Debian Patches

Status for iva/1.0.11+ds-6

Patch Description Author Forwarded Bugs Origin Last update
syntax-warning.patch raw strings for regexes. Starting with at least Python 3.13, bytecode compilation of iva
scripts results in multiple syntax warnings:
.
Setting up iva (1.0.11+ds-5) ...
/usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\('
'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
/usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\('
'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
/usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\('
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
/usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\('
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
/usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d'
'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
/usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.'
self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
/usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W'
return re.sub('\W', '_', s).strip('_')
/usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^'
s = re.sub('\^.', '', s)
.
This change goes through regexes occurrences to make them raw strings,
in order to make them more robust to backslash usage.		 Étienne Mollier <emollier@debian.org> yes debian 2024-12-04
disable-multithreaded-test.patch disable multithreaded test One of the tests uses Python's multiprocessing, which on some machines causes
FTBFS due to problematic permissions on /dev/shm, resulting in:
PermissionError: [Errno 13] Permission denied
This patch disables this test to allow building at the minor expense of this
missing test.		 Sascha Steinbiss <satta@debian.org> not-needed
perl-shebang.patch Use Debian's Perl path Sascha Steinbiss <satta@debian.org> not-needed
samtools1.10 Fix samtools version parsing so that 1.10 > 1.2 Michael R. Crusoe <michael.crusoe@gmail.com> yes
disable-ram-test.patch disable tests that run KMC KMC needs a lot of memory (multi-gigabyte) and fails hard when that
memory cannot be allocated, which can cause builds to fail when
tests are crashing because of that on low-spec buildds.
Let's disable these tests for now.		 Sascha Steinbiss <satta@debian.org> not-needed 2020-02-09
python3.12.patch Python3.12 compatibility by avoiding usage of distutils Andreas Tille <tille@debian.org> yes debian 2024-02-01

All known versions for source package 'iva'

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