Debian Patches

Status for ivar/1.4.4+dfsg-4

Patch Description Author Forwarded Bugs Origin Last update
Fix-warning.patch Initialise array in testfile explicitly to empty string array Nilesh Patra <nilesh@debian.org> yes 2021-08-28
forward-build-options.patch inject Debian build options Étienne Mollier <emollier@debian.org> not-needed 2021-08-28
privacy-breach.patch fix privacy-breach-generic in cookbookpage.html The document refers to a diagram hosted on github, but there is a local copy
readily available for use, so lets use this one.
.
The file layout is somewhat odd, so I refrained to forward upstream.		 Étienne Mollier <emollier@debian.org> not-needed 2021-09-16
gcc-13-2.patch Remove -std=c++11 to fix autopkgtest failure with gcc 13 Adrian Bunk <bunk@debian.org> no debian 2023-08-04
enable_make-shuffle-reverse.patch check_removereads: do not depend on check_getmasked having run first test_removereads.cpp reads ../data/test.masked_primer_indices.txt but never
generates it. That file is only ever written by check_getmasked (via
get_primers_with_mismatches(), tests/test_getmasked.cpp), so check_removereads
has always silently relied on check_getmasked having run earlier in the same
tests/Makefile.am TESTS list and left the file behind.
.
In the shipped TESTS order this happens to hold, so the test passes. Under
dpkg-buildpackage's shuffle=reverse reproducible-builds variation the TESTS
execution order is reversed, check_removereads then runs before
check_getmasked has (re)created the file, amp ends up empty/stale,
rmv_reads_from_amplicon() filters no reads ("0 reads were removed" instead of
the expected 8), and the test's own sanity check on the output BAM fails:
.
FAIL: check_removereads
.
Fix this at the root: have check_removereads regenerate the masked-primer
file itself (the same call check_getmasked makes), removing the hidden
inter-test dependency entirely, independent of execution order. This needs
get_masked_amplicons.cpp linked into check_removereads as well.		 Andreas Tille <tille@debian.org> no debian 2026-09-05

All known versions for source package 'ivar'

Links