[med-svn] [Git][med-team/libsis-base-java][master] Upload to unstable
Pierre Gruet pushed to branch master at Debian Med / libsis-base-java Commits: 73b8cbe8 by Pierre Gruet at 2020-12-07T08:11:29+01:00 Upload to unstable - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,4 +1,4 @@ -libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-2) UNRELEASED; urgency=medium +libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-2) unstable; urgency=medium * Team upload * Deactivate tests that have a symlink point to nothing (Closes: #976490) View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/commit/73b8cbe8e70624d7ecacda4d5d3e1329e5f251af -- View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/commit/73b8cbe8e70624d7ecacda4d5d3e1329e5f251af 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/libsis-base-java] Pushed new tag debian/18.09_pre1+git20180928.45fbd31+dfsg-2
Pierre Gruet pushed new tag debian/18.09_pre1+git20180928.45fbd31+dfsg-2 at Debian Med / libsis-base-java -- View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/tree/debian/18.09_pre1+git20180928.45fbd31+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/community/helper-scripts][master] automatic update
Andreas Tille pushed to branch master at Debian Med / community / helper-scripts Commits: d1246971 by Andreas Tille at 2020-12-07T01:45:57+00:00 automatic update - - - - - 2 changed files: - debian-med-tests.txt - outdated_med-packages.txt Changes: = debian-med-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Sun, 06 Dec 2020 13:42:03 + +Last-Update: Mon, 07 Dec 2020 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = outdated_med-packages.txt = The diff for this file was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/d1246971d94378c5b5d4d3c9ccada30875d64b01 -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/d1246971d94378c5b5d4d3c9ccada30875d64b01 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/libsis-base-java][master] 4 commits: Deactivate tests that cause a symlink point to nothing
Pierre Gruet pushed to branch master at Debian Med / libsis-base-java
Commits:
78ad5c70 by Pierre Gruet at 2020-12-06T22:01:15+01:00
Deactivate tests that cause a symlink point to nothing
- - - - -
c41220a4 by Pierre Gruet at 2020-12-06T22:08:47+01:00
Updating Forwarded information in headers of patches
- - - - -
cc192f6a by Pierre Gruet at 2020-12-06T22:11:41+01:00
Standards version 4.5.1 (no changes needed)
- - - - -
6cdcca8f by Pierre Gruet at 2020-12-06T22:26:23+01:00
Update changelog
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/patches/deactivate_tests_causing_fail_dut_to_commons-io.patch
- debian/patches/load_native_debian.patch
- debian/patches/remove_ch_rinn_imports.patch
- debian/patches/series
- debian/patches/skip_testGetLinkInfoDirectory.patch
- debian/patches/skip_testGetLinkInfoSymLinkDanglingLink.patch
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-2) UNRELEASED;
urgency=medium
+
+ * Team upload
+ * Deactivate tests that have a symlink point to nothing (Closes: #976490)
+ * Standards version 4.5.1 (no changes needed)
+
+ -- Pierre Gruet Sun, 06 Dec 2020 22:12:39 +0100
+
libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-1) unstable;
urgency=medium
* New upstream version
=
debian/control
=
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
testng,
libtool,
procps
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/libsis-base-java
Vcs-Git: https://salsa.debian.org/med-team/libsis-base-java.git
Homepage: https://sissource.ethz.ch/sispub/base
=
debian/patches/deactivate_tests_causing_fail_dut_to_commons-io.patch
=
@@ -0,0 +1,81 @@
+Description: deactivate tests that cause a symlink pointing to nothing
+ In the concerned tests, a file named sameOtherFile is created, and at some
+ point in the afterClass method in AbstractFileSystemTestCase.java, this
+ symlink points to nothing, which is due to a bug in commons-io 2.8.0.
+ Those tests are deactivated, but should be activated again once the bug in
+ commons-io has been fixed.
+ See bug IO-692 in the bug dashboard on issues.apache.org website.
+Author: Pierre Gruet
+Forwarded: not-needed
+Last-Update: 2020-12-06
+
+--- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
+@@ -93,6 +93,7 @@
+ { "skip_this_test" })
+ public void testGetLinkInfoSymLink() throws IOException
+ {
++/*
+ final File f = new File(workingDirectory, "someOtherFile");
+ final String content = "someMoreText\n";
+ FileUtils.writeStringToFile(f, content, Charset.defaultCharset());
+@@ -112,12 +113,14 @@
+ assertEquals(FileLinkType.REGULAR_FILE, info2.getLinkType());
+ assertFalse(info2.isSymbolicLink());
+ assertNull(info2.tryGetSymbolicLink());
++*/
+ }
+
+ @Test(groups =
+-{ "requires_unix" })
++{ "skip_this_test" })
+ public void testTouchSymLinkAndFileRealtimeTimer() throws IOException,
InterruptedException
+ {
++/*
+ if (BuildAndEnvironmentInfo.INSTANCE.getOS().contains("2.6.32"))
+ {
+ System.out.println(" ...skipping as CentOS6 does not yet support
the realtime timer.");
+@@ -173,12 +176,14 @@
+ assertNotEquals(lastMicros,
info3.getLastModifiedTime().getMicroSecPart());
+ assertNotEquals(lastMicros,
info3.getLastAccessTime().getMicroSecPart());
+
++*/
+ }
+
+ @Test(groups =
+-{ "requires_unix" })
++{ "skip_this_test" })
+ public void testTouchSymLinkAndFile() throws IOException,
InterruptedException
+ {
++/*
+ Unix.setUseUnixRealtimeTimer(false);
+ final File f = new File(workingDirectory, "someOtherFile");
+ final String content = "someMoreText\n";
+@@ -230,6 +235,7 @@
+ assertNotEquals(lastMicros,
info3.getLastModifiedTime().getMicroSecPart());
+ assertNotEquals(lastMicros,
info3.getLastAccessTime().getMicroSecPart());
+
++*/
+ }
+
+ @Test(groups =
+@@ -280,9 +286,10 @@
+ }
+
+ @Test(groups =
+-{ "requires_unix" })
++{ "skip_this_test" })
+ public void testGetLinkInfoHardLink() throws IOException
+ {
++/*
+ final File f = new File(workingDirectory, "someOtherFile");
+ f.createNewFile();
+ final File s = new File(workingDirectory, "someLink");
+@@ -292,6 +299,7 @@
+ assertEquals(FileLinkType.REGULAR_FILE, info.getLinkType());
+ assertFalse(info.isSymbolicLink());
+ assertNull(info.tryGetSymbolicLink());
++*/
+ }
+
+ @Test(groups =
[med-svn] [Git][med-team/kmc] Pushed new tag debian/2.3+dfsg-9
Étienne Mollier pushed new tag debian/2.3+dfsg-9 at Debian Med / kmc -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/tree/debian/2.3+dfsg-9 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/kmc] Deleted tag debian/2.3+dfsg-9
Étienne Mollier deleted tag debian/2.3+dfsg-9 at Debian Med / kmc -- 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/kmc] Pushed new tag debian/2.3+dfsg-9
Étienne Mollier pushed new tag debian/2.3+dfsg-9 at Debian Med / kmc -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/tree/debian/2.3+dfsg-9 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/kmc][master] 11 commits: routine-update: Standards-Version: 4.5.1
Étienne Mollier pushed to branch master at Debian Med / kmc Commits: ea9e49ae by Étienne Mollier at 2020-12-06T16:49:18+01:00 routine-update: Standards-Version: 4.5.1 - - - - - efa49f19 by Étienne Mollier at 2020-12-06T16:49:19+01:00 routine-update: debhelper-compat 13 - - - - - 4b49451e by Étienne Mollier at 2020-12-06T16:49:22+01:00 routine-update: Add salsa-ci file - - - - - 1a11ebb0 by Étienne Mollier at 2020-12-06T16:49:22+01:00 routine-update: Rules-Requires-Root: no - - - - - 085d921c by Étienne Mollier at 2020-12-06T16:49:28+01:00 Set upstream metadata fields: Repository, Repository-Browse. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - fb37544c by Étienne Mollier at 2020-12-06T16:51:05+01:00 routine-update: Ready to upload to unstable - - - - - f5b77276 by Étienne Mollier at 2020-12-06T17:13:35+01:00 verbose autopkgtest - - - - - b4491446 by Étienne Mollier at 2020-12-06T17:41:01+01:00 d/watch: version=4 - - - - - 31a5d8f0 by Étienne Mollier at 2020-12-06T17:49:34+01:00 revert readyness for upload - - - - - deea97c1 by Étienne Mollier at 2020-12-06T17:57:14+01:00 allow autopkgtest output to stderr - - - - - 09040963 by Étienne Mollier at 2020-12-06T18:53:19+01:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - debian/changelog - debian/control - + debian/salsa-ci.yml - debian/tests/build-lib - debian/tests/control - debian/upstream/metadata - debian/watch Changes: = debian/changelog = @@ -1,3 +1,18 @@ +kmc (2.3+dfsg-9) unstable; urgency=medium + + * Team upload. + * Standards-Version: 4.5.1 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Repository, Repository-Browse. + * Autopkgtest changes: +- increase verbosity in hope to see more things in case #954270 reoccurs, +- allow output to standard error. + * Update d/watch to format version 4. + + -- Étienne Mollier Sun, 06 Dec 2020 18:51:47 +0100 + kmc (2.3+dfsg-8) unstable; urgency=medium * Add ref to conda (Thanks Steffen Moeller). = debian/control = @@ -6,17 +6,18 @@ Uploaders: Andreas Tille , Kevin Murray Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-exec, zlib1g-dev, libbz2-dev, help2man, asciidoctor, d-shlibs -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/kmc Vcs-Git: https://salsa.debian.org/med-team/kmc.git Homepage: http://sun.aei.polsl.pl/kmc +Rules-Requires-Root: no Package: kmc Architecture: any = debian/salsa-ci.yml = @@ -0,0 +1,4 @@ +--- +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 = debian/tests/build-lib = @@ -7,6 +7,7 @@ ORIGDIR=$(pwd) WORKDIR=$(mktemp -d) trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM +set -v g++ kmc_dump/*cpp -std=c++11 -lkmc -o $WORKDIR/my_kmcdump [ -x $WORKDIR/my_kmcdump ] echo "build: OK" = debian/tests/control = @@ -1,2 +1,3 @@ Tests: build-lib Depends: @, build-essential +Restrictions: allow-stderr = debian/upstream/metadata = @@ -1,6 +1,6 @@ Bug-Database: https://github.com/refresh-bio/KMC/issues Bug-Submit: https://github.com/refresh-bio/KMC/issues/new -Repository: http://github.com/refresh-bio/KMC +Repository: https://github.com/refresh-bio/KMC.git Reference: Author: > S. Deorowicz and M. Kokot and Sz. Grabowski and A. Debudaj-Grabysz @@ -22,3 +22,4 @@ Registry: Entry: KMC - Name: conda:bioconda Entry: kmc +Repository-Browse: https://github.com/refresh-bio/KMC = debian/watch = @@ -1,3 +1,5 @@ -version=3 -opts="repacksuffix=+dfsg,dversionmangle=s/.dfsg//,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/kmc_$1.tar.gz/" \ - https://github.com/marekkokot/KMC/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +version=4 + +opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/kmc_$1.tar.gz/" \ + https://github.com/marekkokot/KMC/releases \ + .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab:
[med-svn] [Git][med-team/signalalign][master] Update metadata - added ref to bio.tools
Steffen Möller pushed to branch master at Debian Med / signalalign Commits: 9ae08180 by Steffen Möller at 2020-12-06T17:18:51+00:00 Update metadata - added ref to bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -1,3 +1,7 @@ Registry: - Name: conda:bioconda Entry: NA + - Name: bio.tools +Entry: signalalign + - Name: SciCrunch +Entry: NA View it on GitLab: https://salsa.debian.org/med-team/signalalign/-/commit/9ae08180951ca0841f1e460ae0c7e6852749f6d7 -- View it on GitLab: https://salsa.debian.org/med-team/signalalign/-/commit/9ae08180951ca0841f1e460ae0c7e6852749f6d7 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/peptidebuilder] Pushed new tag debian/1.1.0-2
Nilesh Patra pushed new tag debian/1.1.0-2 at Debian Med / peptidebuilder -- View it on GitLab: https://salsa.debian.org/med-team/peptidebuilder/-/tree/debian/1.1.0-2 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/peptidebuilder][master] 2 commits: Update changelog
Nilesh Patra pushed to branch master at Debian Med / peptidebuilder Commits: ad8e3ae6 by Nilesh Patra at 2020-12-06T22:21:18+05:30 Update changelog - - - - - 4b8a6956 by Nilesh Patra at 2020-12-06T22:22:58+05:30 Update changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,9 @@ +peptidebuilder (1.1.0-2) unstable; urgency=medium + + * Source-only-upload for testing migration. + + -- Nilesh Patra Sun, 06 Dec 2020 22:20:43 +0530 + peptidebuilder (1.1.0-1) unstable; urgency=medium * Initial release (Closes: #976051) View it on GitLab: https://salsa.debian.org/med-team/peptidebuilder/-/compare/4d845590265e4bd9d3167285f6b02f23f75cefdb...4b8a6956f3a67a1084f6f87e48cf9b85b2a95421 -- View it on GitLab: https://salsa.debian.org/med-team/peptidebuilder/-/compare/4d845590265e4bd9d3167285f6b02f23f75cefdb...4b8a6956f3a67a1084f6f87e48cf9b85b2a95421 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/q2-sample-classifier] Pushed new tag debian/2020.11.1-1
Andreas Tille pushed new tag debian/2020.11.1-1 at Debian Med / q2-sample-classifier -- View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/tree/debian/2020.11.1-1 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/q2-sample-classifier] Pushed new tag upstream/2020.11.1
Andreas Tille pushed new tag upstream/2020.11.1 at Debian Med / q2-sample-classifier -- View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/tree/upstream/2020.11.1 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/q2-sample-classifier][upstream] New upstream version 2020.11.1
Andreas Tille pushed to branch upstream at Debian Med / q2-sample-classifier
Commits:
bd1405ab by Andreas Tille at 2020-12-06T17:10:39+01:00
New upstream version 2020.11.1
- - - - -
1 changed file:
- q2_sample_classifier/_version.py
Changes:
=
q2_sample_classifier/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "ceca1ef65671ec878e973e5f31b23e81a8feba6f"
-git_date = "2020-11-25 17:13:13 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "392e5454b7cb6a91d43968d62178fb6a216e193f"
+git_date = "2020-12-05 20:44:51 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/bd1405ab4f019f49e5708b93b8efa3b794a9475e
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/bd1405ab4f019f49e5708b93b8efa3b794a9475e
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[med-svn] [Git][med-team/q2-sample-classifier][pristine-tar] pristine-tar data for q2-sample-classifier_2020.11.1.orig.tar.gz
Andreas Tille pushed to branch pristine-tar at Debian Med / q2-sample-classifier Commits: b3ec8738 by Andreas Tille at 2020-12-06T17:10:41+01:00 pristine-tar data for q2-sample-classifier_2020.11.1.orig.tar.gz - - - - - 2 changed files: - + q2-sample-classifier_2020.11.1.orig.tar.gz.delta - + q2-sample-classifier_2020.11.1.orig.tar.gz.id Changes: = q2-sample-classifier_2020.11.1.orig.tar.gz.delta = Binary files /dev/null and b/q2-sample-classifier_2020.11.1.orig.tar.gz.delta differ = q2-sample-classifier_2020.11.1.orig.tar.gz.id = @@ -0,0 +1 @@ +f73256064dbd754fcca06aeae97858e4ce3f View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/b3ec8738626d94bfb540232abc71a3907b42e1ff -- View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/b3ec8738626d94bfb540232abc71a3907b42e1ff 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/q2-sample-classifier][master] 4 commits: routine-update: New upstream version
Andreas Tille pushed to branch master at Debian Med / q2-sample-classifier
Commits:
3e9c3b51 by Andreas Tille at 2020-12-06T17:10:38+01:00
routine-update: New upstream version
- - - - -
bd1405ab by Andreas Tille at 2020-12-06T17:10:39+01:00
New upstream version 2020.11.1
- - - - -
2a46b98b by Andreas Tille at 2020-12-06T17:10:41+01:00
Update upstream source from tag upstream/2020.11.1
Update to upstream version 2020.11.1
with Debian dir 7d3d4195c2a7a49c1875bd68e3d0c3ebbaeea0b3
- - - - -
51f1dbc9 by Andreas Tille at 2020-12-06T17:12:32+01:00
routine-update: Ready to upload to unstable
- - - - -
2 changed files:
- debian/changelog
- q2_sample_classifier/_version.py
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+q2-sample-classifier (2020.11.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Andreas Tille Sun, 06 Dec 2020 17:10:46 +0100
+
q2-sample-classifier (2020.11.0-1) unstable; urgency=medium
[ Liubov Chuprikova ]
=
q2_sample_classifier/_version.py
=
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
-git_refnames = " (HEAD -> master, tag: 2020.11.0)"
-git_full = "ceca1ef65671ec878e973e5f31b23e81a8feba6f"
-git_date = "2020-11-25 17:13:13 +"
+git_refnames = " (HEAD -> master, tag: 2020.11.1)"
+git_full = "392e5454b7cb6a91d43968d62178fb6a216e193f"
+git_date = "2020-12-05 20:44:51 +"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab:
https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/ce11327f6c180d7587b16e4ec65e3d6e2a9f8bf9...51f1dbc957466f837f2b3d37337782904627211d
--
View it on GitLab:
https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/ce11327f6c180d7587b16e4ec65e3d6e2a9f8bf9...51f1dbc957466f837f2b3d37337782904627211d
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[med-svn] [Git][med-team/qiime][master] 2 commits: 32-bits.patch forwarded upstream
Étienne Mollier pushed to branch master at Debian Med / qiime Commits: dc4edba4 by Étienne Mollier at 2020-12-06T17:02:28+01:00 32-bits.patch forwarded upstream - - - - - ed12d307 by Étienne Mollier at 2020-12-06T17:03:19+01:00 add myself to Uploaders - - - - - 3 changed files: - debian/changelog - debian/control - debian/patches/32-bits.patch Changes: = debian/changelog = @@ -1,3 +1,10 @@ +qiime (2020.11.0-2) UNRELEASED; urgency=medium + + * Add myself to Uploaders + * 32-bits.patch forwarded upstream. + + -- Étienne Mollier Sun, 06 Dec 2020 16:55:26 +0100 + qiime (2020.11.0-1) unstable; urgency=medium * Team upload. = debian/control = @@ -2,7 +2,8 @@ Source: qiime Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Liubov Chuprikova , - Andreas Tille + Andreas Tille , + Étienne Mollier Section: science Priority: optional Build-Depends: debhelper-compat (= 13), = debian/patches/32-bits.patch = @@ -1,7 +1,7 @@ Description: compatibility with 32-bits architectures Author: Étienne Mollier -Forwarded: no -Last-Update: 2020-12-01 +Forwarded: https://github.com/qiime2/qiime2/pull/555 +Last-Update: 2020-12-06 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- qiime.orig/qiime2/metadata/metadata.py View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/3b30e38c1fd484d5d03a2dfb72b5293aa9b0c912...ed12d3073dc89532900c4158531016f7bf754987 -- View it on GitLab: https://salsa.debian.org/med-team/qiime/-/compare/3b30e38c1fd484d5d03a2dfb72b5293aa9b0c912...ed12d3073dc89532900c4158531016f7bf754987 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/libhmsbeagle] Pushed new tag debian/3.1.2+dfsg-9
Andreas Tille pushed new tag debian/3.1.2+dfsg-9 at Debian Med / libhmsbeagle -- View it on GitLab: https://salsa.debian.org/med-team/libhmsbeagle/-/tree/debian/3.1.2+dfsg-9 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/libhmsbeagle][master] 6 commits: routine-update: Standards-Version: 4.5.1
Andreas Tille pushed to branch master at Debian Med / libhmsbeagle Commits: 42ddb4b7 by Andreas Tille at 2020-12-06T08:22:29+01:00 routine-update: Standards-Version: 4.5.1 - - - - - 1879245a by Andreas Tille at 2020-12-06T08:22:29+01:00 routine-update: debhelper-compat 13 - - - - - ef9d0186 by Andreas Tille at 2020-12-06T08:22:39+01:00 Set upstream metadata fields: Repository, Repository-Browse. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - c389a263 by Andreas Tille at 2020-12-06T12:03:32+01:00 iInstall all *.a files and remove *.la files from debian/tmp - - - - - 261b1d0c by Andreas Tille at 2020-12-06T16:53:06+01:00 Add missing stdlib.h - - - - - 4642e118 by Andreas Tille at 2020-12-06T16:57:54+01:00 Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/control - debian/libhmsbeagle-dev.install - + debian/patches/fix-976567.patch - debian/patches/series - debian/rules - debian/upstream/metadata Changes: = debian/changelog = @@ -1,3 +1,14 @@ +libhmsbeagle (3.1.2+dfsg-9) unstable; urgency=medium + + * Standards-Version: 4.5.1 (routine-update) + * debhelper-compat 13 (routine-update) + * Set upstream metadata fields: Repository, Repository-Browse. + * Install all *.a files and remove *.la files from debian/tmp + * Add missing stdlib.h +Closes: #976567 + + -- Andreas Tille Sun, 06 Dec 2020 16:53:18 +0100 + libhmsbeagle (3.1.2+dfsg-8) unstable; urgency=medium * libhmsbeagle1v5: Architecture: linux-any = debian/control = @@ -4,7 +4,7 @@ Uploaders: Tim Booth , Andreas Tille Section: libs Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), doxygen, graphviz, javahelper, @@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 12), ocl-icd-opencl-dev | opencl-dev, pocl-opencl-icd [amd64] | opencl-icd [amd64], clinfo -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/libhmsbeagle Vcs-Git: https://salsa.debian.org/med-team/libhmsbeagle.git Homepage: https://github.com/beagle-dev/beagle-lib = debian/libhmsbeagle-dev.install = @@ -5,3 +5,5 @@ usr/lib/*/lib*-cpu*.a usr/lib/*/libhmsbeagle.a usr/lib/*/libhmsbeagle.so usr/lib/*/libhmsbeagle-opencl.so +usr/lib/*/lib*jni.a +usr/lib/*/lib*opencl.a = debian/patches/fix-976567.patch = @@ -0,0 +1,16 @@ +Author: Andreas Tille +peter green +Last-Update: Sun, 06 Dec 2020 08:22:29 +0100 +Bug-Debian: https://bugs.debian.org/976567 +Description: Add missing stdlib.h + +--- a/libhmsbeagle/GPU/GPUInterface.h b/libhmsbeagle/GPU/GPUInterface.h +@@ -27,6 +27,7 @@ + #define __GPUInterface__ + + #include ++#include + + #ifdef HAVE_CONFIG_H + #include "libhmsbeagle/config.h" = debian/patches/series = @@ -3,3 +3,4 @@ enable_static.patch gcc-4.7.patch doxygen_update.patch fix-922776.patch +fix-976567.patch = debian/rules = @@ -31,6 +31,10 @@ override_dh_auto_clean: rm -rf doc .config configure rm -rf lib build +override_dh_install: + dh_install + find debian -name "lib*.la" -delete + override_dh_installdocs: dh_installdocs find debian/$(DEB_SOURCE)-dev -name jquery.js -delete = debian/upstream/metadata = @@ -21,3 +21,5 @@ Registry: Entry: beagle-lib Bug-Database: https://github.com/beagle-dev/beagle-lib/issues Bug-Submit: https://github.com/beagle-dev/beagle-lib/issues/new +Repository: https://github.com/beagle-dev/beagle-lib.git +Repository-Browse: https://github.com/beagle-dev/beagle-lib View it on GitLab: https://salsa.debian.org/med-team/libhmsbeagle/-/compare/ea519a8a86799158f20d6f929cd9c4b5298605bf...4642e1181e366fd67db4eaf0210522b03b4d7d85 -- View it on GitLab: https://salsa.debian.org/med-team/libhmsbeagle/-/compare/ea519a8a86799158f20d6f929cd9c4b5298605bf...4642e1181e366fd67db4eaf0210522b03b4d7d85 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/conda-package-handling][master] 4 commits: Extend datetime to Dec 1, 2021 in test_secure_refusal_to_extract_abs_paths to...
Nilesh Patra pushed to branch master at Debian Med / conda-package-handling
Commits:
79478bf4 by Nilesh Patra at 2020-12-06T20:59:12+05:30
Extend datetime to Dec 1, 2021 in test_secure_refusal_to_extract_abs_paths to
prevent failing tests in arm64.
- - - - -
009f85f1 by Nilesh Patra at 2020-12-06T20:59:34+05:30
routine-update: Standards-Version: 4.5.1
- - - - -
75ec3e12 by Nilesh Patra at 2020-12-06T20:59:38+05:30
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
753c6820 by Nilesh Patra at 2020-12-06T20:59:39+05:30
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/extend-test-datetime-to-dec-2021.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,13 @@
+conda-package-handling (1.7.2-2) unstable; urgency=medium
+
+ * Team upload.
+ * Extend datetime to Dec 1, 2021 in api test
+to prevent failing tests in arm64. (Closes: #976506)
+ * Standards-Version: 4.5.1 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+
+ -- Nilesh Patra Sun, 06 Dec 2020 20:59:39 +0530
+
conda-package-handling (1.7.2-1) unstable; urgency=medium
* Team upload.
=
debian/control
=
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest ,
python3-tqdm ,
python3-pytest-mock ,
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/conda-package-handling
Vcs-Git: https://salsa.debian.org/med-team/conda-package-handling.git
Homepage: https://github.com/conda/conda-package-handling
=
debian/patches/extend-test-datetime-to-dec-2021.patch
=
@@ -0,0 +1,17 @@
+Description: Extend datetime to Dec 1, 2021 in
test_secure_refusal_to_extract_abs_paths to prevent failing tests in arm64.
+Upstream has confirmed this here:
https://github.com/conda/conda-package-handling/issues/74#issuecomment-739349646
+Author: Nilesh Patra
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=976506
+Forwarded: https://github.com/conda/conda-package-handling/pull/75
+Last-Update: 2020-12-06
+--- a/tests/test_api.py
b/tests/test_api.py
+@@ -183,7 +183,7 @@
+ assert stat.st_nlink == 1
+
+
+-@pytest.mark.skipif(datetime.now() <= datetime(2020, 12, 1), reason="Don't
understand why this doesn't behave. Punt.")
++@pytest.mark.skipif(datetime.now() <= datetime(2021, 12, 1), reason="Don't
understand why this doesn't behave. Punt.")
+ def test_secure_refusal_to_extract_abs_paths(testing_workdir):
+ with tarfile.open('pinkie.tar.bz2', 'w:bz2') as tf:
+ open('thebrain', 'w').close()
=
debian/patches/series
=
@@ -1,3 +1,4 @@
fix_linking.patch
fix_test.patch
fix-out-dir.patch
+extend-test-datetime-to-dec-2021.patch
View it on GitLab:
https://salsa.debian.org/med-team/conda-package-handling/-/compare/507541229d44626e1f9cf2f253a20617641ae376...753c68206a21e611b0ed046b26ee36422e729154
--
View it on GitLab:
https://salsa.debian.org/med-team/conda-package-handling/-/compare/507541229d44626e1f9cf2f253a20617641ae376...753c68206a21e611b0ed046b26ee36422e729154
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[med-svn] [Git][med-team/conda-package-handling] Pushed new tag debian/1.7.2-2
Nilesh Patra pushed new tag debian/1.7.2-2 at Debian Med / conda-package-handling -- View it on GitLab: https://salsa.debian.org/med-team/conda-package-handling/-/tree/debian/1.7.2-2 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/muscle][master] Update metadata - update d/u/metadata bio.tools
Steffen Möller pushed to branch master at Debian Med / muscle Commits: c4e2ef14 by Steffen Möller at 2020-12-06T15:29:52+00:00 Update metadata - update d/u/metadata bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata = @@ -28,7 +28,7 @@ Registry: - Name: OMICtools Entry: OMICS_00982 - Name: bio.tools - Entry: MUSCLE + Entry: muscle - Name: SciCrunch Entry: SCR_011812 - Name: conda:bioconda View it on GitLab: https://salsa.debian.org/med-team/muscle/-/commit/c4e2ef14496f8f238e532dd4c1b0434339baaac8 -- View it on GitLab: https://salsa.debian.org/med-team/muscle/-/commit/c4e2ef14496f8f238e532dd4c1b0434339baaac8 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-biopython] Pushed new tag debian/1.78+dfsg-4
Étienne Mollier pushed new tag debian/1.78+dfsg-4 at Debian Med / python-biopython -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/tree/debian/1.78+dfsg-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/python-biopython] Deleted tag debian/1.78+dfsg-4
Étienne Mollier deleted tag debian/1.78+dfsg-4 at Debian Med / python-biopython -- 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-biopython][master] bump dssp dependency to v 4.0.0
Étienne Mollier pushed to branch master at Debian Med / python-biopython Commits: b7479c88 by Étienne Mollier at 2020-12-06T15:41:30+01:00 bump dssp dependency to v 4.0.0 - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -2,6 +2,7 @@ python-biopython (1.78+dfsg-4) unstable; urgency=medium * Add mkdssp4.patch. (Closes: #976542) * Standards-Version: 4.5.1 (routine-update) + * Bump dependency on dssp version 4.0.0. -- Étienne Mollier Sat, 05 Dec 2020 23:32:40 +0100 = debian/control = @@ -19,7 +19,7 @@ Build-Depends: debhelper-compat (= 13), clustalo , clustalw , dialign , - dssp , + dssp (>= 4.0.0) , emboss , fasttree , mafft , @@ -64,7 +64,7 @@ Suggests: python3-tk, clustalo, clustalw, dialign, - dssp, + dssp (>= 4.0.0), emboss, fasttree, mafft, View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/b7479c88710121e06b66d443f1f04eface536e46 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/b7479c88710121e06b66d443f1f04eface536e46 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/6.0.25+dfsg
Nilesh Patra pushed new tag upstream/6.0.25+dfsg at Debian Med / proteinortho -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/tree/upstream/6.0.25+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/6.0.25+dfsg-1
Nilesh Patra pushed new tag debian/6.0.25+dfsg-1 at Debian Med / proteinortho -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/tree/debian/6.0.25+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][pristine-tar] pristine-tar data for proteinortho_6.0.25+dfsg.orig.tar.xz
Nilesh Patra pushed to branch pristine-tar at Debian Med / proteinortho Commits: 6c4385c7 by Nilesh Patra at 2020-12-06T20:06:14+05:30 pristine-tar data for proteinortho_6.0.25+dfsg.orig.tar.xz - - - - - 2 changed files: - + proteinortho_6.0.25+dfsg.orig.tar.xz.delta - + proteinortho_6.0.25+dfsg.orig.tar.xz.id Changes: = proteinortho_6.0.25+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/proteinortho_6.0.25+dfsg.orig.tar.xz.delta differ = proteinortho_6.0.25+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +b1d6e550b4e3c08bd9944dc85a22c2e619316408 View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/6c4385c775b958c0e3f12db768fe5deecb031fe9 -- View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/6c4385c775b958c0e3f12db768fe5deecb031fe9 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/plast] Deleted branch simde
Nilesh Patra deleted branch simde at Debian Med / plast -- 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/plast][master] 4 commits: Search binary in obj-* dir to test across all arches
Nilesh Patra pushed to branch master at Debian Med / plast
Commits:
ace8a88a by Nilesh Patra at 2020-12-06T14:46:47+05:30
Search binary in obj-* dir to test across all arches
- - - - -
c01d89a8 by Nilesh Patra at 2020-12-06T09:33:25+00:00
Test only on binary:any package
- - - - -
01856c0d by Nilesh Patra at 2020-12-06T09:38:18+00:00
DEP3
- - - - -
4ec11946 by Nilesh Patra at 2020-12-06T15:13:43+05:30
Update changelog
- - - - -
4 changed files:
- debian/changelog
- debian/patches/adapt_auto_test_script.sh
- debian/patches/simde.patch
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+plast (2.3.2+dfsg-6) unstable; urgency=medium
+
+ * Team Upload.
+ * Search binary in obj-* dir to test across all arches
+ * Test only on binary:any package
+ * DEP3
+
+ -- Nilesh Patra Sun, 06 Dec 2020 15:13:01 +0530
+
plast (2.3.2+dfsg-5) unstable; urgency=medium
* Team Upload.
=
debian/patches/adapt_auto_test_script.sh
=
@@ -12,7 +12,7 @@ Description: Adapt test script to Debian installation
-_result=$_scripts_dir/out.txt
+BUILD_DIR=obj-$(dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DATA_DIR=$(pwd)/db
-+_script=`find $(pwd)/obj-*-linux-gnu/bin -name plast -executable`
++_script=`find $(pwd)/obj-*/bin -name plast -executable`
+_result=`dirname $_script`/out.txt
echo
=
debian/patches/simde.patch
=
@@ -1,3 +1,7 @@
+Description: Use simde for wider portability
+Author: Nilesh Patra
+Forwarded: https://github.com/PLAST-software/plast-library/pull/8
+Last-Update: 2020-12-06
--- a/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp
+++ b/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp
@@ -19,15 +19,8 @@
=
debian/rules
=
@@ -26,10 +26,11 @@ override_dh_auto_build-indep:
override_dh_auto_install-indep:
echo "I: Nothing to do for arch:indep binary"
-override_dh_gencontrol:
+override_dh_gencontrol-arch:
dh_gencontrol -- -Vsimde:Built-Using="$(shell dpkg-query -f
'$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")"
-override_dh_auto_test:
+override_dh_auto_test-indep:
+override_dh_auto_test-arch:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
scripts/test-plast.sh
endif
View it on GitLab:
https://salsa.debian.org/med-team/plast/-/compare/c0faba8d72195c9998fc6b458cae8b12ced2d2f0...4ec11946eea5b8649ca8be2fb2764b87793e1ac3
--
View it on GitLab:
https://salsa.debian.org/med-team/plast/-/compare/c0faba8d72195c9998fc6b458cae8b12ced2d2f0...4ec11946eea5b8649ca8be2fb2764b87793e1ac3
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[med-svn] [Git][med-team/plast] Pushed new tag debian/2.3.2+dfsg-6
Nilesh Patra pushed new tag debian/2.3.2+dfsg-6 at Debian Med / plast -- View it on GitLab: https://salsa.debian.org/med-team/plast/-/tree/debian/2.3.2+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
