[med-svn] [Git][med-team/multiqc] Pushed new tag upstream/1.14+dfsg
Andreas Tille pushed new tag upstream/1.14+dfsg at Debian Med / multiqc -- View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/tree/upstream/1.14+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/multiqc][upstream] New upstream version 1.14+dfsg
Andreas Tille pushed to branch upstream at Debian Med / multiqc Commits: 7a017b32 by Andreas Tille at 2023-01-11T06:37:14+01:00 New upstream version 1.14+dfsg - - - - - 30 changed files: - + .dockerignore - + .pre-commit-config.yaml - CHANGELOG.md - CSP.txt - Dockerfile - README.md - docs/README.md - docs/config.md - docs/customisation.md - docs/installation.md - docs/modules.md - + docs/modules/anglerfish.md - + docs/modules/bbduk.md - docs/modules/bbmap.md - docs/modules/bclconvert.md - docs/modules/ccs.md - + docs/modules/cellranger.md - + docs/modules/diamond.md - docs/modules/dragen.md - + docs/modules/dragen_fastqc.md - + docs/modules/filtlong.md - + docs/modules/gopeaks.md - + docs/modules/hifiasm.md - + docs/modules/humid.md - docs/modules/jellyfish.md - + docs/modules/motus.md - + docs/modules/nextclade.md - docs/modules/picard.md - + docs/modules/porechop.md - + docs/modules/prinseqplusplus.md The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/commit/7a017b32d850005075593f64e37884f0ea22606a -- View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/commit/7a017b32d850005075593f64e37884f0ea22606a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/multiqc] Pushed new tag debian/1.14+dfsg-1
Andreas Tille pushed new tag debian/1.14+dfsg-1 at Debian Med / multiqc -- View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/tree/debian/1.14+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/multiqc][pristine-tar] 2 commits: pristine-tar data for multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / multiqc Commits: a4f92342 by Andreas Tille at 2023-01-11T06:37:23+01:00 pristine-tar data for multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz - - - - - e2f23586 by Andreas Tille at 2023-01-11T06:37:25+01:00 pristine-tar data for multiqc_1.14+dfsg.orig.tar.xz - - - - - 4 changed files: - + multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz.delta - + multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz.id - + multiqc_1.14+dfsg.orig.tar.xz.delta - + multiqc_1.14+dfsg.orig.tar.xz.id Changes: = multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz.delta = Binary files /dev/null and b/multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz.delta differ = multiqc_1.14+dfsg.orig-debian-tests-data.tar.xz.id = @@ -0,0 +1 @@ +24b91a022c090fa6f62f700a174d35af0ecbd1ce = multiqc_1.14+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/multiqc_1.14+dfsg.orig.tar.xz.delta differ = multiqc_1.14+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +adc269b732589cccfe71c53733e4dbc88a10dc9b View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/1a5675a5409aea18e20b4efbe9c4e1c248bd38bb...e2f23586742f955a6ceadbd3882085824ebc6713 -- View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/1a5675a5409aea18e20b4efbe9c4e1c248bd38bb...e2f23586742f955a6ceadbd3882085824ebc6713 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/multiqc][master] 7 commits: python-rich-click was accepted
Andreas Tille pushed to branch master at Debian Med / multiqc Commits: 91da66c1 by Andreas Tille at 2023-01-11T06:34:06+01:00 python-rich-click was accepted - - - - - 38c8be2e by Andreas Tille at 2023-01-11T06:34:24+01:00 routine-update: New upstream version - - - - - 7a017b32 by Andreas Tille at 2023-01-11T06:37:14+01:00 New upstream version 1.14+dfsg - - - - - e4733dda by Andreas Tille at 2023-01-11T06:37:25+01:00 Update upstream source from tag 'upstream/1.14+dfsg' Update to upstream version '1.14+dfsg' with Debian dir f1de797ef2f595f0f75faead359c61fd50c8a994 - - - - - c047c423 by Andreas Tille at 2023-01-11T06:37:47+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 32d0a9bf by Andreas Tille at 2023-01-11T06:38:54+01:00 Remove duplicate line from changelog. Changes-By: lintian-brush - - - - - 329ea269 by Andreas Tille at 2023-01-11T06:41:37+01:00 routine-update: Ready to upload to unstable - - - - - 30 changed files: - + .dockerignore - + .pre-commit-config.yaml - CHANGELOG.md - CSP.txt - Dockerfile - README.md - debian/changelog - debian/control - docs/README.md - docs/config.md - docs/customisation.md - docs/installation.md - docs/modules.md - + docs/modules/anglerfish.md - + docs/modules/bbduk.md - docs/modules/bbmap.md - docs/modules/bclconvert.md - docs/modules/ccs.md - + docs/modules/cellranger.md - + docs/modules/diamond.md - docs/modules/dragen.md - + docs/modules/dragen_fastqc.md - + docs/modules/filtlong.md - + docs/modules/gopeaks.md - + docs/modules/hifiasm.md - + docs/modules/humid.md - docs/modules/jellyfish.md - + docs/modules/motus.md - + docs/modules/nextclade.md - docs/modules/picard.md The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/2fa197bb550f99c3c38a442ed579f9d41c23bf73...329ea269c27ef80c4c325237e6afafa21a33687b -- View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/2fa197bb550f99c3c38a442ed579f9d41c23bf73...329ea269c27ef80c4c325237e6afafa21a33687b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/community/helper-scripts][master] automatic update
Andreas Tille pushed to branch master at Debian Med / community / helper-scripts Commits: 64a9edc0 by Andreas Tille at 2023-01-11T01:42:29+00:00 automatic update - - - - - 4 changed files: - debian-med-tests.txt - debian-science-tests.txt - outdated_med-packages.txt - python-team-tests.txt Changes: = debian-med-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 10 Jan 2023 13:42:05 + +Last-Update: Wed, 11 Jan 2023 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 10 Jan 2023 13:42:07 + +Last-Update: Wed, 11 Jan 2023 01:42:04 + Source | Vote | Tasks |Tags -+++ = outdated_med-packages.txt = The diff for this file was not included because it is too large. = python-team-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 10 Jan 2023 13:42:08 + +Last-Update: Wed, 11 Jan 2023 01:42:05 + Source | Vote | Tags --++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/64a9edc01fe84c99b9dba52aea21dca4ca443cb5 -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/64a9edc01fe84c99b9dba52aea21dca4ca443cb5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-cooler] Pushed new tag debian/0.8.11-7
Étienne Mollier pushed new tag debian/0.8.11-7 at Debian Med / python-cooler -- View it on GitLab: https://salsa.debian.org/med-team/python-cooler/-/tree/debian/0.8.11-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-cooler][master] 2 commits: d/t/control: remove ppc64el from architectures list.
Étienne Mollier pushed to branch master at Debian Med / python-cooler Commits: 72422cb4 by Étienne Mollier at 2023-01-10T20:20:17+01:00 d/t/control: remove ppc64el from architectures list. At least one dependency is missing for that architecture and the package is not installable there, but cannot be removed for that architecture neither since it is architecture independent code. - - - - - 4512b39c by Étienne Mollier at 2023-01-10T20:21:29+01:00 ready to upload to unstable. - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +python-cooler (0.8.11-7) unstable; urgency=medium + + * d/t/control: remove ppc64el from architectures list. + + -- Étienne Mollier Tue, 10 Jan 2023 20:20:52 +0100 + python-cooler (0.8.11-6) unstable; urgency=medium * Team upload. = debian/tests/control = @@ -1,4 +1,4 @@ Tests: run-unit-test Depends: @, python3-pytest, python3-mock, python3-dask Restrictions: allow-stderr -Architecture: any-amd64 arm64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha +Architecture: any-amd64 arm64 mips64el ia64 ppc64 riscv64 sparc64 alpha View it on GitLab: https://salsa.debian.org/med-team/python-cooler/-/compare/e2cf93d0b63c75627d527cc494878f7276feab36...4512b39cdf7c3c276f2f35fbaf680bae594ccc93 -- View it on GitLab: https://salsa.debian.org/med-team/python-cooler/-/compare/e2cf93d0b63c75627d527cc494878f7276feab36...4512b39cdf7c3c276f2f35fbaf680bae594ccc93 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite] Pushed new tag debian/2.4.1-6
Andreas Tille pushed new tag debian/2.4.1-6 at Debian Med / bppsuite -- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/-/tree/debian/2.4.1-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][master] 3 commits: Relax autopkgtest for arm64
Andreas Tille pushed to branch master at Debian Med / bppsuite
Commits:
2f30c3ad by Andreas Tille at 2023-01-10T18:54:50+01:00
Relax autopkgtest for arm64
- - - - -
d9770f09 by Andreas Tille at 2023-01-10T18:55:05+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
f366f4a2 by Andreas Tille at 2023-01-10T19:05:42+01:00
routine-update: Ready to upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+bppsuite (2.4.1-6) unstable; urgency=medium
+
+ * Relax autopkgtest for arm64
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille Tue, 10 Jan 2023 18:55:38 +0100
+
bppsuite (2.4.1-5) unstable; urgency=medium
* Fix watch file
=
debian/control
=
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
libbpp-phyl-dev,
libbpp-popgen-dev,
libeigen3-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/bppsuite
Vcs-Git: https://salsa.debian.org/med-team/bppsuite.git
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
=
debian/tests/run-unit-test
=
@@ -2,6 +2,7 @@
set -e
pkg=bppsuite
+ARCH=$(dpkg --print-architecture)
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ]; then
@@ -36,12 +37,16 @@ run_test() {
# in outfile and refence both
sed -e "s/\([0-9]\.[0-9]\{4\}\)[0-9]\+/\1/g" < $5 > $5.approx
sed -e "s/\([0-9]\.[0-9]\{4\}\)[0-9]\+/\1/g" < $6 > $6.approx
- diff $5.approx $6.approx --suppress-common-lines
- if [ "$?" -ne "0" ]; then
-echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
-exit 1
+ if [ $1 -eq 5 -a "$ARCH" = "arm64" ] ; then
+echo "Test $1 is known to diverge on $ARCH which is accepted here"
+ else
+diff $5.approx $6.approx --suppress-common-lines
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
+ exit 1
+fi
+echo -e "\e[92m\e[1mPassed\e[0m"
fi
- echo -e "\e[92m\e[1mPassed\e[0m"
}
run_test 1 bppml MaximumLikelihood/Codons/BranchModel ML.bpp
lysozymeLarge.ML.dnd ../../../ref/branch-lysozymeLarge.ML.dnd
View it on GitLab:
https://salsa.debian.org/med-team/bppsuite/-/compare/7ae4d1948b7646925a25c42b35bafd25c62644a2...f366f4a21b08650fe6c73c8dbc7e367fb081045e
--
View it on GitLab:
https://salsa.debian.org/med-team/bppsuite/-/compare/7ae4d1948b7646925a25c42b35bafd25c62644a2...f366f4a21b08650fe6c73c8dbc7e367fb081045e
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/gdcm] Pushed new tag debian/3.0.20-3
Mathieu Malaterre pushed new tag debian/3.0.20-3 at Debian Med / gdcm -- View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/tree/debian/3.0.20-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gdcm][master] 2 commits: d/python3-vtkgdcm: Fix hard-coded install path
Mathieu Malaterre pushed to branch master at Debian Med / gdcm Commits: e77f0e95 by Mathieu Malaterre at 2023-01-10T10:03:38+01:00 d/python3-vtkgdcm: Fix hard-coded install path - - - - - f3836363 by Mathieu Malaterre at 2023-01-10T10:09:50+01:00 d/changelog: Upload 3.0.20-3 to unstable - - - - - 2 changed files: - debian/changelog - debian/python3-vtkgdcm.install Changes: = debian/changelog = @@ -1,3 +1,9 @@ +gdcm (3.0.20-3) unstable; urgency=medium + + * d/python3-vtkgdcm: Fix hard-coded install path + + -- Mathieu Malaterre Tue, 10 Jan 2023 10:04:18 +0100 + gdcm (3.0.20-2) unstable; urgency=medium * Team upload. = debian/python3-vtkgdcm.install = @@ -1,2 +1,2 @@ usr/lib/python3*/dist-packages/vtkgdcm/* -usr/lib/x86_64-linux-gnu/vtk-*/hierarchy/vtkgdcm/vtkgdcm-hierarchy.txt +usr/lib/*/vtk-*/hierarchy/vtkgdcm/vtkgdcm-hierarchy.txt View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/compare/3907e889764a1fcf8d0c0b533730ef369f09ec4f...f3836363d5f1bdb09901df6bf9a242c7d7b3ebd6 -- View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/compare/3907e889764a1fcf8d0c0b533730ef369f09ec4f...f3836363d5f1bdb09901df6bf9a242c7d7b3ebd6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
