[med-svn] [Git][med-team/sra-sdk][master] salsa-ci.yml: Add quoting to preclude colon misinterpretation.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 3aac5e63 by Aaron M. Ucko at 2023-01-19T21:21:54-05:00 salsa-ci.yml: Add quoting to preclude colon misinterpretation. - - - - - 1 changed file: - debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -3,9 +3,9 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml before_script: - - echo "Package: ncbi-vdb-data" | tee/etc/apt/preferences.d/exp-data - - echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data - - echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data + - 'echo "Package: ncbi-vdb-data" | tee /etc/apt/preferences.d/exp-data' + - 'echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data' + - 'echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data' - apt-get update variables: RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/3aac5e632a5641ffca698d6df5d799e1b053469d -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/3aac5e632a5641ffca698d6df5d799e1b053469d 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/sra-sdk][master] salsa-ci.yml: Rework before_script to avoid invalid YAML.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: ffa0d09d by Aaron M. Ucko at 2023-01-19T20:28:15-05:00 salsa-ci.yml: Rework before_script to avoid invalid YAML. - - - - - 1 changed file: - debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -3,7 +3,9 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml before_script: - - printf "Package: ncbi-vdb-data\nPin: release a=experimental\nPin-Priority: 999\n" | tee /etc/apt/preferences.d/exp-data + - echo "Package: ncbi-vdb-data" | tee/etc/apt/preferences.d/exp-data + - echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data + - echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data - apt-get update variables: RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/ffa0d09da3077d3141dfd8e02afcbeda85590011 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/ffa0d09da3077d3141dfd8e02afcbeda85590011 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: b8945b64 by Andreas Tille at 2023-01-20T01:42:28+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, 19 Jan 2023 13:42:04 + +Last-Update: Fri, 20 Jan 2023 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Thu, 19 Jan 2023 13:42:06 + +Last-Update: Fri, 20 Jan 2023 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, 19 Jan 2023 13:42:07 + +Last-Update: Fri, 20 Jan 2023 01:42:05 + Source | Vote | Tags --++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/b8945b648394df0b0dbbae53fb6bafe5c5a22126 -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/b8945b648394df0b0dbbae53fb6bafe5c5a22126 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/sra-sdk][master] New salsa-ci taming approach: before_script setting a pin.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
b32b243c by Aaron M. Ucko at 2023-01-19T20:24:07-05:00
New salsa-ci taming approach: before_script setting a pin.
* debian/control: Drop useless explicit dependency on ncbi-vdb-data 3.
* debian/salsa-ci.yml: Reinstate a before_script to favor experimental
ncbi-vdb-data (by pinning a higher preference on it).
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/salsa-ci.yml
Changes:
=
debian/changelog
=
@@ -1,15 +1,17 @@
sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
* NOT RELEASED YET.
- * debian/control: Replace vestigial versioned dependency on
-libncbi-wvdb2 with a temporary one on ncbi-vdb-data 3.x.
+ * debian/control: Drop vestigial versioned dependency on libncbi-wvdb2.
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
- * debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE
-variable rather than a before_script. The new approach is simpler,
-and with any luck will apply to autopkgtest and/or piuparts.
-
- -- Aaron M. Ucko Thu, 19 Jan 2023 19:54:20 -0500
+ * debian/salsa-ci.yml:
+- Pull in experimental ncbi-vdb via a RELEASE variable rather than a
+ before_script. The new approach is simpler, and with any luck will
+ apply to autopkgtest and/or piuparts.
+- Reinstate a before_script to favor experimental ncbi-vdb-data (by
+ pinning a higher preference on it).
+
+ -- Aaron M. Ucko Thu, 19 Jan 2023 20:24:06 -0500
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
=
debian/control
=
@@ -35,7 +35,6 @@ Rules-Requires-Root: no
Package: sra-toolkit
Architecture: any
Depends: ${shlibs:Depends},
- ncbi-vdb-data (>= 3~),
${misc:Depends}
Recommends: med-config
Description: utilities for the NCBI Sequence Read Archive
=
debian/salsa-ci.yml
=
@@ -2,5 +2,8 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+before_script:
+ - printf "Package: ncbi-vdb-data\nPin: release a=experimental\nPin-Priority:
999\n" | tee /etc/apt/preferences.d/exp-data
+ - apt-get update
variables:
RELEASE: 'experimental'
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/b32b243c7dcba4b517eecc988556b5f0189d3741
--
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https://salsa.debian.org/med-team/sra-sdk/-/commit/b32b243c7dcba4b517eecc988556b5f0189d3741
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[med-svn] [Git][med-team/sra-sdk][master] Switch sra-toolkit's explicit versioned dependency.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
2ffd2137 by Aaron M. Ucko at 2023-01-19T19:54:21-05:00
Switch sra-toolkits explicit versioned dependency.
Replace vestigial versioned dependency on libncbi-wvdb2 with a
temporary one on ncbi-vdb-data 3.x.
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,13 +1,15 @@
sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
* NOT RELEASED YET.
+ * debian/control: Replace vestigial versioned dependency on
+libncbi-wvdb2 with a temporary one on ncbi-vdb-data 3.x.
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
* debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE
variable rather than a before_script. The new approach is simpler,
and with any luck will apply to autopkgtest and/or piuparts.
- -- Aaron M. Ucko Thu, 19 Jan 2023 19:13:24 -0500
+ -- Aaron M. Ucko Thu, 19 Jan 2023 19:54:20 -0500
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
=
debian/control
=
@@ -35,7 +35,7 @@ Rules-Requires-Root: no
Package: sra-toolkit
Architecture: any
Depends: ${shlibs:Depends},
- libncbi-wvdb2 (>= 2.10.6+dfsg-3~),
+ ncbi-vdb-data (>= 3~),
${misc:Depends}
Recommends: med-config
Description: utilities for the NCBI Sequence Read Archive
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ffd213775c13eeda47d3a978439d52c36d1dfbf
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ffd213775c13eeda47d3a978439d52c36d1dfbf
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[med-svn] [Git][med-team/sra-sdk][master] d/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE variable
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 2e94098c by Aaron M. Ucko at 2023-01-19T19:13:25-05:00 d/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE variable ... rather than a before_script. The new approach is simpler, and with any luck will apply to autopkgtest and/or piuparts. - - - - - 2 changed files: - debian/changelog - debian/salsa-ci.yml Changes: = debian/changelog = @@ -3,8 +3,11 @@ sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium * NOT RELEASED YET. * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream logic that favored static linkage. + * debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE +variable rather than a before_script. The new approach is simpler, +and with any luck will apply to autopkgtest and/or piuparts. - -- Aaron M. Ucko Wed, 18 Jan 2023 22:47:03 -0500 + -- Aaron M. Ucko Thu, 19 Jan 2023 19:13:24 -0500 sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium = debian/salsa-ci.yml = @@ -2,6 +2,5 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml -before_script: - - echo "deb [trusted=yes] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/3711898/artifacts/raw/aptly unstable main" | tee /etc/apt/sources.list.d/pkga.list - - apt-get update +variables: + RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2e94098c86fe8ad3b736adfa6273a3bfb9301d2a -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2e94098c86fe8ad3b736adfa6273a3bfb9301d2a 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/biosyntax][master] 3 commits: Fix watch file
Andreas Tille pushed to branch master at Debian Med / biosyntax Commits: 26702fb5 by Andreas Tille at 2023-01-19T21:20:24+01:00 Fix watch file - - - - - f8d9a7b1 by Andreas Tille at 2023-01-19T21:20:51+01:00 routine-update: Standards-Version: 4.6.2 - - - - - f86629c3 by Andreas Tille at 2023-01-19T21:52:22+01:00 Upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +biosyntax (1.0.0b-4) unstable; urgency=medium + + * Team upload. + * Fix watch file + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Thu, 19 Jan 2023 21:51:48 +0100 + biosyntax (1.0.0b-3) unstable; urgency=medium * Team upload. = debian/control = @@ -4,7 +4,7 @@ Uploaders: Dylan Aïssi Section: science Priority: optional Build-Depends: debhelper-compat (= 13) -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/biosyntax Vcs-Git: https://salsa.debian.org/med-team/biosyntax.git Homepage: https://biosyntax.org/ = debian/watch = @@ -1,7 +1,6 @@ version=4 -opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/,\ - repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz \ - https://github.com/bioSyntax/bioSyntax/releases .*/bioSyntax-?(\d\S+)\.zip +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%,uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/,repacksuffix=+dfsg,dversionmangle=auto" \ + https://github.com/bioSyntax/bioSyntax/tags .*/v?(\d\S+)\.zip # This is a non standard watch file for GitHub because GH autogenerates tarballs # with empty vim folder. We need to target the zip file which contains all files. \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/biosyntax/-/compare/14f0ce153a80f5a4d4052b4414acf88520a519e2...f86629c30d9160c85fb18d84765d3f8b890364f3 -- View it on GitLab: https://salsa.debian.org/med-team/biosyntax/-/compare/14f0ce153a80f5a4d4052b4414acf88520a519e2...f86629c30d9160c85fb18d84765d3f8b890364f3 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/biosyntax] Pushed new tag debian/1.0.0b-4
Andreas Tille pushed new tag debian/1.0.0b-4 at Debian Med / biosyntax -- View it on GitLab: https://salsa.debian.org/med-team/biosyntax/-/tree/debian/1.0.0b-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/ncbi-igblast] Pushed new tag upstream/1.20.0
Andreas Tille pushed new tag upstream/1.20.0 at Debian Med / ncbi-igblast -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/tree/upstream/1.20.0 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/ncbi-igblast][upstream] New upstream version 1.20.0
Andreas Tille pushed to branch upstream at Debian Med / ncbi-igblast Commits: b8c27a6e by Andreas Tille at 2023-01-19T20:53:57+01:00 New upstream version 1.20.0 - - - - - 30 changed files: - c++/compilers/unix/ICC.sh - c++/compilers/vs2019/build.sh - c++/compilers/vs2019/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - c++/compilers/vs2019/make.bat - c++/compilers/vs2019/retry.sh - c++/compilers/vs2019/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj - c++/compilers/vs2019/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj - c++/compilers/vs2019/static/build/corelib/xncbi.lib.vcxproj - c++/compilers/vs2019/static/build/serial/datatool/datatool.exe.vcxproj - c++/compilers/vs2019/static/build/serial/xser.lib.vcxproj - c++/compilers/vs2019/static/build/util/regexp/regexp.lib.vcxproj - c++/compilers/vs2019/static/build/util/xregexp/xregexp.lib.vcxproj - c++/compilers/vs2019/static/build/util/xutil.lib.vcxproj - c++/compilers/xcode30_prj/postbuild.sh - c++/include/algo/align/util/align_compare.hpp - c++/include/algo/align/util/tabular_fmt.hpp - c++/include/algo/blast/api/magicblast.hpp - c++/include/algo/blast/blast_sra_input/blast_sra_input.hpp - c++/include/algo/blast/blastinput/blast_args.hpp - c++/include/algo/blast/blastinput/cmdline_flags.hpp - c++/include/algo/blast/igblast/igblast.hpp - c++/include/algo/winmask/seq_masker.hpp - c++/include/algo/winmask/seq_masker_istat.hpp - c++/include/algo/winmask/seq_masker_istat_factory.hpp - c++/include/algo/winmask/seq_masker_ostat.hpp - c++/include/algo/winmask/win_mask_config.hpp - c++/include/algo/winmask/win_mask_gen_counts.hpp - c++/include/cgi/cgictx.hpp - c++/include/cgi/ncbicgi.hpp - c++/include/common/config/ncbiconf_msvc.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/b8c27a6ed537f6e43d10388326a104c1c4b60e21 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/b8c27a6ed537f6e43d10388326a104c1c4b60e21 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/ncbi-igblast][pristine-tar] pristine-tar data for ncbi-igblast_1.20.0.orig.tar.gz
Andreas Tille pushed to branch pristine-tar at Debian Med / ncbi-igblast Commits: c12bd476 by Andreas Tille at 2023-01-19T20:55:52+01:00 pristine-tar data for ncbi-igblast_1.20.0.orig.tar.gz - - - - - 2 changed files: - + ncbi-igblast_1.20.0.orig.tar.gz.delta - + ncbi-igblast_1.20.0.orig.tar.gz.id Changes: = ncbi-igblast_1.20.0.orig.tar.gz.delta = Binary files /dev/null and b/ncbi-igblast_1.20.0.orig.tar.gz.delta differ = ncbi-igblast_1.20.0.orig.tar.gz.id = @@ -0,0 +1 @@ +fda8ba19a153c511207406693ca2836cf2b86274 View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/c12bd47666504b1434d94e90c2e7e619966c898f -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/c12bd47666504b1434d94e90c2e7e619966c898f 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/ncbi-igblast][master] 5 commits: routine-update: New upstream version
Andreas Tille pushed to branch master at Debian Med / ncbi-igblast Commits: 4e73a257 by Andreas Tille at 2023-01-19T20:53:56+01:00 routine-update: New upstream version - - - - - b8c27a6e by Andreas Tille at 2023-01-19T20:53:57+01:00 New upstream version 1.20.0 - - - - - 235abb0d by Andreas Tille at 2023-01-19T20:55:52+01:00 Update upstream source from tag upstream/1.20.0 Update to upstream version 1.20.0 with Debian dir bdf20f26266179ce804f9702c2e02a3f433fc8e1 - - - - - 0269475d by Andreas Tille at 2023-01-19T20:55:53+01:00 routine-update: Standards-Version: 4.6.2 - - - - - f1b140f8 by Andreas Tille at 2023-01-19T20:56:00+01:00 Update lintian override info format in d/source/lintian-overrides on line 4-6. Changes-By: lintian-brush Fixes: lintian: mismatched-override See-also: https://lintian.debian.org/tags/mismatched-override.html - - - - - 30 changed files: - c++/compilers/unix/ICC.sh - c++/compilers/vs2019/build.sh - c++/compilers/vs2019/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - c++/compilers/vs2019/make.bat - c++/compilers/vs2019/retry.sh - c++/compilers/vs2019/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj - c++/compilers/vs2019/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj - c++/compilers/vs2019/static/build/corelib/xncbi.lib.vcxproj - c++/compilers/vs2019/static/build/serial/datatool/datatool.exe.vcxproj - c++/compilers/vs2019/static/build/serial/xser.lib.vcxproj - c++/compilers/vs2019/static/build/util/regexp/regexp.lib.vcxproj - c++/compilers/vs2019/static/build/util/xregexp/xregexp.lib.vcxproj - c++/compilers/vs2019/static/build/util/xutil.lib.vcxproj - c++/compilers/xcode30_prj/postbuild.sh - c++/include/algo/align/util/align_compare.hpp - c++/include/algo/align/util/tabular_fmt.hpp - c++/include/algo/blast/api/magicblast.hpp - c++/include/algo/blast/blast_sra_input/blast_sra_input.hpp - c++/include/algo/blast/blastinput/blast_args.hpp - c++/include/algo/blast/blastinput/cmdline_flags.hpp - c++/include/algo/blast/igblast/igblast.hpp - c++/include/algo/winmask/seq_masker.hpp - c++/include/algo/winmask/seq_masker_istat.hpp - c++/include/algo/winmask/seq_masker_istat_factory.hpp - c++/include/algo/winmask/seq_masker_ostat.hpp - c++/include/algo/winmask/win_mask_config.hpp - c++/include/algo/winmask/win_mask_gen_counts.hpp - c++/include/cgi/cgictx.hpp - c++/include/cgi/ncbicgi.hpp - c++/include/common/config/ncbiconf_msvc.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/4d8bbf60775b3cec414670ec3851152bde62280d...f1b140f84d26166d4fa75eb072276a3a118f092d -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/4d8bbf60775b3cec414670ec3851152bde62280d...f1b140f84d26166d4fa75eb072276a3a118f092d 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/jaligner] Pushed new tag debian/1.0+dfsg-10
Andreas Tille pushed new tag debian/1.0+dfsg-10 at Debian Med / jaligner -- View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/tree/debian/1.0+dfsg-10 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/jaligner][master] 3 commits: Fix watch file
Andreas Tille pushed to branch master at Debian Med / jaligner Commits: fbcf8951 by Andreas Tille at 2023-01-19T20:46:16+01:00 Fix watch file - - - - - c4606696 by Andreas Tille at 2023-01-19T20:46:54+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 516e6c5e by Andreas Tille at 2023-01-19T20:48:35+01:00 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +jaligner (1.0+dfsg-10) unstable; urgency=medium + + * Team upload. + * Fix watch file + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Thu, 19 Jan 2023 20:47:15 +0100 + jaligner (1.0+dfsg-9) unstable; urgency=medium * Drop JNLP build-dep = debian/control = @@ -11,7 +11,7 @@ Build-Depends-Indep: junit4, javahelper, asciidoctor, maven-repo-helper -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/jaligner Vcs-Git: https://salsa.debian.org/med-team/jaligner.git Homepage: https://github.com/ahmedmoustafa/JAligner = debian/watch = @@ -1,4 +1,4 @@ version=4 opts="filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/jaligner-$1.tar.gz/,dversionmangle=s/\+dfsg\d*$//,repacksuffix=+dfsg" \ - https://github.com/ahmedmoustafa/JAligner/releases .*/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) + https://github.com/ahmedmoustafa/JAligner/tags .*/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/055a400d3966bed3fd460dbd8deb37aeba5bed9a...516e6c5e6f0d96536888a95b9454d2b5430a61a6 -- View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/055a400d3966bed3fd460dbd8deb37aeba5bed9a...516e6c5e6f0d96536888a95b9454d2b5430a61a6 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/vg] Pushed new tag upstream/1.45.0+ds
Andreas Tille pushed new tag upstream/1.45.0+ds at Debian Med / vg -- View it on GitLab: https://salsa.debian.org/med-team/vg/-/tree/upstream/1.45.0+ds 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/vg][upstream] New upstream version 1.45.0+ds
Andreas Tille pushed to branch upstream at Debian Med / vg Commits: e0515fa7 by Andreas Tille at 2023-01-19T14:32:12+01:00 New upstream version 1.45.0+ds - - - - - 10 changed files: - .github/workflows/testmac.yml - Makefile - README.md - deps/libbdsg/CMakeLists.txt - deps/libbdsg/Makefile - deps/libbdsg/README.md - deps/libbdsg/bdsg/cmake_bindings/bdsg.cpp - deps/libbdsg/bdsg/cmake_bindings/bdsg.sources - − deps/libbdsg/bdsg/cmake_bindings/bdsg/odgi.cpp - deps/libbdsg/bdsg/cmake_bindings/bdsg/overlays/packed_path_position_overlay.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/e0515fa737919ba9f2afb9d5f8ada0c0df03611c -- View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/e0515fa737919ba9f2afb9d5f8ada0c0df03611c 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/vg][master] 8 commits: Standards-Version: 4.6.2
Andreas Tille pushed to branch master at Debian Med / vg Commits: 0ea6e01a by Andreas Tille at 2023-01-19T14:28:23+01:00 Standards-Version: 4.6.2 - - - - - 7804cdf4 by Andreas Tille at 2023-01-19T14:32:07+01:00 routine-update: New upstream version - - - - - e0515fa7 by Andreas Tille at 2023-01-19T14:32:12+01:00 New upstream version 1.45.0+ds - - - - - 7c172287 by Andreas Tille at 2023-01-19T14:35:21+01:00 Update upstream source from tag upstream/1.45.0+ds Update to upstream version 1.45.0+ds with Debian dir 67b83d31209587d2575757277bd0f6a7fd630d64 - - - - - aeb48ca2 by Andreas Tille at 2023-01-19T14:35:49+01:00 Update lintian override info to new format: + debian/source/lintian-overrides: line 2 + debian/vg.lintian-overrides: line 5, 8-12 Changes-By: lintian-brush Fixes: lintian: mismatched-override See-also: https://lintian.debian.org/tags/mismatched-override.html - - - - - e30b59d1 by Andreas Tille at 2023-01-19T14:36:35+01:00 Remove constraints unnecessary since buster (oldstable) * Build-Depends: Replace dependency on transitional package libncurses5-dev with replacement libtinfo6 (= 6.1+20181013-2+deb10u2), libncurses-dev (= 6.1+20181013-2+deb10u2). Changes-By: deb-scrub-obsolete - - - - - b9ac46c3 by Andreas Tille at 2023-01-19T14:51:12+01:00 Refresh patches - - - - - c0989609 by Andreas Tille at 2023-01-19T14:58:11+01:00 Fix broken replacement by lintian-bruch of libtinfo6, libncurses-dev - - - - - 17 changed files: - .github/workflows/testmac.yml - Makefile - README.md - debian/changelog - debian/control - debian/patches/no_rpath - debian/patches/use_packaged_jemalloc - debian/patches/use_packaged_vcflib - debian/source/lintian-overrides - debian/vg.lintian-overrides - deps/libbdsg/CMakeLists.txt - deps/libbdsg/Makefile - deps/libbdsg/README.md - deps/libbdsg/bdsg/cmake_bindings/bdsg.cpp - deps/libbdsg/bdsg/cmake_bindings/bdsg.sources - − deps/libbdsg/bdsg/cmake_bindings/bdsg/odgi.cpp - deps/libbdsg/bdsg/cmake_bindings/bdsg/overlays/packed_path_position_overlay.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/139e0e3bb1e8fd5c2cbde5e372d6dde274ee5100...c0989609f8e4b4ee783a608216d9a9c2f96d649d -- View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/139e0e3bb1e8fd5c2cbde5e372d6dde274ee5100...c0989609f8e4b4ee783a608216d9a9c2f96d649d 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/vg][pristine-tar] pristine-tar data for vg_1.45.0+ds.orig.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / vg Commits: 697be595 by Andreas Tille at 2023-01-19T14:35:21+01:00 pristine-tar data for vg_1.45.0+ds.orig.tar.xz - - - - - 2 changed files: - + vg_1.45.0+ds.orig.tar.xz.delta - + vg_1.45.0+ds.orig.tar.xz.id Changes: = vg_1.45.0+ds.orig.tar.xz.delta = Binary files /dev/null and b/vg_1.45.0+ds.orig.tar.xz.delta differ = vg_1.45.0+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +8fbf5f0c88b54c9d5a08526d6b9b91c56aa8b606 View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/697be595f290466bb19be3612154b3e8ec5f21df -- View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/697be595f290466bb19be3612154b3e8ec5f21df 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/charls][upstream] New upstream version 2.4.1
Mathieu Malaterre pushed to branch upstream at Debian Med / charls Commits: d6ca9caf by Mathieu Malaterre at 2023-01-19T16:16:40+01:00 New upstream version 2.4.1 - - - - - 30 changed files: - .clang-tidy - CHANGELOG.md - CMakeLists.txt - CharLS.sln - CharLS.sln.DotSettings - Directory.Build.props - README.md - SECURITY.md - benchmark/benchmark.cpp - benchmark/benchmark.vcxproj - benchmark/context_regular_mode.cpp - benchmark/context_regular_mode_v220.h - benchmark/log2.cpp - cpp.hint - fuzztest/FuzzTest.vcxproj - fuzztest/main.cpp - include/charls/annotations.h - include/charls/api_abi.h - include/charls/charls.h - include/charls/charls_jpegls_decoder.h - include/charls/charls_jpegls_encoder.h - include/charls/public_types.h - + include/charls/validate_spiff_header.h - include/charls/version.h - samples/convert.c/convert-c.vcxproj - samples/convert.c/main.c - samples/convert.cpp/convert-cpp.vcxproj - samples/convert.cpp/main.cpp - src/CMakeLists.txt - src/CharLS.vcxproj The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/charls/-/commit/d6ca9caf3b7b6324000538957cab1520be8cb300 -- View it on GitLab: https://salsa.debian.org/med-team/charls/-/commit/d6ca9caf3b7b6324000538957cab1520be8cb300 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/charls][master] 4 commits: New upstream version 2.4.1
Mathieu Malaterre pushed to branch master at Debian Med / charls Commits: 1ff04179 by Mathieu Malaterre at 2023-01-19T16:04:39+01:00 New upstream version 2.4.1 - - - - - d64fc82a by Mathieu Malaterre at 2023-01-19T16:04:39+01:00 Update upstream source from tag upstream/2.4.1 Update to upstream version 2.4.1 with Debian dir b55916b4b043552259cddd3aa311966e1a25b01e - - - - - d9ae85dc by Mathieu Malaterre at 2023-01-19T16:13:03+01:00 d/symbols: Add new symbols - - - - - afb7f3ca by Mathieu Malaterre at 2023-01-19T16:15:40+01:00 d/changelog: Upload 2.4.1-1 to unstable - - - - - 30 changed files: - .clang-tidy - CHANGELOG.md - CMakeLists.txt - CharLS.sln - CharLS.sln.DotSettings - Directory.Build.props - README.md - SECURITY.md - benchmark/benchmark.cpp - benchmark/benchmark.vcxproj - benchmark/context_regular_mode.cpp - benchmark/context_regular_mode_v220.h - benchmark/log2.cpp - cpp.hint - debian/changelog - debian/libcharls2.symbols - fuzztest/FuzzTest.vcxproj - fuzztest/main.cpp - include/charls/annotations.h - include/charls/api_abi.h - include/charls/charls.h - include/charls/charls_jpegls_decoder.h - include/charls/charls_jpegls_encoder.h - include/charls/public_types.h - + include/charls/validate_spiff_header.h - include/charls/version.h - samples/convert.c/convert-c.vcxproj - samples/convert.c/main.c - samples/convert.cpp/convert-cpp.vcxproj - samples/convert.cpp/main.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/charls/-/compare/e00d34feb45a649d756c3cb296ed69bbaec06235...afb7f3ca1c0bf0769ac50ced96d62b39b97d8f99 -- View it on GitLab: https://salsa.debian.org/med-team/charls/-/compare/e00d34feb45a649d756c3cb296ed69bbaec06235...afb7f3ca1c0bf0769ac50ced96d62b39b97d8f99 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/barrnap][master] 5 commits: Package was not released
Andreas Tille pushed to branch master at Debian Med / barrnap Commits: 041881b9 by Andreas Tille at 2023-01-19T14:20:37+01:00 Package was not released - - - - - df49ab9e by Andreas Tille at 2023-01-19T14:20:52+01:00 routine-update: Standards-Version: 4.6.2 - - - - - db41175c by Andreas Tille at 2023-01-19T14:21:01+01:00 Update renamed lintian tag names in lintian overrides. Changes-By: lintian-brush Fixes: lintian: renamed-tag See-also: https://lintian.debian.org/tags/renamed-tag.html - - - - - 73950da7 by Andreas Tille at 2023-01-19T14:27:50+01:00 routine-update: watch file standard 4 - - - - - e97e8186 by Andreas Tille at 2023-01-19T14:29:30+01:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - debian/source/lintian-overrides - debian/watch Changes: = debian/changelog = @@ -11,8 +11,11 @@ barrnap (0.9+dfsg-3) unstable; urgency=medium * Set upstream metadata fields: Repository, Repository-Browse. * Deactivate complex and error-prone dh_auto_clean override * Remove invalid lintian-override + * Standards-Version: 4.6.2 (routine-update) + * Update renamed lintian tag names in lintian overrides. + * watch file standard 4 (routine-update) - -- Andreas Tille Fri, 06 Nov 2020 16:48:17 +0100 + -- Andreas Tille Thu, 19 Jan 2023 14:27:50 +0100 barrnap (0.9+dfsg-2) unstable; urgency=medium = debian/control = @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13), hmmer, lua5.1, bedtools -Standards-Version: 4.5.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/barrnap Vcs-Git: https://salsa.debian.org/med-team/barrnap.git Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml = debian/source/lintian-overrides = @@ -1,2 +1,2 @@ # Upstream does not provide signed tarballs. -barrnap source: debian-watch-does-not-check-gpg-signature +barrnap source: debian-watch-does-not-check-openpgp-signature = debian/watch = @@ -1,4 +1,4 @@ -version=3 +version=4 opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/barrnap-$1.tar.gz/,dversionmangle=s/.dfsg// \ https://github.com/Victorian-Bioinformatics-Consortium/barrnap/tags .*/v?(\d\S*)\.tar\.gz View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/compare/bcbe6782e9afedf509018aad74f676670671f587...e97e818693d21ba70de8f8a2014bff854aa4db9a -- View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/compare/bcbe6782e9afedf509018aad74f676670671f587...e97e818693d21ba70de8f8a2014bff854aa4db9a 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/barrnap] Pushed new tag debian/0.9+dfsg-3
Andreas Tille pushed new tag debian/0.9+dfsg-3 at Debian Med / barrnap -- View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/tree/debian/0.9+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/barrnap] Deleted tag debian/0.9+dfsg-3
Andreas Tille deleted tag debian/0.9+dfsg-3 at Debian Med / barrnap -- 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/probalign] Pushed new tag debian/1.4-10
Andreas Tille pushed new tag debian/1.4-10 at Debian Med / probalign -- View it on GitLab: https://salsa.debian.org/med-team/probalign/-/tree/debian/1.4-10 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/probalign][master] 3 commits: Fix Homepage and download location
Andreas Tille pushed to branch master at Debian Med / probalign Commits: 87c2ced0 by Andreas Tille at 2023-01-19T14:14:49+01:00 Fix Homepage and download location - - - - - 97a7d264 by Andreas Tille at 2023-01-19T14:15:00+01:00 routine-update: Standards-Version: 4.6.2 - - - - - b47e15ab by Andreas Tille at 2023-01-19T14:16:15+01:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,10 @@ +probalign (1.4-10) unstable; urgency=medium + + * Fix Homepage and download location + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Thu, 19 Jan 2023 14:15:16 +0100 + probalign (1.4-9) unstable; urgency=medium * Standards-Version: 4.5.1 (routine-update) = debian/control = @@ -5,10 +5,10 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), help2man -Standards-Version: 4.5.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/probalign Vcs-Git: https://salsa.debian.org/med-team/probalign.git -Homepage: http://probalign.njit.edu/standalone.html +Homepage: https://web.njit.edu/~usman/probalign/ Rules-Requires-Root: no Package: probalign = debian/copyright = @@ -1,7 +1,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Probalign Upstream-Contact: Usman Roshan -Source: http://cs.njit.edu/usman/probalign/ +Source: https://web.njit.edu/~usman/probalign/ Files: * Copyright: © 2010 Satish Chikkagoudar and Usman Roshan = debian/watch = @@ -1,2 +1,2 @@ version=4 -http://probalign.njit.edu/standalone.html standalone/probalign([\d\.]+)\.tgz +https://web.njit.edu/~usman/probalign/ @PACKAGE@@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/probalign/-/compare/62c5e08af33e809dc15d54ef520da29780bf80aa...b47e15aba0a4f6f2c129c6e93164223fc567d92d -- View it on GitLab: https://salsa.debian.org/med-team/probalign/-/compare/62c5e08af33e809dc15d54ef520da29780bf80aa...b47e15aba0a4f6f2c129c6e93164223fc567d92d 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/pbcopper][master] 6 commits: New upstream version 2.2.0+dfsg
Andreas Tille pushed to branch master at Debian Med / pbcopper Commits: 506b63c0 by Andreas Tille at 2023-01-19T14:00:14+01:00 New upstream version 2.2.0+dfsg - - - - - a4270e1c by Andreas Tille at 2023-01-19T14:00:14+01:00 routine-update: New upstream version - - - - - 2284c730 by Andreas Tille at 2023-01-19T14:00:17+01:00 Update upstream source from tag upstream/2.2.0+dfsg Update to upstream version 2.2.0+dfsg with Debian dir ee47816849dcafde3ed6b8d04cc8a4e88ffbcd52 - - - - - 1d089ad1 by Andreas Tille at 2023-01-19T14:00:17+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 8ffa16f9 by Andreas Tille at 2023-01-19T14:04:31+01:00 Refresh patch - - - - - 586655ff by Andreas Tille at 2023-01-19T14:08:53+01:00 Build error - - - - - 30 changed files: - .clang-format - CHANGELOG.md - debian/changelog - debian/control - debian/patches/simde.patch - include/meson.build - include/pbcopper/PbcopperConfig.h - include/pbcopper/algorithm/Heteroduplex.h - + include/pbcopper/algorithm/KMerIndex.h - + include/pbcopper/algorithm/LSHIndex.h - src/align/cssw/ssw.h → include/pbcopper/align/cssw/ssw.h - src/align/cssw/ssw_cpp.h → include/pbcopper/align/cssw/ssw_cpp.h - include/pbcopper/align/internal/BCAlignBlocks.h - include/pbcopper/cli2/Interface.h - include/pbcopper/cli2/OptionValue.h - include/pbcopper/cli2/internal/HelpMetrics.h - include/pbcopper/cli2/internal/InterfaceData.h - include/pbcopper/cli2/internal/MultiToolInterfaceData.h - include/pbcopper/cli2/internal/OptionData.h - include/pbcopper/cli2/internal/PositionalArgumentData.h - + include/pbcopper/container/BitContainer.h - + include/pbcopper/container/BitConversion.h - + include/pbcopper/container/BitmaskContainer.h - + include/pbcopper/container/CapacityPointer.h - + include/pbcopper/container/Contains.h - + include/pbcopper/container/DNAString.h - + include/pbcopper/container/RHUnordered.h - + include/pbcopper/container/Unordered.h - + include/pbcopper/cuda/AsciiConversion.h - + include/pbcopper/cuda/Cuda.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/compare/f9bdf2c5d37ab5c6bf5d5866187f3babca5c7eb0...586655ffa1aa2db4578957e91bc830320adf8913 -- View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/compare/f9bdf2c5d37ab5c6bf5d5866187f3babca5c7eb0...586655ffa1aa2db4578957e91bc830320adf8913 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/pbcopper][upstream] New upstream version 2.2.0+dfsg
Andreas Tille pushed to branch upstream at Debian Med / pbcopper Commits: 506b63c0 by Andreas Tille at 2023-01-19T14:00:14+01:00 New upstream version 2.2.0+dfsg - - - - - 30 changed files: - .clang-format - CHANGELOG.md - include/meson.build - include/pbcopper/PbcopperConfig.h - include/pbcopper/algorithm/Heteroduplex.h - + include/pbcopper/algorithm/KMerIndex.h - + include/pbcopper/algorithm/LSHIndex.h - src/align/cssw/ssw.h → include/pbcopper/align/cssw/ssw.h - src/align/cssw/ssw_cpp.h → include/pbcopper/align/cssw/ssw_cpp.h - include/pbcopper/align/internal/BCAlignBlocks.h - include/pbcopper/cli2/Interface.h - include/pbcopper/cli2/OptionValue.h - include/pbcopper/cli2/internal/HelpMetrics.h - include/pbcopper/cli2/internal/InterfaceData.h - include/pbcopper/cli2/internal/MultiToolInterfaceData.h - include/pbcopper/cli2/internal/OptionData.h - include/pbcopper/cli2/internal/PositionalArgumentData.h - + include/pbcopper/container/BitContainer.h - + include/pbcopper/container/BitConversion.h - + include/pbcopper/container/BitmaskContainer.h - + include/pbcopper/container/CapacityPointer.h - + include/pbcopper/container/Contains.h - + include/pbcopper/container/DNAString.h - + include/pbcopper/container/RHUnordered.h - + include/pbcopper/container/Unordered.h - + include/pbcopper/cuda/AsciiConversion.h - + include/pbcopper/cuda/Cuda.h - include/pbcopper/data/CCSTag.h - include/pbcopper/data/Cigar.h - include/pbcopper/data/CigarOperation.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/commit/506b63c06c86b3cf9107459476d733058662bc67 -- View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/commit/506b63c06c86b3cf9107459476d733058662bc67 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/pbcopper] Pushed new tag upstream/2.2.0+dfsg
Andreas Tille pushed new tag upstream/2.2.0+dfsg at Debian Med / pbcopper -- View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/tree/upstream/2.2.0+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/pbcopper][pristine-tar] pristine-tar data for pbcopper_2.2.0+dfsg.orig.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / pbcopper Commits: 72f5d07b by Andreas Tille at 2023-01-19T14:00:17+01:00 pristine-tar data for pbcopper_2.2.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + pbcopper_2.2.0+dfsg.orig.tar.xz.delta - + pbcopper_2.2.0+dfsg.orig.tar.xz.id Changes: = pbcopper_2.2.0+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/pbcopper_2.2.0+dfsg.orig.tar.xz.delta differ = pbcopper_2.2.0+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +cec0a0a13e3c2eef92f1e8e3561010ba34adef5e View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/commit/72f5d07b55b66bc68b98283fdae0a38d4862e0a4 -- View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/commit/72f5d07b55b66bc68b98283fdae0a38d4862e0a4 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/sambamba] Pushed new tag debian/1.0+dfsg-1
Andreas Tille pushed new tag debian/1.0+dfsg-1 at Debian Med / sambamba -- View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/tree/debian/1.0+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/sambamba] Pushed new tag upstream/1.0+dfsg
Andreas Tille pushed new tag upstream/1.0+dfsg at Debian Med / sambamba -- View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/tree/upstream/1.0+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/sambamba][pristine-tar] pristine-tar data for sambamba_1.0+dfsg.orig.tar.xz
Andreas Tille pushed to branch pristine-tar at Debian Med / sambamba Commits: 06eb3c82 by Andreas Tille at 2023-01-19T12:18:08+01:00 pristine-tar data for sambamba_1.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + sambamba_1.0+dfsg.orig.tar.xz.delta - + sambamba_1.0+dfsg.orig.tar.xz.id Changes: = sambamba_1.0+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/sambamba_1.0+dfsg.orig.tar.xz.delta differ = sambamba_1.0+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +8fd58f4c96cb43cd72573498ec75e9b3848e4661 View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/commit/06eb3c82abbd93b078e6e27344e7b3cb08c3b056 -- View it on GitLab: https://salsa.debian.org/med-team/sambamba/-/commit/06eb3c82abbd93b078e6e27344e7b3cb08c3b056 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/libtabixpp] Pushed new tag debian/1.1.2-1
Andreas Tille pushed new tag debian/1.1.2-1 at Debian Med / libtabixpp -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/tree/debian/1.1.2-1 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/libtabixpp] Pushed new tag upstream/1.1.2
Andreas Tille pushed new tag upstream/1.1.2 at Debian Med / libtabixpp -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/tree/upstream/1.1.2 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/libtabixpp][master] 6 commits: New upstream version 1.1.2
Andreas Tille pushed to branch master at Debian Med / libtabixpp
Commits:
7a71f0f6 by Andreas Tille at 2023-01-19T09:54:36+01:00
New upstream version 1.1.2
- - - - -
ec4222b8 by Andreas Tille at 2023-01-19T09:54:36+01:00
routine-update: New upstream version
- - - - -
269131ba by Andreas Tille at 2023-01-19T09:54:36+01:00
Update upstream source from tag upstream/1.1.2
Update to upstream version 1.1.2
with Debian dir c996b962c48053f32a48ecb4cc8ad5a862284f8a
- - - - -
d96ef434 by Andreas Tille at 2023-01-19T09:54:37+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
31fad88a by Andreas Tille at 2023-01-19T09:54:45+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
Changes-By: lintian-brush
- - - - -
cf074041 by Andreas Tille at 2023-01-19T09:55:51+01:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/upstream/metadata
- tabix.hpp
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+libtabixpp (1.1.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
+
+ -- Andreas Tille Thu, 19 Jan 2023 09:54:58 +0100
+
libtabixpp (1.1.1-1) unstable; urgency=medium
[ Andreas Tille ]
=
debian/control
=
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libbz2-dev,
d-shlibs
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libtabixpp
Vcs-Git: https://salsa.debian.org/med-team/libtabixpp.git
Homepage: https://github.com/ekg/tabixpp
=
debian/upstream/metadata
=
@@ -1,5 +1,5 @@
---
-Bug-Database: https://github.com/ekg/tabixpp/issues
-Bug-Submit: https://github.com/ekg/tabixpp/issues/new
+Bug-Database: https://github.com/vcflib/tabixpp/issues
+Bug-Submit: https://github.com/vcflib/tabixpp/issues/new
Repository: https://github.com/ekg/tabixpp.git
-Repository-Browse: https://github.com/ekg/tabixpp
+Repository-Browse: https://github.com/vcflib/tabixpp
=
tabix.hpp
=
@@ -1,3 +1,5 @@
+#pragma once
+
#include
#include
#include
@@ -24,6 +26,30 @@ class Tabix {
bool has_jumped;
vector::iterator current_chrom;
+/* uncompressed file pos
+off_t hts_utell1(htsFile *fp)
+{
+if (fp->is_bgzf) {
+return bgzf_htell(fp->fp.bgzf);
+}
+else
+return htell(fp->fp.hfile);
+}
+*/
+
+// Get file position in compressed file - really on disk
+off_t bgzf_htell1(BGZF *fp) {
+if (fp->mt) {
+return -1; // skip if multithreading
+//pthread_mutex_lock(>mt->job_pool_m);
+//off_t pos = fp->block_address + fp->block_clength;
+//pthread_mutex_unlock(>mt->job_pool_m);
+//return pos;
+} else {
+return htell(fp->fp);
+}
+}
+
public:
string filename;
vector chroms;
@@ -37,5 +63,6 @@ public:
bool setRegion(string& region);
bool getNextLine(string& line);
bool getNextLineKS();
-
+// Specialised function gets actual file position when using bgzf
+long file_pos() { return bgzf_htell1(fn->fp.bgzf); };
};
View it on GitLab:
https://salsa.debian.org/med-team/libtabixpp/-/compare/c28d16d3b0e51f76d54b0409e9659fc89d6b163f...cf0740413b2f665f910c29243604d290e671b674
--
View it on GitLab:
https://salsa.debian.org/med-team/libtabixpp/-/compare/c28d16d3b0e51f76d54b0409e9659fc89d6b163f...cf0740413b2f665f910c29243604d290e671b674
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[med-svn] [Git][med-team/libtabixpp][pristine-tar] pristine-tar data for libtabixpp_1.1.2.orig.tar.gz
Andreas Tille pushed to branch pristine-tar at Debian Med / libtabixpp Commits: 5a2d1bfb by Andreas Tille at 2023-01-19T09:54:36+01:00 pristine-tar data for libtabixpp_1.1.2.orig.tar.gz - - - - - 2 changed files: - + libtabixpp_1.1.2.orig.tar.gz.delta - + libtabixpp_1.1.2.orig.tar.gz.id Changes: = libtabixpp_1.1.2.orig.tar.gz.delta = Binary files /dev/null and b/libtabixpp_1.1.2.orig.tar.gz.delta differ = libtabixpp_1.1.2.orig.tar.gz.id = @@ -0,0 +1 @@ +0e92426cf9b6ec3bad0aaf19c322fdbf7ef7c158 View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/commit/5a2d1bfb1db8c8897dae0f2ea1315d290711cf84 -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/commit/5a2d1bfb1db8c8897dae0f2ea1315d290711cf84 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/libtabixpp][upstream] New upstream version 1.1.2
Andreas Tille pushed to branch upstream at Debian Med / libtabixpp
Commits:
7a71f0f6 by Andreas Tille at 2023-01-19T09:54:36+01:00
New upstream version 1.1.2
- - - - -
1 changed file:
- tabix.hpp
Changes:
=
tabix.hpp
=
@@ -1,3 +1,5 @@
+#pragma once
+
#include
#include
#include
@@ -24,6 +26,30 @@ class Tabix {
bool has_jumped;
vector::iterator current_chrom;
+/* uncompressed file pos
+off_t hts_utell1(htsFile *fp)
+{
+if (fp->is_bgzf) {
+return bgzf_htell(fp->fp.bgzf);
+}
+else
+return htell(fp->fp.hfile);
+}
+*/
+
+// Get file position in compressed file - really on disk
+off_t bgzf_htell1(BGZF *fp) {
+if (fp->mt) {
+return -1; // skip if multithreading
+//pthread_mutex_lock(>mt->job_pool_m);
+//off_t pos = fp->block_address + fp->block_clength;
+//pthread_mutex_unlock(>mt->job_pool_m);
+//return pos;
+} else {
+return htell(fp->fp);
+}
+}
+
public:
string filename;
vector chroms;
@@ -37,5 +63,6 @@ public:
bool setRegion(string& region);
bool getNextLine(string& line);
bool getNextLineKS();
-
+// Specialised function gets actual file position when using bgzf
+long file_pos() { return bgzf_htell1(fn->fp.bgzf); };
};
View it on GitLab:
https://salsa.debian.org/med-team/libtabixpp/-/commit/7a71f0f6097fbe173e40288ffbfece2d02b3bc09
--
View it on GitLab:
https://salsa.debian.org/med-team/libtabixpp/-/commit/7a71f0f6097fbe173e40288ffbfece2d02b3bc09
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[med-svn] [Git][med-team/relion][debian-contrib/master] 3 commits: Fix watch file
Andreas Tille pushed to branch debian-contrib/master at Debian Med / relion Commits: 15ec58a5 by Andreas Tille at 2023-01-19T07:55:18+01:00 Fix watch file - - - - - c293448a by Andreas Tille at 2023-01-19T07:56:31+01:00 Rebuild for the libtiff5 - libtiff6 transition - - - - - 448a255b by Andreas Tille at 2023-01-19T08:20:10+01:00 Upload to unstable - - - - - 2 changed files: - debian/changelog - debian/watch Changes: = debian/changelog = @@ -1,3 +1,12 @@ +relion-cuda (3.1.3-2) unstable; urgency=medium + + * Team upload. + * Fix watch file + * Rebuild for the libtiff5 -> libtiff6 transition +Closes: #1029179 + + -- Andreas Tille Thu, 19 Jan 2023 07:57:26 +0100 + relion-cuda (3.1.3-1) unstable; urgency=medium * Team upload. = debian/watch = @@ -1,4 +1,4 @@ version=4 opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ - https://github.com/3dem/relion/releases .*/(\d[\d.]+)@ARCHIVE_EXT@ + https://github.com/3dem/relion/tags .*/(\d[\d.]+)@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/039c9146bbe02f93aa2ca4df0dd9a4ff32045cf9...448a255b1b7bb7c8b9180e49c1f1de4b54347542 -- View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/039c9146bbe02f93aa2ca4df0dd9a4ff32045cf9...448a255b1b7bb7c8b9180e49c1f1de4b54347542 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/relion] Pushed new tag debian-contrib/3.1.3-2
Andreas Tille pushed new tag debian-contrib/3.1.3-2 at Debian Med / relion -- View it on GitLab: https://salsa.debian.org/med-team/relion/-/tree/debian-contrib/3.1.3-2 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
