[med-svn] [Git][med-team/gffread][master] 4 commits: d/t/*: work around uninstallable packages.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / gffread


Commits:
7f28a236 by Étienne Mollier at 2023-06-20T20:59:36+02:00
d/t/*: work around uninstallable packages.

The change involves not testing gffread anymore against trinityrnaseq
until it is back to testing, and not testing against R BioC modules
until libboost 1.81 transition is finished.

Closes: 1033703

- - - - -
cf246cba by Étienne Mollier at 2023-06-20T21:02:56+02:00
initialize changelog

- - - - -
32c5a6e4 by Étienne Mollier at 2023-06-20T21:03:11+02:00
Update standards version to 4.6.2, no changes needed.

Changes-By: lintian-brush
Fixes: lintian: out-of-date-standards-version
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html

- - - - -
be85c584 by Étienne Mollier at 2023-06-20T21:03:58+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/tests/control
- debian/tests/run-tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+gffread (0.12.7-4) unstable; urgency=medium
+
+  * Team upload.
+  * d/t/*: work around uninstallable packages.
+    The change involves not testing gffread anymore against trinityrnaseq
+    until it is back to testing, and not testing against R BioC modules
+    until libboost 1.81 transition is finished. (Closes: #1033703)
+  * Update standards version to 4.6.2, no changes needed.
+
+ -- Étienne Mollier <emollier at debian.org>  Tue, 20 Jun 2023 21:03:42 +0200
+
 gffread (0.12.7-3) unstable; urgency=medium
 
   * Fix watch file


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libgclib-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/gffread
 Vcs-Git: https://salsa.debian.org/med-team/gffread.git
 Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,6 @@
 Tests: run-tests
-Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit [amd64 arm64 ppc64el], emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir [amd64 arm64 ppc64el], proteinortho [amd64 arm64 ppc64el s390x], python3-gffutils, python3-pybedtools [amd64 arm64 ppc64el], r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades [amd64], trinityrnaseq-examples, dpkg-dev
+# FIXME: put back trinityrnaseq-examples when available in testing.
+# FIXME: put back r-bioc-gviz, r-bioc-genomicfeatures, r-bioc-rhtslib
+#        and r-bioc-rtracklayer, when boost 1.81 transition is ended.
+Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit [amd64 arm64 ppc64el], emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir [amd64 arm64 ppc64el], proteinortho [amd64 arm64 ppc64el s390x], python3-gffutils, python3-pybedtools [amd64 arm64 ppc64el], seqan-apps, spades [amd64], dpkg-dev
 Restrictions: allow-stderr


=====================================
debian/tests/run-tests
=====================================
@@ -10,7 +10,10 @@ cd "$AUTOPKGTEST_TMP"
 # generated via
 # apt-file search --package-only --regexp '\.gff.?$' | grep -v -E "bedops|cct|ugene|gbrowse-data"
 
-PACKAGES="augustus-doc, bedtools-test, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, python3-gffutils, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, trinityrnaseq-examples"
+# FIXME: put back trinityrnaseq-examples when available in testing.
+# FIXME: put back r-bioc-gviz, r-bioc-genomicfeatures, r-bioc-rhtslib,
+#        r-bioc-rtracklayer when boost 1.81 transition is ended.
+PACKAGES="augustus-doc, bedtools-test, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, python3-gffutils, seqan-apps"
 
 if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "amd64" ] ; then
 	PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools, spades"



View it on GitLab: https://salsa.debian.org/med-team/gffread/-/compare/437ad433edf736073aab17f0c712c9697fe08462...be85c58433aa62a1e7754fd5420b5a969df493be

-- 
View it on GitLab: https://salsa.debian.org/med-team/gffread/-/compare/437ad433edf736073aab17f0c712c9697fe08462...be85c58433aa62a1e7754fd5420b5a969df493be
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