[med-svn] [Git][med-team/libzstd][master] 6 commits: New upstream version 1.3.4+dfsg

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: b02a2aa7 by Alexandre Mestiashvili at 2018-04-03T09:29:57+00:00 New upstream version 1.3.4+dfsg - - - - - 075c405a by Alexandre Mestiashvili at 2018-04-03T09:30:00+00:00 Update upstream source from tag 'ups

[med-svn] [Git][med-team/libzstd][pristine-tar] pristine-tar data for libzstd_1.3.4+dfsg.orig.tar.xz

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / libzstd Commits: 4f7e3826 by Alexandre Mestiashvili at 2018-04-03T09:30:00+00:00 pristine-tar data for libzstd_1.3.4+dfsg.orig.tar.xz - - - - - 2 changed files: - + libzstd_1.3.4+dfsg.orig.tar.xz.delta - + libzstd_1.3.4

[med-svn] [Git][med-team/libzstd][upstream] New upstream version 1.3.4+dfsg

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch upstream at Debian Med / libzstd Commits: b02a2aa7 by Alexandre Mestiashvili at 2018-04-03T09:29:57+00:00 New upstream version 1.3.4+dfsg - - - - - 30 changed files: - Makefile - NEWS - README.md - + contrib/adaptive-compression/.gitignore - contrib

[med-svn] [Git][med-team/libzstd][master] 3 commits: Remove indexes from patches

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: fcad1da1 by Alexandre Mestiashvili at 2018-04-03T13:14:11+02:00 Remove indexes from patches - - - - - 6f4685aa by Alexandre Mestiashvili at 2018-04-03T13:33:40+02:00 Remove Multi-Arch field from -udeb section

[med-svn] [Git][med-team/libzstd] Pushed new tag upstream/1.3.4+dfsg

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.3.4+dfsg at Debian Med / libzstd --- View it on GitLab: https://salsa.debian.org/med-team/libzstd/tree/upstream/1.3.4+dfsg You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/libzstd] Pushed new tag debian/1.3.4+dfsg-1

2018-04-03 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.3.4+dfsg-1 at Debian Med / libzstd --- View it on GitLab: https://salsa.debian.org/med-team/libzstd/tree/debian/1.3.4+dfsg-1 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/subread][upstream] New upstream version 1.6.1+dfsg

2018-04-04 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch upstream at Debian Med / subread Commits: 9c61fb61 by Alexandre Mestiashvili at 2018-04-04T16:50:35+00:00 New upstream version 1.6.1+dfsg - - - - - 18 changed files: - doc/SubreadUsersGuide.tex - src/HelperFunctions.c - src/Makefile.FreeBSD - src

[med-svn] [Git][med-team/subread][master] 6 commits: New upstream version 1.6.1+dfsg

2018-04-04 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / subread Commits: 9c61fb61 by Alexandre Mestiashvili at 2018-04-04T16:50:35+00:00 New upstream version 1.6.1+dfsg - - - - - 6cf49bb5 by Alexandre Mestiashvili at 2018-04-04T16:51:19+00:00 Update upstream source from tag 'ups

[med-svn] [Git][med-team/subread][pristine-tar] pristine-tar data for subread_1.6.1+dfsg.orig.tar.xz

2018-04-04 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / subread Commits: bcb87575 by Alexandre Mestiashvili at 2018-04-04T16:51:19+00:00 pristine-tar data for subread_1.6.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + subread_1.6.1+dfsg.orig.tar.xz.delta - + subread_1.6.1

[med-svn] [Git][med-team/subread] Pushed new tag debian/1.6.1+dfsg-1

2018-04-04 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.6.1+dfsg-1 at Debian Med / subread --- View it on GitLab: https://salsa.debian.org/med-team/subread/tree/debian/1.6.1+dfsg-1 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/subread] Pushed new tag upstream/1.6.1+dfsg

2018-04-04 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.6.1+dfsg at Debian Med / subread --- View it on GitLab: https://salsa.debian.org/med-team/subread/tree/upstream/1.6.1+dfsg You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/plip][pristine-tar] pristine-tar data for plip_1.4.0~b+dfsg.orig.tar.xz

2018-04-12 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / plip Commits: b47c2282 by Alexandre Mestiashvili at 2018-04-12T12:05:48+02:00 pristine-tar data for plip_1.4.0~b+dfsg.orig.tar.xz - - - - - 2 changed files: - + plip_1.4.0~b+dfsg.orig.tar.xz.delta - + plip_1.4.0~b

[med-svn] [Git][med-team/plip] Pushed new tag debian/1.4.0_b+dfsg-1

2018-04-12 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.4.0_b+dfsg-1 at Debian Med / plip --- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/debian/1.4.0_b+dfsg-1 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/plip] Pushed new tag upstream/1.4.0_b+dfsg

2018-04-12 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.4.0_b+dfsg at Debian Med / plip --- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/upstream/1.4.0_b+dfsg You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/libzstd][master] 2 commits: Apply patch from Helmut Grohne fixing cross build failure

2018-04-17 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: 7b7d9320 by Alexandre Mestiashvili at 2018-04-17T17:06:04+02:00 Apply patch from Helmut Grohne fixing cross build failure - - - - - 1b564a40 by Alexandre Mestiashvili at 2018-04-17T17:09:09+02:00 Update changelog

[med-svn] [Git][med-team/libzstd][master] Update d/rules, use dh_auto_clean instead of make

2018-04-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: e9974316 by Alexandre Mestiashvili at 2018-04-18T16:51:24+02:00 Update d/rules, use dh_auto_clean instead of make - - - - - 1 changed file: - debian/rules Changes: = debian

[med-svn] [Git][med-team/fasta3][master] 3 commits: Add zlib1g-dev to Build-Depends

2018-04-19 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / fasta3 Commits: 0ddc6997 by Alexandre Mestiashvili at 2018-04-19T11:40:11+02:00 Add zlib1g-dev to Build-Depends - - - - - dc5e2b83 by Alexandre Mestiashvili at 2018-04-19T11:48:56+02:00 Apply cme fix dpkg, fixing indentation, secure

[med-svn] [Git][med-team/libzstd][master] Properly close bug #895925

2018-04-20 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: 8159ace9 by Alexandre Mestiashvili at 2018-04-20T17:26:27+02:00 Properly close bug #895925 - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/libzstd][master] Update d/copyright, starting from 1.3.1 patent claim is removed

2018-04-24 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: 2599a626 by Alexandre Mestiashvili at 2018-04-24T11:19:03+02:00 Update d/copyright, starting from 1.3.1 patent claim is removed - - - - - 1 changed file: - debian/copyright Changes

[med-svn] [Git][med-team/libzstd][master] 2 commits: Add comments to unstable symbols in d/libzstd1.symbols

2018-04-25 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: 4da28ab6 by Alexandre Mestiashvili at 2018-04-25T10:39:13+02:00 Add comments to unstable symbols in d/libzstd1.symbols - - - - - 07194aec by Alexandre Mestiashvili at 2018-04-25T10:40:33+02:00 Update changelog Gbp

[med-svn] [Git][med-team/plip][pristine-tar] pristine-tar data for plip_1.4.1+dfsg.orig.tar.xz

2018-04-26 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / plip Commits: f56bc7ea by Alexandre Mestiashvili at 2018-04-26T15:27:57+02:00 pristine-tar data for plip_1.4.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + plip_1.4.1+dfsg.orig.tar.xz.delta - + plip_1.4.1

[med-svn] [Git][med-team/plip] Pushed new tag debian/1.4.1+dfsg-1

2018-04-27 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.4.1+dfsg-1 at Debian Med / plip --- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/debian/1.4.1+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ d

[med-svn] [Git][med-team/plip] Pushed new tag upstream/1.4.1+dfsg

2018-04-27 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.4.1+dfsg at Debian Med / plip --- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/upstream/1.4.1+dfsg You're receiving this email because of your account on salsa.debian.org. ___ d

[med-svn] [Git][med-team/libzstd][master] Upload to unstable

2018-04-27 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: f951eaf1 by Alexandre Mestiashvili at 2018-04-27T10:16:05+02:00 Upload to unstable - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/libzstd] Pushed new tag debian/1.3.4+dfsg-1

2018-04-27 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.3.4+dfsg-1 at Debian Med / libzstd --- View it on GitLab: https://salsa.debian.org/med-team/libzstd/tree/debian/1.3.4+dfsg-1 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/libzstd][master] 5 commits: Add patch making build reproducible, Closes: #897904

2018-05-09 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: 7f162afc by Alexandre Mestiashvili at 2018-05-09T10:55:19+02:00 Add patch making build reproducible, Closes: #897904 - - - - - 17470bc9 by Alexandre Mestiashvili at 2018-05-09T11:03:08+02:00 Update patch skipping

[med-svn] [Git][med-team/libzstd] Pushed new tag debian/1.3.4+dfsg-3

2018-05-09 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.3.4+dfsg-3 at Debian Med / libzstd --- View it on GitLab: https://salsa.debian.org/med-team/libzstd/tree/debian/1.3.4+dfsg-3 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/libzstd][master] Add attribuition for the patch

2018-05-09 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: e6a1b912 by Alexandre Mestiashvili at 2018-05-09T19:27:40+02:00 Add attribuition for the patch - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/subread][master] 9 commits: New upstream version 1.6.2+dfsg

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / subread Commits: b354f0db by Alexandre Mestiashvili at 2018-05-18T18:12:20+02:00 New upstream version 1.6.2+dfsg - - - - - ce4b7129 by Alexandre Mestiashvili at 2018-05-18T18:13:26+02:00 Update upstream source from tag 'ups

[med-svn] [Git][med-team/subread][upstream] New upstream version 1.6.2+dfsg

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch upstream at Debian Med / subread Commits: b354f0db by Alexandre Mestiashvili at 2018-05-18T18:12:20+02:00 New upstream version 1.6.2+dfsg - - - - - 16 changed files: - doc/SubreadUsersGuide.tex - src/HelperFunctions.c - src/HelperFunctions.h - src

[med-svn] [Git][med-team/subread][pristine-tar] pristine-tar data for subread_1.6.2+dfsg.orig.tar.xz

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / subread Commits: 58604ecc by Alexandre Mestiashvili at 2018-05-18T18:13:26+02:00 pristine-tar data for subread_1.6.2+dfsg.orig.tar.xz - - - - - 2 changed files: - + subread_1.6.2+dfsg.orig.tar.xz.delta - + subread_1.6.2

[med-svn] [Git][med-team/subread] Pushed new tag upstream/1.6.2+dfsg

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.6.2+dfsg at Debian Med / subread --- View it on GitLab: https://salsa.debian.org/med-team/subread/tree/upstream/1.6.2+dfsg You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/subread] Pushed new tag debian/1.6.2+dfsg-1

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.6.2+dfsg-1 at Debian Med / subread --- View it on GitLab: https://salsa.debian.org/med-team/subread/tree/debian/1.6.2+dfsg-1 You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/libzstd][master] Fix varying number of threads in pzstd man page, making build reproducible

2018-05-18 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / libzstd Commits: e1f30233 by Alexandre Mestiashvili at 2018-05-18T21:47:16+02:00 Fix varying number of threads in pzstd man page, making build reproducible - - - - - 1 changed file: - debian/rules Changes

[med-svn] [Git][med-team/pyscanfcs][master] 13 commits: Bump policy 4.1.4, update VCS-* fields to salsa

2018-05-31 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / pyscanfcs Commits: cf68bc18 by Alexandre Mestiashvili at 2018-05-31T10:40:17+02:00 Bump policy 4.1.4, update VCS-* fields to salsa - - - - - 46e80f2f by Alexandre Mestiashvili at 2018-05-31T10:44:25+02:00 Update Files-Excluded list

[med-svn] [Git][med-team/transtermhp][master] 4 commits: Apply cme fix dpkg, bump Policy to 4.1.4, fix VCS-* fields, use https

2018-05-31 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / transtermhp Commits: 6efba8b1 by Alexandre Mestiashvili at 2018-05-31T20:00:20+02:00 Apply cme fix dpkg, bump Policy to 4.1.4, fix VCS-* fields, use https - - - - - 5f5de498 by Alexandre Mestiashvili at 2018-05-31T20:11:34+02:00

[med-svn] [Git][med-team/transtermhp] Pushed new tag debian/2.09-4

2018-06-01 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/2.09-4 at Debian Med / transtermhp -- View it on GitLab: https://salsa.debian.org/med-team/transtermhp/tree/debian/2.09-4 You're receiving this email because of your account on salsa.debian.org. ___ d

[med-svn] [Git][med-team/plip][pristine-tar] pristine-tar data for plip_1.4.2+dfsg.orig.tar.xz

2018-06-08 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / plip Commits: dce20f7a by Alexandre Mestiashvili at 2018-06-07T20:04:11+02:00 pristine-tar data for plip_1.4.2+dfsg.orig.tar.xz - - - - - 2 changed files: - + plip_1.4.2+dfsg.orig.tar.xz.delta - + plip_1.4.2

[med-svn] [Git][med-team/plip] Pushed new tag debian/1.4.2+dfsg-1

2018-06-08 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag debian/1.4.2+dfsg-1 at Debian Med / plip -- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/debian/1.4.2+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ d

[med-svn] [Git][med-team/plip] Pushed new tag upstream/1.4.2+dfsg

2018-06-08 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.4.2+dfsg at Debian Med / plip -- View it on GitLab: https://salsa.debian.org/med-team/plip/tree/upstream/1.4.2+dfsg You're receiving this email because of your account on salsa.debian.org. ___ d

[med-svn] [Git][med-team/pycorrfit] Pushed new tag upstream/1.1.1+dfsg

2018-06-14 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed new tag upstream/1.1.1+dfsg at Debian Med / pycorrfit -- View it on GitLab: https://salsa.debian.org/med-team/pycorrfit/tree/upstream/1.1.1+dfsg You're receiving this email because of your account on salsa.debia

[med-svn] [Git][med-team/pycorrfit][master] 12 commits: Update Files-Excluded, add .readthedocs.yml to the list

2018-06-14 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / pycorrfit Commits: 49ccda18 by Alexandre Mestiashvili at 2018-06-13T14:25:53+02:00 Update Files-Excluded, add .readthedocs.yml to the list - - - - - 78ef6455 by Alexandre Mestiashvili at 2018-06-13T14:26:33+02:00 Bump policy to

[med-svn] [Git][med-team/pycorrfit][pristine-tar] pristine-tar data for pycorrfit_1.1.1+dfsg.orig.tar.gz

2018-06-14 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch pristine-tar at Debian Med / pycorrfit Commits: 9b6868ba by Alexandre Mestiashvili at 2018-06-13T14:27:03+02:00 pristine-tar data for pycorrfit_1.1.1+dfsg.orig.tar.gz - - - - - 2 changed files: - + pycorrfit_1.1.1+dfsg.orig.tar.gz.delta

[med-svn] [Git][med-team/pycorrfit][upstream] New upstream version 1.1.1+dfsg

2018-06-14 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch upstream at Debian Med / pycorrfit Commits: 2dfb3b2e by Alexandre Mestiashvili at 2018-06-13T14:26:57+02:00 New upstream version 1.1.1+dfsg - - - - - 30 changed files: - + CHANGELOG - ChangeLog.txt - MANIFEST.in - README.rst - + docs/README.md - + docs

[med-svn] [Git][med-team/gmap][master] Update d/rules, remove find needed for debugging

2018-07-17 Thread Alexandre Mestiashvili
Alexandre Mestiashvili pushed to branch master at Debian Med / gmap Commits: ecd23f09 by Alexandre Mestiashvili at 2018-07-17T18:29:47+02:00 Update d/rules, remove find needed for debugging - - - - - 1 changed file: - debian/rules Changes: = debian

[med-svn] [SCM] bowtie2 branch, master, created. b3d919be41c7309e37ab9b5d1ea0f07b9ec23ec1

2012-02-21 Thread Alexandre Mestiashvili
The branch, master has been created at b3d919be41c7309e37ab9b5d1ea0f07b9ec23ec1 (commit) - Shortlog commit b3d919be41c7309e37ab9b5d1ea0f07b9ec23ec1 Author: Alexandre Mestiashvili Date: Tue Feb 21 18:10:56 2012 +0100

[med-svn] [SCM] bowtie2 branch, upstream, created. 4b732fc3aa3fa95ee87904aff06325a38a804fb6

2012-02-21 Thread Alexandre Mestiashvili
The branch, upstream has been created at 4b732fc3aa3fa95ee87904aff06325a38a804fb6 (commit) - Shortlog --- -- ultrafast memory-efficient short read aligner __

[med-svn] [SCM] bowtie2 branch, pristine-tar, created. c9b3332baf6cefab6db53a379e0e3a6ad70278f2

2012-02-21 Thread Alexandre Mestiashvili
The branch, pristine-tar has been created at c9b3332baf6cefab6db53a379e0e3a6ad70278f2 (commit) - Shortlog commit c9b3332baf6cefab6db53a379e0e3a6ad70278f2 Author: Alexandre Mestiashvili Date: Tue Feb 21 15:13:13 2012 +

[med-svn] [SCM] bowtie2 annotated tag, upstream/2.0.0-beta5, created. upstream/2.0.0-beta5

2012-02-21 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0-beta5 has been created at 4c2fdc061c6f33b05c9e9237177155f97cc87fb0 (tag) tagging 4b732fc3aa3fa95ee87904aff06325a38a804fb6 (commit) tagged by Alexandre Mestiashvili on Tue Feb 21 15:13:14 2012 + - Shortlog

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-3-g4cbe5c0

2012-02-21 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 4cbe5c0bcda26d66da8fc5a4b77654701ef32de6 Author: Alexandre Mestiashvili Date: Tue Feb 21 18:52:00 2012 +0100 set to UNRELEASED, debian/rules help2man for missing man pages diff --git a/debian/bowtie2.dirs b/debian/bowtie2

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

2012-02-22 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 99c8c05231df67ccb037cc6e75a3dd7aee0ca53b Merge: 1c63e02dccb400fd7cc8e61c4e8783950aafa036 c7c402a1f85d7a9d9726c869dfb0ac36ef594360 Author: Alexandre Mestiashvili Date: Wed Feb 22 11:01:53 2012 +0100 Merge branch 'maste

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

2012-02-22 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 5cc8819596b0a92dd5ba16623f5e69740d37ecaf Author: Alexandre Mestiashvili Date: Wed Feb 22 11:15:52 2012 +0100 NEWS removed from bowtie2.docs and used as Upstream's changelog diff --git a/debian/bowtie2.docs b/debian/bo

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

2012-02-22 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 1c63e02dccb400fd7cc8e61c4e8783950aafa036 Author: Alexandre Mestiashvili Date: Wed Feb 22 08:42:40 2012 +0100 Fixed minor linitan complains , added ls.h to debain/copyright License is GPL3 and not GPL2. Added manual

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

2012-02-22 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 2e113a6bcb544bd8c0355042a2a4124125602cee Author: Alexandre Mestiashvili Date: Wed Feb 22 11:22:45 2012 +0100 Added debian/upstream diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 000..c46ccf9

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-9-g794bafa

2012-02-22 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 794bafae716cb47616d750a321585ebaf497565d Author: Alexandre Mestiashvili Date: Wed Feb 22 12:35:04 2012 +0100 debian/rules using commit of Andreas diff --git a/debian/rules b/debian/rules index 559fce6..2f74e57 100755 --- a

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-12-g6ecb1b2

2012-03-10 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 6ecb1b218db9a353f4d71f9f80f80f0eb3a7ed0e Author: Alexandre Mestiashvili Date: Sat Mar 10 20:58:14 2012 +0100 added information about sse_util.h with mising license statement patch to disable unknown flags for certain

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-13-gfc9cd68

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 8fda61551c53650a8fddb1ae76fcc15056663710 Merge: d8c3c758a2ec1badb986b3f77aba2c5e45827035 747fa7b771bc17cc627fddde0737ffd1d5d10c6f Author: Alexandre Mestiashvili Date: Sat Apr 14 10:12:40 2012 +0200 Merge tag 'upstream/

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-13-gfc9cd68

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 45c55eba4f5486191184aeaf21e6c16c9b34b725 Author: Alexandre Mestiashvili Date: Sat Apr 14 10:41:37 2012 +0200 updated debian/patches updated debian/changelog diff --git a/debian/changelog b/debian/changelog index 3ce9c42

[med-svn] [SCM] tophat branch, pristine-tar, updated. 9054e5e332922ec0b025feca0529436a00a5115e

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the pristine-tar branch: commit 9054e5e332922ec0b025feca0529436a00a5115e Author: Alexandre Mestiashvili Date: Sat Apr 14 10:12:40 2012 +0200 pristine-tar data for tophat_2.0.0.orig.tar.gz diff --git a/tophat_2.0.0.orig.tar.gz.delta b/tophat_2.0.0

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-13-gfc9cd68

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit fc9cd68bea90178a2b2e44d505f48e4b0e77a2d9 Author: Alexandre Mestiashvili Date: Sat Apr 14 11:20:51 2012 +0200 debian/control added libboost-thread-dev dependency Suggests: bowtie2 diff --git a/debian/control b/debian

[med-svn] [SCM] tophat annotated tag, upstream/2.0.0, created. upstream/2.0.0

2012-04-14 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0 has been created at 24044d215254ef6f7673cfce4ac3664d4d4b3b74 (tag) tagging 747fa7b771bc17cc627fddde0737ffd1d5d10c6f (commit) replaces upstream/1.4.1 tagged by Alexandre Mestiashvili on Sat Apr 14 10:12:40 2012 +0200 - Shortlog

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-14-g1ebd078

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 1ebd0789996a9eb1d9c576039ad2a433522058bb Author: Alexandre Mestiashvili Date: Sat Apr 14 11:52:34 2012 +0200 debian/control Standards-Version: 3.9.3 Depends: bowtie2 debian/copyright updated Format, removed seqan

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-15-g8a94679

2012-04-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 8a94679e5edd27fa72308d20d161a774c6e374f5 Author: Alexandre Mestiashvili Date: Sat Apr 14 12:45:45 2012 +0200 debian/get-orig-source - removes shipped with tophat SeqAn files. diff --git a/debian/changelog b/debian/changelog

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

2012-05-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 63de8d6638c5c54675387b2e96a46b8351436639 Author: Alexandre Mestiashvili Date: Wed May 9 14:07:27 2012 +0200 uname -m doesn't detect 32 bit chroot env diff --git a/debian/patches/fix_makefile_machine_detection.pat

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

2012-05-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit bc61822d516c2ca19e74ed47e0e76dd20bb05ab3 Author: Alexandre Mestiashvili Date: Wed May 9 14:22:08 2012 +0200 fixed too-long line in changelog, added versioned URI format for copyright removed bug close statement (not sure

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

2012-05-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 2f459ff23e4544f9fd469c9b51b7d390221dcabd Author: Alexandre Mestiashvili Date: Wed May 9 14:47:46 2012 +0200 updated changelog to reflect git changes diff --git a/debian/changelog b/debian/changelog index 8d6ee53..756a464

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

2012-05-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit d374b906850002f364610c535789e2bc85b1fd12 Author: Alexandre Mestiashvili Date: Wed May 9 14:10:45 2012 +0200 added patch fixing #672090 updated DEP3 headers bumperd Standards-Version to 3.9.3 diff --git a/debian

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-22-gf8cec87

2012-05-11 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 7814d8dd094102bcd80c5dd0ef3e5254b48f70c8 Author: Alexandre Mestiashvili Date: Fri May 11 08:36:20 2012 +0200 updated debian/watch and get-orig-source to track -source suffix diff --git a/debian/get-orig-source b/debian/get

[med-svn] [SCM] bowtie2 branch, pristine-tar, updated. a0da20969cc65056a30bda55b6e3b11b281c095c

2012-05-11 Thread Alexandre Mestiashvili
The following commit has been merged in the pristine-tar branch: commit a0da20969cc65056a30bda55b6e3b11b281c095c Author: Alexandre Mestiashvili Date: Fri May 11 08:41:50 2012 +0200 pristine-tar data for bowtie2_2.0.0-beta6.orig.tar.gz diff --git a/bowtie2_2.0.0-beta6.orig.tar.gz.delta b

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-22-gf8cec87

2012-05-11 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit f8cec87fd958ee813ab2b127b099da4f233e30bf Merge: 7814d8dd094102bcd80c5dd0ef3e5254b48f70c8 98900480623909d99a6eb707422d84033401b320 Author: Alexandre Mestiashvili Date: Fri May 11 08:41:50 2012 +0200 Merge tag 'upstream/

[med-svn] [SCM] bowtie2 annotated tag, upstream/2.0.0-beta6, created. upstream/2.0.0-beta6

2012-05-11 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0-beta6 has been created at bc543a4df6196d1f4fb212cb8a255c54b3e5922f (tag) tagging 98900480623909d99a6eb707422d84033401b320 (commit) replaces upstream/2.0.0-beta5 tagged by Alexandre Mestiashvili on Fri May 11 08:41:50 2012 +0200

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-23-gfc15174

2012-05-13 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 9dd9b1985619244b609496ded13c51c4cfdebc39 Author: Alexandre Mestiashvili Date: Sat May 12 12:07:06 2012 +0200 add -msse2 only for intel architectures diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-23-gfc15174

2012-05-13 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit fc15174e3a5d23d862ad07cb8a66b9943690917c Author: Alexandre Mestiashvili Date: Sun May 13 14:01:21 2012 +0200 updated debian/changelog diff --git a/debian/changelog b/debian/changelog index 4ecd78b..ce0c0b1 100644 --- a

[med-svn] [SCM] bowtie2 tag, debian/2.0.0-beta6-1, created. upstream/2.0.0-beta6-23-gfc15174

2012-05-13 Thread Alexandre Mestiashvili
The tag, debian/2.0.0-beta6-1 has been created at fc15174e3a5d23d862ad07cb8a66b9943690917c (commit) - Shortlog commit fc15174e3a5d23d862ad07cb8a66b9943690917c Author: Alexandre Mestiashvili Date: Sun May 13 14:01:21 2012

[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-1-11-g6fa162f

2012-05-14 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 6fa162f402a4a0350fa162ae6e5f4320c9857ff5 Author: Alexandre Mestiashvili Date: Mon May 14 10:21:21 2012 +0200 Bumped Standards-Version: 3.9.3 diff --git a/debian/control b/debian/control index 259a7c5..884234a 100644 --- a

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-24-g5117c55

2012-05-31 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 5117c55213ddfda5fe2879530da0fb06e08472f1 Author: Alexandre Mestiashvili Date: Thu May 31 17:52:40 2012 +0200 normalized output of dpkg-architecture, so for example kfreebsd-amd64 is detected as an amd64 architecture

[med-svn] [SCM] bowtie2 tag, debian/2.0.0-beta6-2, created. upstream/2.0.0-beta6-24-g5117c55

2012-05-31 Thread Alexandre Mestiashvili
The tag, debian/2.0.0-beta6-2 has been created at 5117c55213ddfda5fe2879530da0fb06e08472f1 (commit) - Shortlog commit 5117c55213ddfda5fe2879530da0fb06e08472f1 Author: Alexandre Mestiashvili Date: Thu May 31 17:52:40 2012

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-26-g3318120

2012-06-01 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 0f973db67421a63cfbb864ff7ca3be738e2f1920 Author: Alexandre Mestiashvili Date: Fri Jun 1 21:36:55 2012 +0200 normalized architecture detection so for example kfreebsd-amd64 is detected as an amd64 architecture and

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-26-g3318120

2012-06-01 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 3318120c5db61abc6717f8629198fcd9f0bea05d Author: Alexandre Mestiashvili Date: Fri Jun 1 21:59:39 2012 +0200 updated changelog diff --git a/debian/changelog b/debian/changelog index 3f2c60c..da61ada 100644 --- a/debian

[med-svn] [SCM] bowtie2 tag, debian/2.0.0-beta6-3, created. upstream/2.0.0-beta6-26-g3318120

2012-06-01 Thread Alexandre Mestiashvili
The tag, debian/2.0.0-beta6-3 has been created at 3318120c5db61abc6717f8629198fcd9f0bea05d (commit) - Shortlog commit 3318120c5db61abc6717f8629198fcd9f0bea05d Author: Alexandre Mestiashvili Date: Fri Jun 1 21:59:39 2012

[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-1-gb01514b

2012-06-05 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit b01514b30354dccc6a7f43e6acc002aec9f5b64b Author: Alexandre Mestiashvili Date: Tue Jun 5 10:44:18 2012 +0200 debian/patches imported 0004-fix-m64-usage-and-lfs.patch from Ubuntu diff --git a/debian/patches/0004-fix-m64-usage

[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-10-ga2b0324

2012-06-08 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit a2b03244dce1226a91c9f1a2ee08bf2cb7dd5aec Author: Alexandre Mestiashvili Date: Sat Jun 9 08:43:14 2012 +0200 debian/changelog imported patch closes #675985 diff --git a/debian/changelog b/debian/changelog index 1aecd62

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-26-g3b790e2

2012-06-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 83c54a812cb07b7ccc4a166ed515f789b6e97b7b Merge: 9b8f8b203f50787eb66471ac34063399e577ad9b 556c8c77f9d4e5d380bb05c1fb333c40fed89f13 Author: Alexandre Mestiashvili Date: Sat Jun 9 11:06:09 2012 +0200 Merge tag 'upstream/

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-26-g3b790e2

2012-06-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 858f4330e26145ea76048e224d12dc80a8027164 Author: Alexandre Mestiashvili Date: Sat Jun 9 11:06:46 2012 +0200 tophat depends on bowtie or bowtie2 diff --git a/debian/changelog b/debian/changelog index 819b0c0..82cc7a6 100644

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-26-g3b790e2

2012-06-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 3b790e2081a927077186a31dbc8409e5d2ee476e Author: Alexandre Mestiashvili Date: Sat Jun 9 11:19:55 2012 +0200 unreleased->unstable diff --git a/debian/changelog b/debian/changelog index 82cc7a6..6564817 100644 --- a/deb

[med-svn] [SCM] tophat branch, pristine-tar, updated. 139d0320cf49e3e8bd38d5e93ec86078b3b3be84

2012-06-09 Thread Alexandre Mestiashvili
The following commit has been merged in the pristine-tar branch: commit 139d0320cf49e3e8bd38d5e93ec86078b3b3be84 Author: Alexandre Mestiashvili Date: Sat Jun 9 11:06:09 2012 +0200 pristine-tar data for tophat_2.0.3.orig.tar.gz diff --git a/tophat_2.0.3.orig.tar.gz.delta b/tophat_2.0.3

[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-26-g3b790e2

2012-06-09 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 67f4e8162b71be8a202d7aa1accee99dc0f21443 Author: Alexandre Mestiashvili Date: Sat Jun 9 11:09:49 2012 +0200 refreshed debian/patches/fix_includes_path.patch diff --git a/debian/patches/fix_includes_path.patch b/debian

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-30-gde0c32f

2012-07-03 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit e045e8b24e55af4d85410004aaf3e73b2046d976 Author: Alexandre Mestiashvili Date: Mon Jun 25 15:35:51 2012 +0200 debian/control only i386* and amd64* architecures are supported diff --git a/debian/changelog b/debian/changelog

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-30-gde0c32f

2012-07-03 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 991b8398d88a7e1c2eeec183d0306a039785dfe6 Author: Alexandre Mestiashvili Date: Mon Jul 2 16:21:25 2012 +0200 debhelper v9 diff --git a/debian/compat b/debian/compat index 45a4fb7..ec63514 100644 --- a/debian/compat +++ b

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-30-gde0c32f

2012-07-03 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit fb08d9d238035e71725939b8a3e36d9b41aa5e53 Author: Alexandre Mestiashvili Date: Mon Jul 2 16:28:05 2012 +0200 debian/rules added hardening flags diff --git a/debian/changelog b/debian/changelog index 6307548..f53825c 100644

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-30-gde0c32f

2012-07-03 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit de0c32fc6c3d0e92ce98eaafa09ed863df34b488 Author: Alexandre Mestiashvili Date: Tue Jul 3 10:23:06 2012 +0200 hardening.patch to inject hardening CPPFLAGS diff --git a/debian/changelog b/debian/changelog index f53825c

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-32-g246c7d7

2012-07-17 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit 246c7d7efaa90790f2ca04880adf2605539fc42c Merge: de0c32fc6c3d0e92ce98eaafa09ed863df34b488 da842779f3d21d2e844a3ea0bdb10f060787f607 Author: Alexandre Mestiashvili Date: Tue Jul 17 09:39:57 2012 +0200 Merge tag 'upstream/

[med-svn] [SCM] bowtie2 branch, pristine-tar, updated. 4680cc05ab62186309f8ea9f7f344bdf412d1a7f

2012-07-17 Thread Alexandre Mestiashvili
The following commit has been merged in the pristine-tar branch: commit 4680cc05ab62186309f8ea9f7f344bdf412d1a7f Author: Alexandre Mestiashvili Date: Tue Jul 17 09:39:57 2012 +0200 pristine-tar data for bowtie2_2.0.0-beta7.orig.tar.gz diff --git a/bowtie2_2.0.0-beta7.orig.tar.gz.delta b

[med-svn] [SCM] bowtie2 annotated tag, upstream/2.0.0-beta7, created. upstream/2.0.0-beta7

2012-07-17 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0-beta7 has been created at 5663db6012ceb2b7516e2dae0575ef9227601e63 (tag) tagging da842779f3d21d2e844a3ea0bdb10f060787f607 (commit) replaces upstream/2.0.0-beta6 tagged by Alexandre Mestiashvili on Tue Jul 17 09:39:57 2012 +0200

[med-svn] [SCM] bowtie2 annotated tag, upstream/2.0.0-beta7, deleted. upstream/2.0.0-beta6-1-gda84277

2012-07-30 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0-beta7 has been deleted was 5663db6012ceb2b7516e2dae0575ef9227601e63 --- tag upstream/2.0.0-beta7 Upstream version 2.0.0-beta7 da842779f3d21d2e844a3ea0bdb10f060787f607 Imported Upstream ve

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-33-gdb5e7eb

2012-07-30 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit fece62a8bf7619bb6d1e09019fed86b429ef6295 Merge: de0c32fc6c3d0e92ce98eaafa09ed863df34b488 7b518c0a4b114723c20180de160fc111c35bd577 Author: Alexandre Mestiashvili Date: Mon Jul 30 13:37:59 2012 +0200 Merge tag 'upstream/

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-33-gdb5e7eb

2012-07-30 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit db5e7eb8a1ddce5b6191163e2c80a5135fcc Author: Alexandre Mestiashvili Date: Mon Jul 30 13:53:59 2012 +0200 changelog update diff --git a/debian/changelog b/debian/changelog index 344b17e..eca3256 100644 --- a/debian

[med-svn] [SCM] bowtie2 branch, pristine-tar, updated. 3b2d29a149a660db00acc0c512ceb093a5e2d02a

2012-07-30 Thread Alexandre Mestiashvili
The following commit has been merged in the pristine-tar branch: commit 3b2d29a149a660db00acc0c512ceb093a5e2d02a Author: Alexandre Mestiashvili Date: Mon Jul 30 13:37:59 2012 +0200 pristine-tar data for bowtie2_2.0.0-beta7.orig.tar.gz diff --git a/bowtie2_2.0.0-beta7.orig.tar.gz.delta b

[med-svn] [SCM] bowtie2 annotated tag, upstream/2.0.0-beta7, created. upstream/2.0.0-beta7

2012-07-30 Thread Alexandre Mestiashvili
The annotated tag, upstream/2.0.0-beta7 has been created at d23620f90d0dccbec4a445670556b69d8a1affdf (tag) tagging 7b518c0a4b114723c20180de160fc111c35bd577 (commit) replaces upstream/2.0.0-beta6 tagged by Alexandre Mestiashvili on Mon Jul 30 13:37:59 2012 +0200

[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta7-33-gfdec80e

2012-08-03 Thread Alexandre Mestiashvili
The following commit has been merged in the master branch: commit fdec80e23ed8f8417db21aa7c6feae6f8bb68e55 Author: Alexandre Mestiashvili Date: Fri Aug 3 15:43:56 2012 +0200 overrided lintian's warning diff --git a/debian/bowtie2-examples.lintian-overrides b/debian/bo

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