[med-svn] [Git][med-team/python-biopython][master] 3 commits: skip-scipy-in-codonalign.patch: also skip on mips64el.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Oct 18 10:30:46 BST 2024
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 <emollier at debian.org> 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
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