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 <[email protected]> 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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