Source: python-biopython Version: 1.83+dfsg1-3 Severity: important I've been looking at why debci appears to be stuck on riscv64 for the python-biopython package:
https://ci.debian.net/packages/p/python-biopython/testing/riscv64/ For that reason, I've been trying to reproduce it on the debian porter machine. When trying to build the package manually, the build was stuck exactly like on debci: env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/home python3.12 run_tests.py --offline Skipping any tests requiring internet access Python version: 3.12.5 (main, Aug 7 2024, 13:49:14) [GCC 14.1.0] Operating system: posix linux test_Ace ... ok test_Affy ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Align_Alignment ... ok test_Align_a2m ... ok test_Align_bed ... ok test_Align_bigbed ... ok test_Align_bigmaf ... ok test_Align_bigpsl ... ok test_Align_chain ... ok test_Align_clustal ... ok I managed to capture a process tree at the time it was stuck: siretart@ricci:~$ pstree 3014984 -ac -St dh /usr/bin/dh binary --with python3 --buildsystem=pybuild └─rules -f debian/rules override_dh_auto_test └─sh -c... └─dh_auto_test /usr/bin/dh_auto_test -- --test --system=custom... └─pybuild /usr/bin/pybuild --test -i python{version} -p 3.12 --test --system=custom... └─sh -c... └─python3.12 run_tests.py --offline siretart 3014731 0.0 0.1 18980 17016 pts/2 S+ Aug22 0:00 | \_ /usr/bin/perl /usr/bin/dpkg-buildpackage -b -us -uc siretart 3014975 0.0 0.0 2200 1608 pts/2 S+ Aug22 0:00 | \_ /usr/bin/make -f debian/rules binary siretart 3014984 0.0 0.0 14148 11968 pts/2 S+ Aug22 0:00 | \_ /usr/bin/perl /usr/bin/dh binary --with python3 --buildsystem=pybuild siretart 3024296 0.0 0.0 2204 1400 pts/2 S+ Aug22 0:00 | \_ /usr/bin/make -f debian/rules override_dh_auto_test siretart 3024324 0.0 0.0 1980 1080 pts/2 S+ Aug22 0:00 | \_ /bin/sh -c LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \ ?--test-args='set -e; \ siretart 3024325 0.0 0.0 18488 16268 pts/2 S+ Aug22 0:00 | \_ /usr/bin/perl /usr/bin/dh_auto_test -- --test --system=custom --test-args=set -e; \ siretart 3024333 0.0 0.0 20824 15860 pts/2 S+ Aug22 0:00 | \_ /usr/bin/python3 /usr/bin/pybuild --test -i python{version} -p 3.12 --test --system siretart 3024336 0.0 0.0 1980 1160 pts/2 S+ Aug22 0:00 | \_ /bin/sh -c set -e; \ mkdir -p /home/siretart/pytho siretart 3024343 99.9 0.5 115704 97700 pts/2 R+ Aug22 801:57 | \_ python3.12 run_tests.py --offline This tells me that there is unlikely a single test that could be disabled get the build unstuck. Rather, the issue seems triggered by the run_tests.py, and might require a change to either run_tests.py [1] or the python interpreter on riscv64? [1] https://sources.debian.org/src/python-biopython/1.83%2Bdfsg1-3/Tests/run_tests.py/ -- System Information: Debian Release: trixie/sid APT prefers testing APT policy: (500, 'testing'), (50, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 6.10.4-amd64 (SMP w/8 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
