Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: 3fb9c7ee by Étienne Mollier at 2024-10-18T11:27:10+02:00 skip-scipy-in-codonalign.patch: also skip on mips64el. The symptom of scipy processing hanging up appeared already in riscv64, now on mips64el. - - - - - 415b471a by Étienne Mollier at 2024-10-18T11:28:14+02:00 d/rules: skip test of BWA on mips64el. - - - - - fc95017a by Étienne Mollier at 2024-10-18T11:30:20+02:00 Ready for upload to unstable. - - - - - 3 changed files: - debian/changelog - debian/patches/skip-scipy-in-codonalign.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +python-biopython (1.84+dfsg-3) unstable; urgency=medium + + * skip-scipy-in-codonalign.patch: also skip on mips64el. + The symptom of scipy processing hanging up appeared already in + riscv64, now on mips64el. + * d/rules: skip test of BWA on mips64el. + + -- Étienne Mollier <[email protected]> Fri, 18 Oct 2024 11:30:13 +0200 + python-biopython (1.84+dfsg-2) unstable; urgency=medium * d/t/run-unit-test: disable PDB_binary_cif for s390x in autopkgtest too. ===================================== debian/patches/skip-scipy-in-codonalign.patch ===================================== @@ -18,9 +18,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ + import os + import sys -+ if os.uname().machine == 'riscv64': ++ if os.uname().machine == 'riscv64' or os.uname().machine == 'mips64': + print('note: tests involving scipy skipped, ' -+ 'they hang on riscv64.', file=sys.stderr) ++ 'they hang on riscv64 and mips64.', file=sys.stderr) + return try: import scipy @@ -35,9 +35,9 @@ index d4bcd52..2f9c41d 100644 + import os + import sys -+ if os.uname().machine == 'riscv64': ++ if os.uname().machine == 'riscv64' or os.uname().machine == 'mips64': + print('note: tests involving scipy skipped, ' -+ 'they hang on riscv64.', file=sys.stderr) ++ 'they hang on riscv64 and mips64.', file=sys.stderr) + return try: import scipy ===================================== debian/rules ===================================== @@ -49,6 +49,17 @@ ifeq ($(BUILDARCH),riscv64) EXCLUDEARCH+=NCBI_BLAST_tools endif +ifeq ($(BUILDARCH),mips64el) + # FIXME: bwa on mips64el is affected by the following issue, so + # skipping for now: + # + # Bio.Application.ApplicationError: Non-zero return code 138 from + # 'bwa mem BWA/human_g1k_v37_truncated.fasta + # BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq', + # message '[M::bwa_idx_load_from_disk] read 0 ALT contigs' + EXCLUDEARCH+=BWA_tool +endif + ifeq ($(BUILDARCH),s390x) # PDB binary cif parsing is non-working on big endian platforms. # The parsing is fed to C code which would need potientially View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b02520908486d28e92cf86004312338cfca4c7bb...fc95017a23de6ead7be57971126bdda35a2504d9 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b02520908486d28e92cf86004312338cfca4c7bb...fc95017a23de6ead7be57971126bdda35a2504d9 You're receiving this email because of your account on salsa.debian.org.
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