Debian Patches

Status for spades/3.15.5+dfsg-8

Patch Description Author Forwarded Bugs Origin Last update
fix-gcc13.patch fix gcc-13 build issue Bo YU <tsu.yubo@gmail.com> yes upstream 2023-07-19
0002_use_debian_packaged_python-joblib.patch We are using Debian packaged python-joblib Debian has its own way to distinguish Python versions and there is no point
in doing this inside the code.
.
The patch is non-intrusive since it conserves the original code and uses
Debian pyyaml only if the original method fails.
Andreas Tille <tille@debian.org> not-needed
0003_accept-system-bwa.patch Enable using Debian packaged bwa instead of bwa-spades Users might have installed a local version of bwa which is used independently
from SPAdes. This is specifically true on Debian systems where the
dependency system ensures the installation of bwa. This patch uses the
local installed bwa as fallback if bwa-spades is not found.
.
The patch is non-intrusive since it conserves the original code and uses
Debian bwa only if bwa-spades is not available.
.
Note: The duplicated which() in two files is for sure not the best solution.
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
Andreas Tille <tille@debian.org> not-needed
0101_cmake_ignore_removed_python-yaml.patch Since we are using Debian packaged python-yaml (see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
excluded
Andreas Tille <tille@debian.org> not-needed
0102_cmake_ignore_removed_python-joblib.patch Since we are using Debian packaged python-joblib (see 0002_use_debian_packaged_python-joblib.patch) the dir needs to be
excluded
Andreas Tille <tille@debian.org> not-needed
0103_use-debian-packaged-bwa.patch SPAdes originally contained a code copy of bwa since the version of bwa which was current of the time of release did not builded with recent
gcc versions. Since this is not the case with Debian shipped bwa this code
copy is skipped.
.
See https://lists.debian.org/debian-med/2014/02/msg00192.html
.
Note: I tried to patch the Python scripts which were calling bwa-spades to
rather call /usr/bin/bwa but the test suite failed. So as an alternative
the package contains a symlink
ln -s /usr/bin/bwa /usr/libexec/spades/bwa-spades
which enables successful run of the test suite
Andreas Tille <tille@debian.org> not-needed
0114_use_debian_provided_libs.patch use more Debian packaged libraries Michael R. Crusoe <michael.crusoe@gmail.com> Sascha Steinbiss <satta@debian.org>, not-needed
0118_adjust_spades_home_again.patch Adjust spades_home var to install files under /usr/share/spades Alex Mestiashvili <amestia@rsh2.donotuse.de> not-needed
fix-bool-cast Make explicit cast to bool Michael R. Crusoe <crusoe@debian.org> no
python3.patch Make sure Python3 interpreter is used in scripts Andreas Tille <tille@debian.org> not-needed 2019-11-12
yaml_load.patch Specify yaml loader see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation Andreas Tille <tille@debian.org> no debian 2022-10-23
debuginfo.patch want debug info for the deb package Juhani Numminen <juhaninumminen0@gmail.com> not-needed
debian_bwa_zlib.patch due to debian changes, bwa now refers to a system-wide libbwa.a and we need to manually link with zlib Juhani Numminen <juhaninumminen0@gmail.com> no
workdir_for_test.patch set working directory so that the test finds its data Juhani Numminen <juhaninumminen0@gmail.com> no
disable_local_convertutf.patch removal of ConvertUTF.cpp makes it necessary to link spades's LLVM with system-provided LLVMSupport.a Juhani Numminen <juhaninumminen0@gmail.com> not-needed
fix-sigill-on-non-popcnt-cpus.patch fix baseline violation caused by asm calling popcnt Étienne Mollier <etienne.mollier@mailoo.org> yes 2021-02-27
fix-privacy-breaches.patch fix privacy breaches identified by lintian. These breaches are caused by various badges, they may be safely remove. Étienne Mollier <emollier@debian.org> not-needed 2022-06-25
typos.patch fix typo caught by lintian. Étienne Mollier <emollier@debian.org> no 2022-06-25
python3.12.patch Replace distutils which is removed in Python3.12 Andreas Tille <tille@debian.org> no debian 2024-02-02
raw_regex_pattern.patch passing regex patterns as raw strings to avoid SyntaxWarnings with Python 3 Pierre Gruet <pgt@debian.org> no debian 2024-12-14

All known versions for source package 'spades'

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