[Debian-med-packaging] Bug#1079439: python-biopython: autopkgtest stuck on riscv64

[Reinhard Tartler]

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 at 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