[med-svn] [Git][med-team/ska] Pushed new tag debian/1.0+dfsg-3
Andreas Tille pushed new tag debian/1.0+dfsg-3 at Debian Med / ska -- View it on GitLab: https://salsa.debian.org/med-team/ska/-/tree/debian/1.0+dfsg-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/ska][master] 5 commits: Cleanup after testing
Andreas Tille pushed to branch master at Debian Med / ska Commits: f2b29802 by Andreas Tille at 2024-01-12T07:26:45+01:00 Cleanup after testing - - - - - 2de1004d by Andreas Tille at 2024-01-12T07:27:13+01:00 routine-update: Standards-Version: 4.6.2 - - - - - b6250652 by Andreas Tille at 2024-01-12T07:31:22+01:00 Needs DEB_CXXFLAGS_MAINT_APPEND = -std=c++14 for successful building - - - - - a9907fb4 by Andreas Tille at 2024-01-12T08:20:16+01:00 Fix clean target - - - - - 2043fb52 by Andreas Tille at 2024-01-12T08:22:27+01:00 Upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +ska (1.0+dfsg-3) unstable; urgency=medium + + * Cleanup after testing +Closes: #1048122 + * Standards-Version: 4.6.2 (routine-update) + * Needs DEB_CXXFLAGS_MAINT_APPEND = -std=c++14 for successful building + + -- Andreas Tille Fri, 12 Jan 2024 08:21:49 +0100 + ska (1.0+dfsg-2) unstable; urgency=medium * Packaging update = debian/control = @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper-compat (= 13), zlib1g-dev, googletest -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ska Vcs-Git: https://salsa.debian.org/med-team/ska.git Homepage: https://github.com/simonrharris/SKA = debian/rules = @@ -3,6 +3,8 @@ # DH_VERBOSE := 1 export LC_ALL=C.UTF-8 +export DEB_CXXFLAGS_MAINT_APPEND = -std=c++14 + %: dh $@ @@ -11,6 +13,8 @@ override_dh_auto_install: override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + cp -a tests tests.bak cd tests && ln -s /usr/src/googletest/googletest && make && \ ./general_unittest && ./kmers_unittest && ./DNA_unittest + rm -rf tests && mv tests.bak tests endif View it on GitLab: https://salsa.debian.org/med-team/ska/-/compare/da0bff58b91fd7a9f8d948287fea17c9a5320b32...2043fb52617bff74ef40b6a8ca4b6a24dec0b218 -- View it on GitLab: https://salsa.debian.org/med-team/ska/-/compare/da0bff58b91fd7a9f8d948287fea17c9a5320b32...2043fb52617bff74ef40b6a8ca4b6a24dec0b218 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/varna][master] 3 commits: Fix clean target
Andreas Tille pushed to branch master at Debian Med / varna Commits: 324098c4 by Andreas Tille at 2024-01-12T07:16:55+01:00 Fix clean target - - - - - 466adb0a by Andreas Tille at 2024-01-12T07:17:19+01:00 routine-update: Standards-Version: 4.6.2 - - - - - c2c62de1 by Andreas Tille at 2024-01-12T07:18:39+01:00 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - + debian/clean - debian/control Changes: = debian/changelog = @@ -1,3 +1,12 @@ +varna (3-93+ds-5) unstable; urgency=medium + + * Team upload. + * Fix clean target +Closes: #1048125 + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Fri, 12 Jan 2024 07:17:32 +0100 + varna (3-93+ds-4) unstable; urgency=medium * Update my email address. = debian/clean = @@ -0,0 +1 @@ +out.png = debian/control = @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13), javahelper, default-jdk, help2man -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/varna Vcs-Git: https://salsa.debian.org/med-team/varna.git Homepage: https://varna.lri.fr/ View it on GitLab: https://salsa.debian.org/med-team/varna/-/compare/9032c03f4c12a9d77aa242f6b1a1777257630f47...c2c62de1f814e4dd58aa02a9937ddd17d8c9bc0e -- View it on GitLab: https://salsa.debian.org/med-team/varna/-/compare/9032c03f4c12a9d77aa242f6b1a1777257630f47...c2c62de1f814e4dd58aa02a9937ddd17d8c9bc0e 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/varna] Pushed new tag debian/3-93+ds-5
Andreas Tille pushed new tag debian/3-93+ds-5 at Debian Med / varna -- View it on GitLab: https://salsa.debian.org/med-team/varna/-/tree/debian/3-93+ds-5 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/libatomicbitvector] Pushed new tag debian/0.0+git20200519.e295358-3
Andreas Tille pushed new tag debian/0.0+git20200519.e295358-3 at Debian Med / libatomicbitvector -- View it on GitLab: https://salsa.debian.org/med-team/libatomicbitvector/-/tree/debian/0.0+git20200519.e295358-3 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/libatomicbitvector][master] 6 commits: Fix clean target
Andreas Tille pushed to branch master at Debian Med / libatomicbitvector
Commits:
3f2f36bb by Andreas Tille at 2024-01-12T07:11:41+01:00
Fix clean target
- - - - -
8696e99c by Andreas Tille at 2024-01-12T07:12:04+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
4007636d by Andreas Tille at 2024-01-12T07:12:11+01:00
Set upstream metadata fields: Repository-Browse.
Changes-By: lintian-brush
- - - - -
4e48d3cf by Andreas Tille at 2024-01-12T07:12:13+01:00
Apply multi-arch hints.
+ libatomicbitvector-dev: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
089b5f08 by Andreas Tille at 2024-01-12T07:13:15+01:00
Cleanup changelog
- - - - -
ea61847d by Andreas Tille at 2024-01-12T07:13:59+01:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/upstream/metadata
Changes:
=
debian/changelog
=
@@ -1,3 +1,14 @@
+libatomicbitvector (0.0+git20200519.e295358-3) unstable; urgency=medium
+
+ * Fix clean target
+Closes: #1047857
+ * Standards-Version: 4.6.2 (routine-update)
+ * Set upstream metadata fields: Repository-Browse.
+ * Apply multi-arch hints.
++ libatomicbitvector-dev: Add Multi-Arch: foreign.
+
+ -- Andreas Tille Fri, 12 Jan 2024 07:13:26 +0100
+
libatomicbitvector (0.0+git20200519.e295358-2) unstable; urgency=medium
* Remove trailing whitespace in debian/copyright (routine-update)
=
debian/clean
=
@@ -0,0 +1 @@
+bin/test_atomicbitvector
=
debian/control
=
@@ -5,7 +5,7 @@ Section: libdevel
Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libatomicbitvector
Vcs-Git: https://salsa.debian.org/med-team/libatomicbitvector.git
Homepage: https://github.com/ekg/atomicbitvector
@@ -14,6 +14,7 @@ Rules-Requires-Root: no
Package: libatomicbitvector-dev
Architecture: all
Depends: ${misc:Depends}
+Multi-Arch: foreign
Description: atomic bitset/bitvector with size determined at runtime
This header-only library encodes a bitvector class with size fixed at
runtime. Atomic operations allow for concurrent access and modification
=
debian/upstream/metadata
=
@@ -1,3 +1,4 @@
---
Bug-Database: https://github.com/ekg/atomicbitvector/issues
Bug-Submit: https://github.com/ekg/atomicbitvector/issues/new
+Repository-Browse: https://github.com/ekg/atomicbitvector
View it on GitLab:
https://salsa.debian.org/med-team/libatomicbitvector/-/compare/35165885f2059c7e408359cddef5b8a5250d0e79...ea61847dfc7a14962928bbdf3cfe3705134d224d
--
View it on GitLab:
https://salsa.debian.org/med-team/libatomicbitvector/-/compare/35165885f2059c7e408359cddef5b8a5250d0e79...ea61847dfc7a14962928bbdf3cfe3705134d224d
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[med-svn] [Git][med-team/piler] Pushed new tag debian/0_20140707-4
Andreas Tille pushed new tag debian/0_20140707-4 at Debian Med / piler -- View it on GitLab: https://salsa.debian.org/med-team/piler/-/tree/debian/0_20140707-4 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/piler][master] 4 commits: Fix clean target
Andreas Tille pushed to branch master at Debian Med / piler Commits: b929222d by Andreas Tille at 2024-01-12T07:03:10+01:00 Fix clean target - - - - - 11014d60 by Andreas Tille at 2024-01-12T07:03:36+01:00 routine-update: Standards-Version: 4.6.2 - - - - - f8b3ab19 by Andreas Tille at 2024-01-12T07:06:30+01:00 Also cleanup executable - - - - - 9b4b1b6c by Andreas Tille at 2024-01-12T07:07:24+01:00 Upload to unstable - - - - - 3 changed files: - debian/changelog - + debian/clean - debian/control Changes: = debian/changelog = @@ -1,3 +1,11 @@ +piler (0~20140707-4) unstable; urgency=medium + + * Fix clean target +Closes: #1047737 + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Fri, 12 Jan 2024 07:07:01 +0100 + piler (0~20140707-3) unstable; urgency=medium [ Afif Elghraoui ] = debian/clean = @@ -0,0 +1,2 @@ +*.o +piler2 = debian/control = @@ -4,7 +4,7 @@ Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13) -Standards-Version: 4.5.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/piler Vcs-Git: https://salsa.debian.org/med-team/piler.git Homepage: https://www.drive5.com/piler/ View it on GitLab: https://salsa.debian.org/med-team/piler/-/compare/124cb420332c0e6a223df1c96e8ac144c1369962...9b4b1b6c72120975b6b80a5abd29b58837f3ccf7 -- View it on GitLab: https://salsa.debian.org/med-team/piler/-/compare/124cb420332c0e6a223df1c96e8ac144c1369962...9b4b1b6c72120975b6b80a5abd29b58837f3ccf7 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/smalt][master] 3 commits: Fix clean target
Andreas Tille pushed to branch master at Debian Med / smalt Commits: 26b1857d by Andreas Tille at 2024-01-12T06:59:12+01:00 Fix clean target - - - - - 4dad8f28 by Andreas Tille at 2024-01-12T06:59:44+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 110b2a11 by Andreas Tille at 2024-01-12T07:02:58+01:00 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = @@ -1,3 +1,11 @@ +smalt (0.7.6-13) unstable; urgency=medium + + * Fix clean target +Closes: #1047681 + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Fri, 12 Jan 2024 07:00:11 +0100 + smalt (0.7.6-12) unstable; urgency=medium * Team Upload. = debian/control = @@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13), python3 , samtools, libbambamc-dev -Standards-Version: 4.6.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/smalt Vcs-Git: https://salsa.debian.org/med-team/smalt.git Homepage: https://www.sanger.ac.uk/science/tools/smalt-0 = debian/rules = @@ -26,6 +26,7 @@ override_dh_install-indep: override_dh_auto_clean: dh_auto_clean rm -rf test/*.pyc misc/*.pyc test/tmp + find . -type d -name __pycache__ | xargs rm -rf override_dh_auto_build-arch: dh_auto_build -a View it on GitLab: https://salsa.debian.org/med-team/smalt/-/compare/a41b94e90586efc5ba4deeb87f446d707e6b293d...110b2a11564723d15803dee55a0934b316fd5dbc -- View it on GitLab: https://salsa.debian.org/med-team/smalt/-/compare/a41b94e90586efc5ba4deeb87f446d707e6b293d...110b2a11564723d15803dee55a0934b316fd5dbc 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/smalt] Pushed new tag debian/0.7.6-13
Andreas Tille pushed new tag debian/0.7.6-13 at Debian Med / smalt -- View it on GitLab: https://salsa.debian.org/med-team/smalt/-/tree/debian/0.7.6-13 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/htseq] Pushed new tag upstream/2.0.5
Andreas Tille pushed new tag upstream/2.0.5 at Debian Med / htseq -- View it on GitLab: https://salsa.debian.org/med-team/htseq/-/tree/upstream/2.0.5 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/htseq][upstream] New upstream version 2.0.5
Andreas Tille pushed to branch upstream at Debian Med / htseq Commits: 289668d7 by Andreas Tille at 2024-01-12T06:23:48+01:00 New upstream version 2.0.5 - - - - - 30 changed files: - + .ci_deploy.sh - + .ci_deps.sh - + .ci_install.sh - + .ci_postdeploy_install.sh - + .ci_test.sh - + .github/ISSUE_TEMPLATE/bug_report.md - + .github/workflows/ci.yml - + .github/workflows/deploy.yml - + .gitignore - + .readthedocs.yaml - + .travis.yml - + .travis_pypirc - HTSeq/_version.py - HTSeq/scripts/count_features/count_features_per_file.py - HTSeq/scripts/count_features/reads_io_processor.py - PKG-INFO - README.md - + RELEASE_CHECKOUT - VERSION - + buildwheels.sh - + deploywheels.sh - + doc/GenomicArrayOfSets.svg - + doc/Makefile - + doc/add_counter.py - + doc/alignments.rst - + doc/code_examples/tss1.py - + doc/code_examples/tss2.py - + doc/code_examples/tss3.py - + doc/conf.py - + doc/contrib.rst The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/htseq/-/commit/289668d7ec4a8aff43907776b8e417b2d4740e48 -- View it on GitLab: https://salsa.debian.org/med-team/htseq/-/commit/289668d7ec4a8aff43907776b8e417b2d4740e48 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/htseq] Pushed new tag debian/2.0.5-1
Andreas Tille pushed new tag debian/2.0.5-1 at Debian Med / htseq -- View it on GitLab: https://salsa.debian.org/med-team/htseq/-/tree/debian/2.0.5-1 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/htseq][pristine-tar] pristine-tar data for htseq_2.0.5.orig.tar.gz
Andreas Tille pushed to branch pristine-tar at Debian Med / htseq Commits: 2415c4c1 by Andreas Tille at 2024-01-12T06:24:45+01:00 pristine-tar data for htseq_2.0.5.orig.tar.gz - - - - - 2 changed files: - + htseq_2.0.5.orig.tar.gz.delta - + htseq_2.0.5.orig.tar.gz.id Changes: = htseq_2.0.5.orig.tar.gz.delta = Binary files /dev/null and b/htseq_2.0.5.orig.tar.gz.delta differ = htseq_2.0.5.orig.tar.gz.id = @@ -0,0 +1 @@ +ceb604b9651fba7133522d4aafdc7ecfbbac95cf View it on GitLab: https://salsa.debian.org/med-team/htseq/-/commit/2415c4c1f2501bb7520c9719090a47f67ca18c67 -- View it on GitLab: https://salsa.debian.org/med-team/htseq/-/commit/2415c4c1f2501bb7520c9719090a47f67ca18c67 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/htseq][master] 7 commits: New upstream version 2.0.5
Andreas Tille pushed to branch master at Debian Med / htseq Commits: 289668d7 by Andreas Tille at 2024-01-12T06:23:48+01:00 New upstream version 2.0.5 - - - - - df3d613e by Andreas Tille at 2024-01-12T06:23:48+01:00 routine-update: New upstream version - - - - - dee5e965 by Andreas Tille at 2024-01-12T06:24:45+01:00 Update upstream source from tag upstream/2.0.5 Update to upstream version 2.0.5 with Debian dir ed55e293622bd79c29c7b7ed10d1fb493becc782 - - - - - 1b8fa67e by Andreas Tille at 2024-01-12T06:24:49+01:00 routine-update: Build-Depends: s/dh-python/dh-sequence-python3/ - - - - - 3351e894 by Andreas Tille at 2024-01-12T06:43:43+01:00 Ensure proper numpy ABI - - - - - dd549af9 by Andreas Tille at 2024-01-12T06:53:57+01:00 Fix clean target - - - - - 49926a03 by Andreas Tille at 2024-01-12T06:56:37+01:00 Upload to unstable - - - - - 30 changed files: - + .ci_deploy.sh - + .ci_deps.sh - + .ci_install.sh - + .ci_postdeploy_install.sh - + .ci_test.sh - + .github/ISSUE_TEMPLATE/bug_report.md - + .github/workflows/ci.yml - + .github/workflows/deploy.yml - + .gitignore - + .readthedocs.yaml - + .travis.yml - + .travis_pypirc - HTSeq/_version.py - HTSeq/scripts/count_features/count_features_per_file.py - HTSeq/scripts/count_features/reads_io_processor.py - PKG-INFO - README.md - + RELEASE_CHECKOUT - VERSION - + buildwheels.sh - debian/changelog - debian/clean - debian/control - debian/rules - + deploywheels.sh - + doc/GenomicArrayOfSets.svg - + doc/Makefile - + doc/add_counter.py - + doc/alignments.rst - + doc/code_examples/tss1.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/htseq/-/compare/a256fbb3df6c5f34a1bab40fc22ddb59d6f4b06b...49926a0310df0fbb547d9d2903b04d842e3de307 -- View it on GitLab: https://salsa.debian.org/med-team/htseq/-/compare/a256fbb3df6c5f34a1bab40fc22ddb59d6f4b06b...49926a0310df0fbb547d9d2903b04d842e3de307 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/proteinortho] Pushed new tag upstream/6.3.1+dfsg
Andreas Tille pushed new tag upstream/6.3.1+dfsg at Debian Med / proteinortho -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/tree/upstream/6.3.1+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/proteinortho] Pushed new tag debian/6.3.1+dfsg-1
Andreas Tille pushed new tag debian/6.3.1+dfsg-1 at Debian Med / proteinortho -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/tree/debian/6.3.1+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/proteinortho][upstream] New upstream version 6.3.1+dfsg
Andreas Tille pushed to branch upstream at Debian Med / proteinortho Commits: 7d7e6624 by Andreas Tille at 2024-01-12T06:35:33+01:00 New upstream version 6.3.1+dfsg - - - - - 5 changed files: - CHANGELOG - CHANGEUID - Makefile - README.md - manual.html The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/7d7e6624fa868fe54538bfcad3e44d28162a1563 -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/7d7e6624fa868fe54538bfcad3e44d28162a1563 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/proteinortho][pristine-tar] pristine-tar data for proteinortho_6.3.1+dfsg.orig.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / proteinortho Commits: 5819311d by Andreas Tille at 2024-01-12T06:35:34+01:00 pristine-tar data for proteinortho_6.3.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + proteinortho_6.3.1+dfsg.orig.tar.xz.delta - + proteinortho_6.3.1+dfsg.orig.tar.xz.id Changes: = proteinortho_6.3.1+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/proteinortho_6.3.1+dfsg.orig.tar.xz.delta differ = proteinortho_6.3.1+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +4770e79bce0d0ecb6e72461bcf50210668e687cc View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/5819311d7386728f083b14ccb3cc42dfcf540fb6 -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/5819311d7386728f083b14ccb3cc42dfcf540fb6 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/proteinortho][master] 7 commits: Keep copy of test dir before testing to clean up after testing
Andreas Tille pushed to branch master at Debian Med / proteinortho Commits: 92fd5132 by Andreas Tille at 2024-01-12T06:35:08+01:00 Keep copy of test dir before testing to clean up after testing - - - - - 7d7e6624 by Andreas Tille at 2024-01-12T06:35:33+01:00 New upstream version 6.3.1+dfsg - - - - - 45bd7f59 by Andreas Tille at 2024-01-12T06:35:33+01:00 routine-update: New upstream version - - - - - da32488d by Andreas Tille at 2024-01-12T06:35:34+01:00 Update upstream source from tag upstream/6.3.1+dfsg Update to upstream version 6.3.1+dfsg with Debian dir 07bdaa97689e7c9e24728559e5f3aea57a5e953b - - - - - 60f2448e by Andreas Tille at 2024-01-12T06:36:36+01:00 UPdate patches - - - - - 292286af by Andreas Tille at 2024-01-12T06:50:11+01:00 Proper clean up after testing - - - - - c05a3564 by Andreas Tille at 2024-01-12T06:52:17+01:00 Upload to unstable - - - - - 8 changed files: - CHANGELOG - CHANGEUID - Makefile - README.md - debian/changelog - debian/patches/deb_diamond - debian/rules - manual.html The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/4bb9880b7072dcb3e85112467a94b78fd1e7f6fa...c05a35649b97fb6b88db42b0f4d8383486fc7377 -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/4bb9880b7072dcb3e85112467a94b78fd1e7f6fa...c05a35649b97fb6b88db42b0f4d8383486fc7377 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: a09e5fc3 by Andreas Tille at 2024-01-12T01:42:31+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: Thu, 11 Jan 2024 13:42:05 + +Last-Update: Fri, 12 Jan 2024 01:42:04 + Source| Vote | Tasks | Tags ---+++-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Thu, 11 Jan 2024 13:42:08 + +Last-Update: Fri, 12 Jan 2024 01:42:05 + 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: Thu, 11 Jan 2024 13:42:10 + +Last-Update: Fri, 12 Jan 2024 01:42:05 + Source | Vote | Tags ++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a09e5fc383216607b55dca2581f2e5252c7e33a4 -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a09e5fc383216607b55dca2581f2e5252c7e33a4 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-cogent][master] Add build support for loongarch64
Andreas Tille pushed to branch master at Debian Med / python-cogent
Commits:
68f2ea53 by Andreas Tille at 2024-01-11T22:47:38+01:00
Add build support for loongarch64
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -4,6 +4,8 @@ python-cogent (2023.12.15a1+dfsg-1) UNRELEASED; urgency=medium
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Build-Depends: python3-sphinxcontrib.bibtex, python3-sphinx-design,
python3-pydata-sphinx-theme
+ * Add build support for loongarch64
+Closes: #1059557
TODO: Wait for working numba
-- Andreas Tille Sat, 16 Dec 2023 22:25:27 +0100
=
debian/control
=
@@ -44,7 +44,7 @@ Homepage: https://github.com/cogent3/cogent3
Rules-Requires-Root: no
Package: python3-cogent3
-Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64
sparc64 alpha
+Architecture: any-amd64 arm64 loong64 mips64el ppc64el s390x ia64 ppc64
riscv64 sparc64 alpha
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
View it on GitLab:
https://salsa.debian.org/med-team/python-cogent/-/commit/68f2ea53a01190b9456a2f7f27e3b750113343b3
--
View it on GitLab:
https://salsa.debian.org/med-team/python-cogent/-/commit/68f2ea53a01190b9456a2f7f27e3b750113343b3
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[med-svn] [Git][med-team/gdcm][master] Add build support for loongarch64 (no intend to upload this package but trying...
Andreas Tille pushed to branch master at Debian Med / gdcm
Commits:
ff6595a3 by Andreas Tille at 2024-01-11T22:44:20+01:00
Add build support for loongarch64 (no intend to upload this package but trying
to make sure this bug is closed at next upload)
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/control.in
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+gdcm (3.0.22-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Add build support for loongarch64
+Closes: #1059517
+
+ -- Andreas Tille Thu, 11 Jan 2024 22:43:46 +0100
+
gdcm (3.0.22-2) unstable; urgency=medium
* d/patches: Revert changes breaking binary ABI. Closes: #1056953
=
debian/control
=
@@ -185,7 +185,7 @@ Description: Grassroots DICOM documentation
This is the documentation for gdcm and vtkgdcm
Package: libgdcm-java
-Architecture: alpha amd64 arm64 armel armhf i386 ia64 m68k mips64el mipsel
powerpc ppc64 ppc64el riscv64 s390x sh4 sparc64 x32
+Architecture: alpha amd64 arm64 armel armhf i386 ia64 loong64 m68k mips64el
mipsel powerpc ppc64 ppc64el riscv64 s390x sh4 sparc64 x32
Section: java
Depends: ${java:Depends}, ${misc:Depends}, ${shlibs:Depends}
Suggests: java-virtual-machine
=
debian/control.in
=
@@ -185,7 +185,7 @@ Description: Grassroots DICOM documentation
This is the documentation for gdcm and vtkgdcm
Package: libgdcm-java
-Architecture: alpha amd64 arm64 armel armhf i386 ia64 m68k mips64el mipsel
powerpc ppc64 ppc64el riscv64 s390x sh4 sparc64 x32
+Architecture: alpha amd64 arm64 armel armhf i386 ia64 loong64 m68k mips64el
mipsel powerpc ppc64 ppc64el riscv64 s390x sh4 sparc64 x32
Section: java
Depends: ${java:Depends}, ${misc:Depends}, ${shlibs:Depends}
Suggests: java-virtual-machine
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/commit/ff6595a39a205bfed26c053fb87116673233b8cc
--
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/commit/ff6595a39a205bfed26c053fb87116673233b8cc
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[med-svn] [Git][med-team/snap-aligner][master] 4 commits: Add loong64 to list of architectures
Andreas Tille pushed to branch master at Debian Med / snap-aligner
Commits:
4a40af66 by Andreas Tille at 2023-08-25T09:10:16+02:00
Add loong64 to list of architectures
- - - - -
1d52ab66 by Andreas Tille at 2023-08-25T09:12:30+02:00
Upload to unstable
- - - - -
6326594d by Andreas Tille at 2024-01-11T21:47:47+01:00
For some reason this package was not uploaded
- - - - -
6681dc57 by Andreas Tille at 2024-01-11T21:50:39+01:00
Upload to unstable
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+snap-aligner (2.0.3+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Add loong64 to list of architectures
+Closes: #1050330, #1059989
+
+ -- Andreas Tille Thu, 11 Jan 2024 21:49:06 +0100
+
snap-aligner (2.0.3+dfsg-1) unstable; urgency=medium
* Team upload.
=
debian/control
=
@@ -15,7 +15,7 @@ Homepage: https://snap.cs.berkeley.edu/
Rules-Requires-Root: no
Package: snap-aligner
-Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64
riscv64 sparc64
+Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64
riscv64 sparc64 loong64
Depends: ${shlibs:Depends},
${misc:Depends}
Description: Scalable Nucleotide Alignment Program
View it on GitLab:
https://salsa.debian.org/med-team/snap-aligner/-/compare/6b8d176f3a4ad34de0fc50229dd1bd57d0416a5a...6681dc5749ca21e79b7a7f9b8ff9c39763b7f336
--
View it on GitLab:
https://salsa.debian.org/med-team/snap-aligner/-/compare/6b8d176f3a4ad34de0fc50229dd1bd57d0416a5a...6681dc5749ca21e79b7a7f9b8ff9c39763b7f336
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[med-svn] [Git][med-team/snap-aligner] Pushed new tag debian/2.0.3+dfsg-2
Andreas Tille pushed new tag debian/2.0.3+dfsg-2 at Debian Med / snap-aligner -- View it on GitLab: https://salsa.debian.org/med-team/snap-aligner/-/tree/debian/2.0.3+dfsg-2 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/ghmm][master] Try harder to port to LAPACKE, but failed anyway
Andreas Tille pushed to branch master at Debian Med / ghmm Commits: 8e490e66 by Andreas Tille at 2024-01-11T17:42:27+01:00 Try harder to port to LAPACKE, but failed anyway - - - - - 1 changed file: - debian/patches/lapacke.patch Changes: = debian/patches/lapacke.patch = @@ -44,3 +44,30 @@ FIXME: This is not sufficient and needs more changes inside the code #endif /**/ +@@ -99,7 +99,7 @@ int ighmm_invert_det(double *sigmainv, d + memcpy(sigmainv, cov, length * length * sizeof *cov); + + /* perform in-place LU factorization of covariance matrix */ +- info = clapack_dgetrf(CblasRowMajor, length, length, sigmainv, length, ipiv); ++ info = LAPACKE_dgetrf(LAPACK_ROW_MAJOR, length, length, sigmainv, length, ipiv); + + /* determinant */ + sign = 1; +@@ -112,7 +112,7 @@ int ighmm_invert_det(double *sigmainv, d + *det = det_tmp * sign; + + /* use the LU factorization to get inverse */ +- info = clapack_dgetri(CblasRowMajor, length, sigmainv, length, ipiv); ++ info = LAPACKE_dgetri(LAPACK_ROW_MAJOR, length, sigmainv, length, ipiv); + + free(ipiv); + #else +@@ -235,7 +235,7 @@ int ighmm_cholesky_decomposition (double + int info; + /* copy cov. matrix entries to result matrix, the rest is done in-place */ + memcpy(sigmacd, cov, dim * dim * sizeof *cov); +- info = clapack_dpotrf(CblasRowMajor, CblasUpper, dim, sigmacd, dim); ++ info = LAPACK_dpotrf(LAPACK_ROW_MAJOR, LAPACK_UPPER, dim, sigmacd, dim); + #else + int row, j, k; + double sum; View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/8e490e66cddbbbd6146c50aad0b686e770973324 -- View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/8e490e66cddbbbd6146c50aad0b686e770973324 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/ghmm][master] 5 commits: Do not build-depends on atlas
Andreas Tille pushed to branch master at Debian Med / ghmm
Commits:
01f86ba2 by Andreas Tille at 2024-01-11T17:07:06+01:00
Do not build-depends on atlas
- - - - -
b32b9a03 by Andreas Tille at 2024-01-11T17:07:25+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
c3368687 by Andreas Tille at 2024-01-11T17:07:42+01:00
Avoid explicitly specifying -Wl,--as-needed linker flag.
Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also:
https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html
- - - - -
a5f0b10f by Andreas Tille at 2024-01-11T17:10:30+01:00
Typo
- - - - -
b3e5f923 by Andreas Tille at 2024-01-11T17:30:52+01:00
First attempt to use LAPACKE instead of ATLAS
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/lapacke.patch
- debian/patches/series
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,13 @@
+ghmm (0.9~rc3-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Do not build-depends on atlas
+Closes: #1056673
+ * Standards-Version: 4.6.2 (routine-update)
+ * Avoid explicitly specifying -Wl,--as-needed linker flag.
+
+ -- Andreas Tille Thu, 11 Jan 2024 17:06:32 +0100
+
ghmm (0.9~rc3-4) unstable; urgency=medium
* Team upload.
=
debian/control
=
@@ -9,11 +9,11 @@ Build-Depends: debhelper-compat (= 13),
pkg-config,
libxml2-dev,
libgsl-dev,
- libatlas-base-dev,
- liblapack-dev,
+ libblas-dev | libblas.so,
+ liblapacke-dev,
zlib1g-dev,
swig
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ghmm
Vcs-Git: https://salsa.debian.org/med-team/ghmm.git
Homepage: https://sourceforge.net/p/ghmm/wiki/Home/
@@ -25,6 +25,7 @@ Depends: ${shlibs:Depends},
${misc:Depends},
python3,
libghmm1
+Recommends: libopenblas0 | libblis4
Description: General Hidden-Markov-Model library - tools
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
=
debian/patches/lapacke.patch
=
@@ -0,0 +1,46 @@
+Description: Use LAPACKE instead of ATLAS
+Bug-Debian: https://bugs.debian.org/1056673
+Author: Andreas Tille
+Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
+FIXME: This is not sufficient and needs more changes inside the code
+
+--- a/configure.in
b/configure.in
+@@ -226,7 +226,7 @@ AC_ARG_ENABLE(atlas,
+
+ dnl checking for clapack_dgetrf
+ AC_MSG_CHECKING([for clapack_dgetrf in -llapack])
+-AC_TRY_COMPILE([#include ],
++AC_TRY_COMPILE([#include ],
+ [
+ double a;
+ int ipiv;
+@@ -239,7 +239,7 @@ AC_ARG_ENABLE(atlas,
+
+ dnl checking for clapack_dgetri
+ AC_MSG_CHECKING([for clapack_dgetri in -llapack])
+-AC_TRY_COMPILE([#include ],
++AC_TRY_COMPILE([#include ],
+ [
+ double a;
+ int ipiv;
+@@ -252,7 +252,7 @@ AC_ARG_ENABLE(atlas,
+
+ dnl checking for clapack_dpotrf
+ AC_MSG_CHECKING([for clapack_dpotrf in -llapack])
+-AC_TRY_COMPILE([#include ],
++AC_TRY_COMPILE([#include ],
+ [
+ double a;
+ int x = clapack_dpotrf(0, 0, 0, , 0);
+--- a/ghmm/matrixop.c
b/ghmm/matrixop.c
+@@ -45,7 +45,7 @@
+ #endif
+
+ #ifdef DO_WITH_ATLAS
+-#include
++#include
+ #endif
+
+
/**/
=
debian/patches/series
=
@@ -3,3 +3,4 @@ pythonpaths.patch
fix_libxml2_config.patch
2to3.patch
python3_build_system.patch
+lapacke.patch
=
debian/rules
=
@@ -3,8 +3,6 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-
%:
dh $@
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/d1a2418dac35111ee2b48dc873d421537791d7eb...b3e5f923ccd894bb550404fefe4a893512b61ec3
--
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/d1a2418dac35111ee2b48dc873d421537791d7eb...b3e5f923ccd894bb550404fefe4a893512b61ec3
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[med-svn] [Git][med-team/plink1-9] Pushed new tag debian/1.90_b7.2-231211-1
Andreas Tille pushed new tag debian/1.90_b7.2-231211-1 at Debian Med / plink1.9 -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/tree/debian/1.90_b7.2-231211-1 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/plink1-9][master] 3 commits: routine-update: Standards-Version: 4.6.2
Andreas Tille pushed to branch master at Debian Med / plink1.9 Commits: b11a7fc4 by Andreas Tille at 2024-01-11T16:53:51+01:00 routine-update: Standards-Version: 4.6.2 - - - - - c784eb61 by Andreas Tille at 2024-01-11T16:57:51+01:00 Update patch - - - - - 7a152fc8 by Andreas Tille at 2024-01-11T17:02:00+01:00 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - debian/patches/blas.patch Changes: = debian/changelog = @@ -1,12 +1,13 @@ -plink1.9 (1.90~b7.2-231211-1) UNRELEASED; urgency=medium +plink1.9 (1.90~b7.2-231211-1) unstable; urgency=medium * Team upload. * New upstream version * Do not Build-Depends on atlas Closes: #1056682 * Fix debian/get-orig-source + * Standards-Version: 4.6.2 (routine-update) - -- Andreas Tille Thu, 11 Jan 2024 16:14:58 +0100 + -- Andreas Tille Thu, 11 Jan 2024 16:57:57 +0100 plink1.9 (1.90~b6.26-220402-1) unstable; urgency=medium = debian/control = @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13), libblas-dev | libblas.so, liblapack-dev | liblapack.so, zlib1g-dev -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/plink1-9 Vcs-Git: https://salsa.debian.org/med-team/plink1-9.git Homepage: https://www.cog-genomics.org/plink/1.9/ = debian/patches/blas.patch = @@ -12,5 +12,5 @@ Last-Update: Thu, 11 Jan 2024 16:14:58 +0100 -BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas +BLASFLAGS ?= -llapack -lblas LDFLAGS ?=-lm -lpthread -ldl - ZLIB ?= -L. ../zlib-1.2.11/libz.so.1.2.11 + ZLIB ?= -L. ../zlib-1.3/libz.so.1.3 View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/ea2b8a7e8ba580ac6e8dc8a8f47bff8ebaeeb170...7a152fc88d5079225ea54ecd0045b2d46d44abc5 -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/ea2b8a7e8ba580ac6e8dc8a8f47bff8ebaeeb170...7a152fc88d5079225ea54ecd0045b2d46d44abc5 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/plink1-9][upstream] New upstream version 1.90~b7.2-231211
Andreas Tille pushed to branch upstream at Debian Med / plink1.9 Commits: e9532b6e by Andreas Tille at 2024-01-11T16:52:51+01:00 New upstream version 1.90~b7.2-231211 - - - - - 3 changed files: - Makefile - Rconnection.cc - pigz.c The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/e9532b6eb6716b57f782f67025d7de02e02a766f -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/e9532b6eb6716b57f782f67025d7de02e02a766f 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/plink1-9][pristine-tar] pristine-tar data for plink1.9_1.90~b7.2-231211.orig.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / plink1.9 Commits: b5547958 by Andreas Tille at 2024-01-11T16:52:53+01:00 pristine-tar data for plink1.9_1.90~b7.2-231211.orig.tar.xz - - - - - 2 changed files: - + plink1.9_1.90~b7.2-231211.orig.tar.xz.delta - + plink1.9_1.90~b7.2-231211.orig.tar.xz.id Changes: = plink1.9_1.90~b7.2-231211.orig.tar.xz.delta = Binary files /dev/null and b/plink1.9_1.90~b7.2-231211.orig.tar.xz.delta differ = plink1.9_1.90~b7.2-231211.orig.tar.xz.id = @@ -0,0 +1 @@ +da6b510a798b41a9501aaa7e0cf1b17cca0e9ed2 View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/b5547958c7071dd9141104af76ca471aaabedc63 -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/b5547958c7071dd9141104af76ca471aaabedc63 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/plink1-9] Pushed new tag upstream/1.90_b7.2-231211
Andreas Tille pushed new tag upstream/1.90_b7.2-231211 at Debian Med / plink1.9 -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/tree/upstream/1.90_b7.2-231211 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/plink1-9][master] 4 commits: Fix debian/get-orig-source
Andreas Tille pushed to branch master at Debian Med / plink1.9 Commits: 85a9680f by Andreas Tille at 2024-01-11T16:51:33+01:00 Fix debian/get-orig-source - - - - - a8f3c896 by Andreas Tille at 2024-01-11T16:52:31+01:00 New upstream version - - - - - e9532b6e by Andreas Tille at 2024-01-11T16:52:51+01:00 New upstream version 1.90~b7.2-231211 - - - - - ea2b8a7e by Andreas Tille at 2024-01-11T16:52:53+01:00 Update upstream source from tag upstream/1.90_b7.2-231211 Update to upstream version 1.90~b7.2-231211 with Debian dir e32894677868b90964ecaf421b8683189d48860c - - - - - 5 changed files: - Makefile - Rconnection.cc - debian/changelog - debian/get-orig-source - pigz.c The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/56b6a54e7992f3adbd013f0c5e8c22f0caf07f1b...ea2b8a7e8ba580ac6e8dc8a8f47bff8ebaeeb170 -- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/56b6a54e7992f3adbd013f0c5e8c22f0caf07f1b...ea2b8a7e8ba580ac6e8dc8a8f47bff8ebaeeb170 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/plink1-9][master] 2 commits: Do not Build-Depends on atlas
Andreas Tille pushed to branch master at Debian Med / plink1.9
Commits:
e8c4bba6 by Andreas Tille at 2024-01-11T16:15:49+01:00
Do not Build-Depends on atlas
- - - - -
56b6a54e by Andreas Tille at 2024-01-11T16:26:21+01:00
Do not try to link against atlas
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/blas.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+plink1.9 (1.90~b6.26-220402-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Do not Build-Depends on atlas
+Closes: #1056682
+
+ -- Andreas Tille Thu, 11 Jan 2024 16:14:58 +0100
+
plink1.9 (1.90~b6.26-220402-1) unstable; urgency=medium
* New upstream release.
=
debian/control
=
@@ -4,8 +4,8 @@ Uploaders: Dylan Aïssi
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- libatlas-base-dev,
- liblapack-dev,
+ libblas-dev | libblas.so,
+ liblapack-dev | liblapack.so,
zlib1g-dev
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/plink1-9
@@ -17,6 +17,7 @@ Package: plink1.9
Architecture: any-amd64 any-i386 armel armhf mipsel
Depends: ${misc:Depends},
${shlibs:Depends}
+Recommends: libopenblas0 | libblis4
Description: whole-genome association analysis toolset
plink expects as input the data from SNP (single nucleotide polymorphism)
chips of many individuals and their phenotypical description of a disease.
=
debian/patches/blas.patch
=
@@ -0,0 +1,16 @@
+Description: Do not try to link against atlas
+Bug-Debian: https://bugs.debian.org/1056682
+Author: Andreas Tille
+Last-Update: Thu, 11 Jan 2024 16:14:58 +0100
+
+--- a/Makefile
b/Makefile
+@@ -62,7 +62,7 @@ ifeq ($(SYS), WIN)
+ endif
+
+ # These must appear after the MAC/WIN-specific ?= statements.
+-BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
++BLASFLAGS ?= -llapack -lblas
+ LDFLAGS ?=-lm -lpthread -ldl
+ ZLIB ?= -L. ../zlib-1.2.11/libz.so.1.2.11
+
=
debian/patches/series
=
@@ -1 +1,2 @@
fix_makefile.patch
+blas.patch
View it on GitLab:
https://salsa.debian.org/med-team/plink1-9/-/compare/a32b0f06fc374a959b0e852a42e06bd9f4fa8ce5...56b6a54e7992f3adbd013f0c5e8c22f0caf07f1b
--
View it on GitLab:
https://salsa.debian.org/med-team/plink1-9/-/compare/a32b0f06fc374a959b0e852a42e06bd9f4fa8ce5...56b6a54e7992f3adbd013f0c5e8c22f0caf07f1b
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[med-svn] [Git][med-team/dcmtk] Pushed new tag upstream/3.6.8
Mathieu Malaterre pushed new tag upstream/3.6.8 at Debian Med / dcmtk -- View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/tree/upstream/3.6.8 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/dcmtk] Pushed new tag debian/3.6.8-1
Mathieu Malaterre pushed new tag debian/3.6.8-1 at Debian Med / dcmtk -- View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/tree/debian/3.6.8-1 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/dcmtk][debian/experimental] 4 commits: New upstream version 3.6.8
Mathieu Malaterre pushed to branch debian/experimental at Debian Med / dcmtk Commits: 2ffc893b by Mathieu Malaterre at 2024-01-11T15:40:43+01:00 New upstream version 3.6.8 - - - - - 67a6f7c4 by Mathieu Malaterre at 2024-01-11T15:40:43+01:00 Update upstream source from tag upstream/3.6.8 Update to upstream version 3.6.8 with Debian dir 9197f93b8f3af0afd6f1f4f0edb87e66c45db77f - - - - - 33a56d33 by Mathieu Malaterre at 2024-01-11T15:41:58+01:00 d/patches: Refresh patches - - - - - b5de3ce3 by Mathieu Malaterre at 2024-01-11T16:08:30+01:00 d/changelog: Upload 3.6.8-1 to experimental - - - - - 12 changed files: - ANNOUNCE - CMake/3rdparty.cmake - CMake/GenerateDCMTKConfigure.cmake - CMake/dcmtkPrepare.cmake - INSTALL - VERSION - config/configure - config/configure.in - config/confmod - config/include/dcmtk/config/osconfig.h.in - dcmdata/apps/Makefile.dep - dcmdata/docs/dcm2json.man The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/compare/0ea5fd8da1ae341de09c6d3b7e52756412d8ee0a...b5de3ce34821fb7526b1c0eabd0f1ffe5fe112e1 -- View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/compare/0ea5fd8da1ae341de09c6d3b7e52756412d8ee0a...b5de3ce34821fb7526b1c0eabd0f1ffe5fe112e1 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/dcmtk][upstream] New upstream version 3.6.8
Mathieu Malaterre pushed to branch upstream at Debian Med / dcmtk Commits: 2ffc893b by Mathieu Malaterre at 2024-01-11T15:40:43+01:00 New upstream version 3.6.8 - - - - - 12 changed files: - ANNOUNCE - CMake/3rdparty.cmake - CMake/GenerateDCMTKConfigure.cmake - CMake/dcmtkPrepare.cmake - INSTALL - VERSION - config/configure - config/configure.in - config/confmod - config/include/dcmtk/config/osconfig.h.in - dcmdata/apps/Makefile.dep - dcmdata/docs/dcm2json.man The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/commit/2ffc893bd2908fc7292313d53c5bdcee3f2951b1 -- View it on GitLab: https://salsa.debian.org/med-team/dcmtk/-/commit/2ffc893bd2908fc7292313d53c5bdcee3f2951b1 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/cat-bat][master] 2 commits: Slightly cleanup run-unit-test, install the script as doc as well as an...
Andreas Tille pushed to branch master at Debian Med / cat-bat
Commits:
d1288009 by Andreas Tille at 2024-01-11T10:40:54+01:00
Slightly cleanup run-unit-test, install the script as doc as well as an
accompanying README.test to inform users how to test the program on their local
system.
- - - - -
32e95cbf by Andreas Tille at 2024-01-11T11:19:41+01:00
Team upload to unstable
- - - - -
4 changed files:
- + debian/README.test
- debian/changelog
- debian/docs
- debian/tests/run-unit-test
Changes:
=
debian/README.test
=
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by running the provided test:
+
+sh run-unit-test
+
+in order to confirm its integrity.
=
debian/changelog
=
@@ -1,4 +1,6 @@
-cat-bat (5.3-2) UNRELEASED; urgency=medium
+cat-bat (5.3-2) unstable; urgency=medium
+
+ * Team upload.
[ Andreas Tille ]
* Prevent Salsa CI from building under i386 which is prevented by
@@ -7,7 +9,7 @@ cat-bat (5.3-2) UNRELEASED; urgency=medium
[ Komolehin Israel Timilehin ]
* Added autopkgtest
- -- Andreas Tille Mon, 27 Nov 2023 12:06:16 +0100
+ -- Komolehin Israel Timilehin Thu, 11 Jan 2024
10:42:08 +0100
cat-bat (5.3-1) unstable; urgency=medium
=
debian/docs
=
@@ -1 +1,3 @@
README*
+debian/tests/run-unit-test
+debian/README.test
=
debian/tests/run-unit-test
=
@@ -1,6 +1,5 @@
#!/bin/bash
-CUR_DIR=`pwd`
pkg=cat-bat
if [ "$AUTOPKGTEST_TMP" = "" ]; then
@@ -10,16 +9,12 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
fi
-mkdir -p "$AUTOPKGTEST_TMP"/data
-
# Copy tests data
-cp -a /usr/share/doc/"${pkg}"/examples/data/* "$AUTOPKGTEST_TMP"/data
-
+cp -a /usr/share/doc/"${pkg}"/examples/data "$AUTOPKGTEST_TMP"
# Change directory into data
cd "$AUTOPKGTEST_TMP"/data/
-
# Extract fasta
gunzip prepare/small.fa.gz
@@ -60,4 +55,4 @@ else
echo "One or both classification files not generated"
rm -rf out.*
exit 1
-fi
\ No newline at end of file
+fi
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/423538633ca6d0cf9f280e4befa5afbdd3cdef41...32e95cbf3aa9e46ca6962fa9e6ae5ff29265d854
--
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/423538633ca6d0cf9f280e4befa5afbdd3cdef41...32e95cbf3aa9e46ca6962fa9e6ae5ff29265d854
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[med-svn] [Git][med-team/cat-bat] Pushed new tag debian/5.3-2
Andreas Tille pushed new tag debian/5.3-2 at Debian Med / cat-bat -- View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/tree/debian/5.3-2 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/cat-bat][master] Updated Tests
Israel Komolehin pushed to branch master at Debian Med / cat-bat Commits: 42353863 by Komolehin Israel Timilehin at 2024-01-11T08:53:18+00:00 Updated Tests - - - - - 1 changed file: - debian/tests/control Changes: = debian/tests/control = @@ -1,3 +1,3 @@ -Tests: run-bat-unit-test, run-cat-unit-test +Tests: run-unit-test Depends: cat-bat Restrictions: allow-stderr \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/423538633ca6d0cf9f280e4befa5afbdd3cdef41 -- View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/423538633ca6d0cf9f280e4befa5afbdd3cdef41 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/cat-bat][master] 2 commits: Run CAT and BAT test in a single file
Israel Komolehin pushed to branch master at Debian Med / cat-bat
Commits:
8ce616af by Komolehin Israel Timilehin at 2024-01-11T08:04:13+00:00
Run CAT and BAT test in a single file
- - - - -
c9329b6b by Komolehin Israel Timilehin at 2024-01-11T08:04:47+00:00
Added examples
- - - - -
3 changed files:
- + debian/examples
- − debian/tests/run-bat-unit-test
- debian/tests/run-cat-unit-test → debian/tests/run-unit-test
Changes:
=
debian/examples
=
@@ -0,0 +1 @@
+tests/data
\ No newline at end of file
=
debian/tests/run-bat-unit-test deleted
=
@@ -1,44 +0,0 @@
-#!/bin/bash
-
-CUR_DIR=`pwd`
-
-if [ "$AUTOPKGTEST_TMP" = "" ]; then
-
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
- trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
-
-fi
-
-mkdir -p "$AUTOPKGTEST_TMP"/data
-
-# Copy tests data
-cp -a "${CUR_DIR}"/tests/data/* "$AUTOPKGTEST_TMP"/data
-
-# Change directory into data
-cd "$AUTOPKGTEST_TMP"/data/
-
-# Extract fasta
-gunzip prepare/small.fa.gz
-
-# Prepare CAT database
-CAT prepare \
---db_fasta ./prepare/small.fa \
---names ./prepare/names.dmp \
---nodes ./prepare/nodes.dmp \
---acc2tax ./prepare/prot2acc.txt \
---db_dir ./output_db
-
-# Run BAT on single MAG
-CAT bins -b prepare/small.fa \
- -d output_db/db \
- -t output_db/tax
-
-# Check final classification files (output files)
-if [ -f "out.BAT.ORF2LCA.txt" ] && [ -f "out.BAT.bin2classification.txt" ];
then
-echo "Final Classification Files Generated"
-rm -rf *
-else
-echo "One or both classification files not generated"
-rm -rf *
-exit 1
-fi
\ No newline at end of file
=
debian/tests/run-cat-unit-test → debian/tests/run-unit-test
=
@@ -1,6 +1,7 @@
#!/bin/bash
CUR_DIR=`pwd`
+pkg=cat-bat
if [ "$AUTOPKGTEST_TMP" = "" ]; then
@@ -12,11 +13,13 @@ fi
mkdir -p "$AUTOPKGTEST_TMP"/data
# Copy tests data
-cp -a "${CUR_DIR}"/tests/data/* "$AUTOPKGTEST_TMP"/data
+cp -a /usr/share/doc/"${pkg}"/examples/data/* "$AUTOPKGTEST_TMP"/data
+
# Change directory into data
cd "$AUTOPKGTEST_TMP"/data/
+
# Extract fasta
gunzip prepare/small.fa.gz
@@ -37,9 +40,24 @@ CAT contigs \
# Check final classification files (output files)
if [ -f "out.CAT.ORF2LCA.txt" ] && [ -f "out.CAT.contig2classification.txt" ];
then
echo "Final Classification Files Generated"
-rm -rf *
+rm -rf out.*
+else
+echo "One or both classification files not generated"
+rm -rf out.*
+exit 1
+fi
+
+# Run BAT on single MAG
+CAT bins -b prepare/small.fa \
+ -d output_db/db \
+ -t output_db/tax
+
+# Check final classification files (output files)
+if [ -f "out.BAT.ORF2LCA.txt" ] && [ -f "out.BAT.bin2classification.txt" ];
then
+echo "Final Classification Files Generated"
+rm -rf out.*
else
echo "One or both classification files not generated"
-rm -rf *
+rm -rf out.*
exit 1
fi
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/446fb2f7966393f2e3a6346921fcb95960ab8fe1...c9329b6bb448cd2f54e3448118aeb03581a18a54
--
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/446fb2f7966393f2e3a6346921fcb95960ab8fe1...c9329b6bb448cd2f54e3448118aeb03581a18a54
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