Michael R. Crusoe pushed to branch master at Debian Med / gffread
Commits:
f9c4fc76 by Michael R. Crusoe at 2024-07-31T12:41:20+02:00
d/tests/control: add skip-not-installable so that s390x's lack of
python3-pysam (for cnvkit) isn't a problem.
- - - - -
0c7e6fc0 by Michael R. Crusoe at 2024-07-31T12:54:09+02:00
Merge remote-tracking branch 'origin/master'
- - - - -
2117f286 by Michael R. Crusoe at 2024-07-31T12:56:48+02:00
d/tests/{control,run-tests}: instead, we explictly skip cnvkit on s390x
- - - - -
3 changed files:
- debian/changelog
- debian/tests/control
- debian/tests/run-tests
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+gffread (0.12.7-8) unstable; urgency=medium
+
+ [ Charles Plessy ]
+ * Remove Breaks/Replace on cufflinks (<< 2.2.1+dfsg.1-4), as oldstable
already has 2.2.1+dfsg.1-8+b1
+
+ [ Michael R. Crusoe ]
+ * d/tests/{control,run-tests}: instead, we explictly skip cnvkit on s390x
+
+ -- Michael R. Crusoe <[email protected]> Wed, 31 Jul 2024 12:54:36 +0200
+
+gffread (0.12.7-7) unstable; urgency=medium
+
+ * d/tests/control: add skip-not-installable so that s390x's lack of
+ python3-pysam (for cnvkit) isn't a problem.
+
+ -- Michael R. Crusoe <[email protected]> Wed, 31 Jul 2024 12:41:17 +0200
+
gffread (0.12.7-6) unstable; urgency=medium
* d/tests: adjust architecture lists, enable more testing with riscv64
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-tests
-Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit, emboss-data,
emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test,
libbio-graphics-perl, optimir [amd64 arm64 ppc64el riscv64], proteinortho
[amd64 arm64 ppc64el riscv64 s390x], python3-gffutils, python3-pybedtools
[amd64 arm64 ppc64el riscv64], r-bioc-genomicfeatures [amd64 arm64 ppc64el
riscv64 s390x], r-bioc-gviz [amd64 arm64 ppc64el riscv64 s390x], r-bioc-rhtslib
[amd64 arm64 ppc64el riscv64 s390x], r-bioc-rtracklayer [amd64 arm64 ppc64el
riscv64 s390x], seqan-apps [amd64 arm64 ppc64el riscv64 s390x], spades [amd64],
trinityrnaseq-examples [amd64 arm64 ppc64el riscv64], dpkg-dev
+Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit [amd64 arm64
ppc64el riscv64], emboss-data, emboss-test, gbrowse, genometools-common,
gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir [amd64 arm64
ppc64el riscv64], proteinortho [amd64 arm64 ppc64el riscv64 s390x],
python3-gffutils, python3-pybedtools [amd64 arm64 ppc64el riscv64],
r-bioc-genomicfeatures [amd64 arm64 ppc64el riscv64 s390x], r-bioc-gviz [amd64
arm64 ppc64el riscv64 s390x], r-bioc-rhtslib [amd64 arm64 ppc64el riscv64
s390x], r-bioc-rtracklayer [amd64 arm64 ppc64el riscv64 s390x], seqan-apps
[amd64 arm64 ppc64el riscv64 s390x], spades [amd64], trinityrnaseq-examples
[amd64 arm64 ppc64el riscv64], dpkg-dev
Restrictions: allow-stderr
=====================================
debian/tests/run-tests
=====================================
@@ -10,22 +10,22 @@ 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, cnvkit, emboss-data, emboss-test,
gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test,
libbio-graphics-perl, python3-gffutils"
+PACKAGES="augustus-doc, bedtools-test, emboss-data, emboss-test, gbrowse,
genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl,
python3-gffutils"
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "amd64" ] ; then
- PACKAGES+=", optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, spades, trinityrnaseq-examples"
+ PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, spades, trinityrnaseq-examples"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "arm64" ] ; then
- PACKAGES+=", optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
+ PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "ppc64el" ] ; then
- PACKAGES+=", optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
+ PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "riscv64" ] ; then
- PACKAGES+=", optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
+ PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools,
r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer,
seqan-apps, trinityrnaseq-examples"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "s390x" ] ; then
View it on GitLab:
https://salsa.debian.org/med-team/gffread/-/compare/bc17436366002e3466cfdf057adeafcf3d1d7c45...2117f2860f7bc69763e401505f213a5d5da75779
--
View it on GitLab:
https://salsa.debian.org/med-team/gffread/-/compare/bc17436366002e3466cfdf057adeafcf3d1d7c45...2117f2860f7bc69763e401505f213a5d5da75779
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