[med-svn] [Git][med-team/gffread][master] 5 commits: Skip two failing tests from gff2aplot

[Graham Inggs]

Graham Inggs pushed to branch master at Debian Med / gffread


Commits:
66b7741a by Graham Inggs at 2020-12-06T01:48:55+02:00
Skip two failing tests from gff2aplot

- - - - -
e10e1814 by Graham Inggs at 2020-12-06T01:51:13+02:00
Adjust autopkgtest dependencies for various architectures

- - - - -
4f9c2091 by Graham Inggs at 2020-12-06T01:56:24+02:00
Bump Standards-Version to 4.5.1

- - - - -
d8d253ff by Graham Inggs at 2020-12-06T01:57:12+02:00
Prepare for upload to unstable

- - - - -
e814fa35 by Graham Inggs at 2020-12-06T08:11:21+02:00
Fix a typo in ppc64el autopkgtest, upload to unstable

- - - - -


4 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+gffread (0.12.1-3) unstable; urgency=medium
+
+  * Team upload
+  * Fix a typo in ppc64el autopkgtest
+
+ -- Graham Inggs <ginggs at debian.org>  Sun, 06 Dec 2020 06:09:58 +0000
+
+gffread (0.12.1-2) unstable; urgency=medium
+
+  * Team upload
+  * Skip two failing tests from gff2aplot that were not run
+    previously due to being compressed (Closes: #962553)
+  * Adjust autopkgtest dependencies for various architectures
+  * Bump Standards-Version to 4.5.1, no changes
+
+ -- Graham Inggs <ginggs at debian.org>  Sat, 05 Dec 2020 23:56:29 +0000
+
 gffread (0.12.1-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libgclib-dev (>= 0.11.10)
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
 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
=====================================
@@ -1,2 +1,2 @@
 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, proteinortho, python3-gffutils, python3-pybedtools, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades [amd64], trinityrnaseq-examples, dpkg-dev
+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


=====================================
debian/tests/run-tests
=====================================
@@ -10,10 +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, optimir, proteinortho, python3-gffutils, python3-pybedtools, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, trinityrnaseq-examples"
+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"
 
 if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "amd64" ] ; then
-	PACKAGES+=", spades"
+	PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools, spades"
+fi
+
+if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "arm64" ] ; then
+	PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools"
+fi
+
+if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "ppc64el" ] ; then
+	PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools"
+fi
+
+if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "s390x" ] ; then
+	PACKAGES+=", proteinortho"
 fi
 
 IFS=", " read -r -a pkgs <<< ${PACKAGES}
@@ -101,7 +113,7 @@ IFS=", " read -r -a pkgs <<< ${PACKAGES}
 # gffread /usr/lib/python3/dist-packages/pybedtools/test/data/c.gff
 # Error: discarding overlapping duplicate mRNA feature (496-576) with ID=AT1G01010.mRNA
 
-SKIPS="/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1\+2/yeast_chr1\+2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff"
+SKIPS="/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1\+2/yeast_chr1\+2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff"
 
 for package in "${pkgs[@]}"
 do



View it on GitLab: https://salsa.debian.org/med-team/gffread/-/compare/d719fba162be014938c92a2cad7558260fe37731...e814fa3541aa2bc0365228cbe8b72aa5f6a001a9

-- 
View it on GitLab: https://salsa.debian.org/med-team/gffread/-/compare/d719fba162be014938c92a2cad7558260fe37731...e814fa3541aa2bc0365228cbe8b72aa5f6a001a9
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