[med-svn] [Git][med-team/abyss][master] 8 commits: gcc-16.patch: new: fix ftbfs with Gcc 16.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Mar 28 20:30:09 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / abyss
Commits:
6d8a33c1 by Étienne Mollier at 2026-03-28T21:28:55+01:00
gcc-16.patch: new: fix ftbfs with Gcc 16.
Closes: #1132058
- - - - -
5ce7bec0 by Étienne Mollier at 2026-03-28T21:29:03+01:00
d/watch: convert to Github uscan template v5.
- - - - -
83d6aca2 by Étienne Mollier at 2026-03-28T21:29:03+01:00
d/control: drop redundant Priority: optional.
- - - - -
8384c990 by Étienne Mollier at 2026-03-28T21:29:04+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
8de7c60a by Étienne Mollier at 2026-03-28T21:29:04+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
6885bcd6 by Étienne Mollier at 2026-03-28T21:29:04+01:00
abyss-pe.patch: fix a typo caught by lintian in description.
- - - - -
b8cd351a by Étienne Mollier at 2026-03-28T21:29:05+01:00
d/copyright: remove the old fsf mail address.
- - - - -
0ea0298e by Étienne Mollier at 2026-03-28T21:29:44+01:00
d/changelog: ready for upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/abyss-pe.patch
- + debian/patches/gcc-16.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-abyss (2.3.10-2) UNRELEASED; urgency=medium
+abyss (2.3.10-2) unstable; urgency=medium
[ Michael R. Crusoe ]
* 'btllib' is no longer included in the upstream sources, so the
@@ -7,7 +7,16 @@ abyss (2.3.10-2) UNRELEASED; urgency=medium
[ Andreas Tille ]
* Replace pkg-config with pkgconf in Build-Depends
- -- Michael R. Crusoe <crusoe at debian.org> Mon, 13 Jan 2025 09:16:40 +0100
+ [ Étienne Mollier ]
+ * gcc-16.patch: new: fix ftbfs with Gcc 16. (Closes: #1132058)
+ * d/watch: convert to Github uscan template v5.
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * abyss-pe.patch: fix a typo caught by lintian in description.
+ * d/copyright: remove the old fsf mail address.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 28 Mar 2026 21:29:14 +0100
abyss (2.3.10-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -4,7 +4,6 @@ Uploaders: Andreas Tille <tille at debian.org>,
Michael R. Crusoe <crusoe at debian.org>,
Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
architecture-is-64-bit,
libboost-graph-dev,
@@ -16,11 +15,10 @@ Build-Depends: debhelper-compat (= 13),
pkgconf,
help2man,
debhelper
-Standards-Version: 4.7.0
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/abyss
Vcs-Git: https://salsa.debian.org/med-team/abyss.git
Homepage: https://github.com/bcgsc/abyss
-Rules-Requires-Root: no
Package: abyss
Architecture: any
=====================================
debian/copyright
=====================================
@@ -52,10 +52,6 @@ License: LGPL-2.1+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
.
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
- .
Amarendran R. Subramanian, hereby disclaims all copyright interest in the
DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
.
=====================================
debian/patches/abyss-pe.patch
=====================================
@@ -1,6 +1,6 @@
Author: Shaun Jackman <sjackman at debian.org>
Description: Add internal PATH to find abyss tools
- This change is to accomodate file layout in the Debian package, thus
+ This change is to accommodate file layout in the Debian package, thus
unnecessary upstream.
Reviewed-By: Étienne Mollier <emollier at debian.org>
Forwarded: not-needed
=====================================
debian/patches/gcc-16.patch
=====================================
@@ -0,0 +1,83 @@
+Description: fix build failure with Gcc 16
+ Starting with Gcc 16, unused but set variables have become error. This
+ results in the following build failure in abyss.
+ .
+ Consensus.cpp:379:18: error: variable ‘numIgnored’ set but not used [-Werror=unused-but-set-variable=]
+ 379 | unsigned numIgnored = 0;
+ .
+ This change drops occurrences of the numIgnored variable, since it is
+ unused.
+ .
+ This feels either like a work in progress functionality, or a leftover
+ of a removed functionality, which may require discussion upstream
+ before forwarding the patch.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1132058
+Forwarded: no
+Last-Update: 2026-03-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- abyss.orig/Consensus/Consensus.cpp
++++ abyss/Consensus/Consensus.cpp
+@@ -376,7 +376,6 @@
+ : (pileupFile.open(pileupPath.c_str()), pileupFile);
+ assert_good(pileupOut, pileupPath);
+
+- unsigned numIgnored = 0;
+ for (ContigMap::const_iterator it = g_contigs.begin();
+ it != g_contigs.end(); ++it) {
+ const ContigCount& contig = it->second;
+@@ -397,7 +396,6 @@
+ float percentAgreement
+ = sumBest / (float)(sumBest + sumSecond);
+ if (isnan(percentAgreement) || percentAgreement < .9) {
+- numIgnored++;
+ if (opt::csToNt) {
+ if (opt::verbose > 0)
+ cerr << "warning: Contig " << it->first
+--- abyss.orig/SimpleGraph/SimpleGraph.cpp
++++ abyss/SimpleGraph/SimpleGraph.cpp
+@@ -516,7 +516,7 @@
+ = makeDistanceMap(g, origin, *solIter);
+
+ // Remove solutions whose distance estimates are not correct.
+- unsigned validCount = 0, invalidCount = 0, ignoredCount = 0;
++ unsigned validCount = 0, invalidCount = 0;
+ for (Estimates::const_iterator iter
+ = er.estimates[dirIdx].begin();
+ iter != er.estimates[dirIdx].end(); ++iter) {
+@@ -528,7 +528,6 @@
+ = distanceMap.find(v);
+ if (dmIter == distanceMap.end()) {
+ // This contig is a repeat.
+- ignoredCount++;
+ vout << "ignored\n";
+ continue;
+ }
+@@ -541,11 +540,9 @@
+ bool invalid = (unsigned)abs(diff) > buffer;
+ bool repeat = repeats.count(v.contigIndex()) > 0;
+ bool ignored = invalid && repeat;
+- if (ignored)
+- ignoredCount++;
+- else if (invalid)
++ if (invalid)
+ invalidCount++;
+- else
++ else if (!ignored)
+ validCount++;
+ vout << "dist: " << actualDistance
+ << " diff: " << diff
+--- abyss.orig/RResolver/BloomFilters.cpp
++++ abyss/RResolver/BloomFilters.cpp
+@@ -141,10 +141,8 @@
+ {
+ ReadSize::readsSampleSize = 0;
+ ReadSize::current.sampleCount = 0;
+- int i = 0;
+ for (auto& b : ReadSize::readSizes) {
+ b.sampleCount = 0;
+- i++;
+ }
+
+ for (const auto& path : readFilepaths) {
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ abyss-pe.patch
# gtest.patch
#abyss-32-bit.patch
fix-privacy-breach.patch
+gcc-16.patch
=====================================
debian/watch
=====================================
@@ -1,4 +1,6 @@
-version=4
-opts="mode=git,dversionmangle=auto" \
-https://github.com/bcgsc/abyss.git \
-refs/tags/v?([\d\.\d]+)
+Version: 5
+
+Template: Github
+Project: abyss
+Owner: bcgsc
+Dversion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/46cb8166cd6ab23b2de2adf310e64ad178af0350...0ea0298e405d2e016a8026f84deb63e53a6679f2
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/46cb8166cd6ab23b2de2adf310e64ad178af0350...0ea0298e405d2e016a8026f84deb63e53a6679f2
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