[med-svn] [Git][med-team/biosquid][master] 11 commits: d/rules: normalise the permissions of examples.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Jan 12 21:20:34 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / biosquid
Commits:
bba1dd3c by Chris Lamb at 2026-01-12T21:26:37+01:00
d/rules: normalise the permissions of examples.
This makes the build reproducible.
Closes: #1120351
Signed-off-by: Étienne Mollier <emollier at debian.org>
- - - - -
d23b407b by Étienne Mollier at 2026-01-12T21:27:21+01:00
d/control: drop redundant Priority: optional.
- - - - -
b4540b61 by Étienne Mollier at 2026-01-12T21:27:36+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
8f83ae1b by Étienne Mollier at 2026-01-12T21:27:57+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
5483d663 by Étienne Mollier at 2026-01-12T21:28:47+01:00
d/watch: convert to watch file version 5.
- - - - -
91a830fb by Étienne Mollier at 2026-01-12T21:30:56+01:00
d/rules: deduplicate --t64 option.
Gbp-Dch: ignore
- - - - -
1e1db2f0 by Étienne Mollier at 2026-01-12T21:42:42+01:00
d/control: hardcode conflicting libsquid1 version.
This unconfuses a lintian error about version substitution variable on
an external package.
- - - - -
28e86cc9 by Étienne Mollier at 2026-01-12T21:46:03+01:00
d/patches/*: normalise the Last-Update timestamp.
- - - - -
55abf94d by Étienne Mollier at 2026-01-12T22:13:46+01:00
d/t/run-unit-test: make bug-1-sfetch-paths executable.
- - - - -
03e97cc3 by Étienne Mollier at 2026-01-12T22:14:11+01:00
d/*lintian-overrides: update to different tag.
The context is the same: avoid raising alarms due to t64 transition
specificities.
- - - - -
f23a0d90 by Étienne Mollier at 2026-01-12T22:15:40+01:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/libsquid1t64.lintian-overrides
- debian/patches/automake.patch
- debian/patches/pkg-config.patch
- debian/rules
- debian/tests/run-unit-test
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,31 @@
+biosquid (1.9g+cvs20050121-16) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Andreas Tille ]
+ * Restore changes targeting at experimental
+
+ [ Chris Lamb ]
+ * d/rules: normalise the permissions of examples.
+ This makes the build reproducible.
+ Signed-off-by: Étienne Mollier <emollier at debian.org> (Closes: #1120351)
+
+ [ Étienne Mollier ]
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/watch: convert to watch file version 5.
+ * d/control: hardcode conflicting libsquid1 version.
+ This unconfuses a lintian error about version substitution variable on
+ an external package.
+ * d/patches/*: normalise the Last-Update timestamp.
+ * d/t/run-unit-test: make bug-1-sfetch-paths executable.
+ * d/*lintian-overrides: update to different tag.
+ The context is the same: avoid raising alarms due to t64 transition
+ specificities.
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 12 Jan 2026 22:15:22 +0100
+
biosquid (1.9g+cvs20050121-15.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/control
=====================================
@@ -2,14 +2,12 @@ Source: biosquid
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
d-shlibs (>= 0.106)
-Standards-Version: 4.6.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/biosquid
Vcs-Git: https://salsa.debian.org/med-team/biosquid.git
Homepage: http://eddylab.org/software.html
-Rules-Requires-Root: no
Package: biosquid
Architecture: any
@@ -31,7 +29,7 @@ Description: utilities for biological sequence analysis
Package: libsquid1t64
Provides: ${t64:Provides}
Replaces: libsquid1
-Conflicts: libsquid1 (<< ${source:Version})
+Conflicts: libsquid1 (<< 1.9g+cvs20050121-15.1)
Architecture: any
Section: libs
Depends: ${shlibs:Depends},
=====================================
debian/libsquid1t64.lintian-overrides
=====================================
@@ -1 +1 @@
-libsquid1t64: package-name-doesnt-match-sonames libsquid1
+libsquid1t64: conflicts-with-version libsquid1 (<< 1.9g+cvs20050121-15.1)
=====================================
debian/patches/automake.patch
=====================================
@@ -1,6 +1,6 @@
Description: Use automake
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 12 Aug 2020 22:30:00 +0200
+Last-Update: 2020-08-12
--- /dev/null
+++ b/Makefile.am
=====================================
debian/patches/pkg-config.patch
=====================================
@@ -1,6 +1,6 @@
Description: Provide pkg-config input file
Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 23 Mar 2017 21:55:15 +0100
+Last-Update: 2017-03-23
--- /dev/null
+++ b/libsquid.pc.in
=====================================
debian/rules
=====================================
@@ -32,7 +32,6 @@ override_dh_install:
mv $(CURDIR)/debian/tmp/usr/bin/translate $(CURDIR)/debian/tmp/usr/bin/stranslate
dh_install
d-shlibmove --commit \
- --t64 \
--multiarch \
--devunversioned \
--t64 \
@@ -54,6 +53,7 @@ override_dh_install:
done
override_dh_installexamples:
+ chmod 644 Testsuite/*
dh_installexamples
cd $(CURDIR)/debian/biosquid-dev/usr/share/doc/biosquid-dev/examples/Testsuite; make clean
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(CURDIR)/debian/$(LIBNAME)-dev/usr/share/doc/$(LIBNAME)-dev/examples/Formats/*.pl
=====================================
debian/tests/run-unit-test
=====================================
@@ -21,6 +21,7 @@ find . -name "*.gz" -exec gunzip \{\} \;
cd Testsuite
sed -i 's#-I../#-I/usr/include/biosquid#' Makefile
chmod +x x-base*
+chmod +x ./bug-1-sfetch-paths
make
chmod +x iospeed rndspeed sqdconfig
for tool in $TOOLS ; do ln -s /usr/bin/$tool ../$tool ; done
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
-version=4
-opts="dversionmangle=s/\+.*//" \
-http://eddylab.org/software/squid/ squid-(.*)\.tar\.gz
+Version: 5
+
+Source: http://eddylab.org/software/squid/
+Matching-Pattern: squid-(.*)\.tar\.gz
+Dversionmangle: s/\+.*//
View it on GitLab: https://salsa.debian.org/med-team/biosquid/-/compare/43621939b751d38bf6ab200ef3636ae91354e7fd...f23a0d90c744463da975a971a88730243902668c
--
View it on GitLab: https://salsa.debian.org/med-team/biosquid/-/compare/43621939b751d38bf6ab200ef3636ae91354e7fd...f23a0d90c744463da975a971a88730243902668c
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