/12/05/openstructure_2.2.0-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking 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 me
so that we can identify if something relevant changed in the meantime.

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.