[med-svn] [Git][med-team/canu] Pushed new tag debian/1.7+dfsg-1

[Afif Elghraoui]

Afif Elghraoui pushed new tag debian/1.7+dfsg-1 at Debian Med / canu

---
View it on GitLab: https://salsa.debian.org/med-team/canu/tree/debian/1.7+dfsg-1
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[med-svn] [Git][med-team/canu][master] releasing package canu version 1.7+dfsg-1

[Afif Elghraoui]

Afif Elghraoui pushed to branch master at Debian Med / canu


Commits:
52a3f22d by Afif Elghraoui at 2018-03-17T18:16:14-04:00
releasing package canu version 1.7+dfsg-1

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
-canu (1.7+dfsg-1) UNRELEASED; urgency=medium
+canu (1.7+dfsg-1) unstable; urgency=medium
 
-  * New upstream version 1.7+dfsg
+  * New upstream version
   * Update handling of mhap bundled copy
   * Refresh patches
   * Use a wrapper script for main program
@@ -8,7 +8,7 @@ canu (1.7+dfsg-1) UNRELEASED; urgency=medium
   * Bump mhap minimum version
   * Bump Standards-Version to 4.1.3
 
- -- Afif Elghraoui   Sat, 10 Mar 2018 23:44:12 -0500
+ -- Afif Elghraoui   Sat, 17 Mar 2018 18:09:13 -0400
 
 canu (1.6+dfsg-2) unstable; urgency=medium
 



View it on GitLab: 
https://salsa.debian.org/med-team/canu/commit/52a3f22d7bb368afb9a5d64b5a16c531fd6f1ad4

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[med-svn] [Git][med-team/libseqlib][master] 2 commits: Add missing -lz to pkg-config for linking with zlib

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / libseqlib


Commits:
459a0118 by Andreas Tille at 2018-03-17T10:51:41+01:00
Add missing -lz to pkg-config for linking with zlib

- - - - -
75c30508 by Andreas Tille at 2018-03-17T12:09:35+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/patches/pkg-config.patch
- debian/patches/use_private_htslib_headers.patch


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+libseqlib (1.1.1+dfsg-5) unstable; urgency=medium
+
+  [ Adam Conrad ]
+  * Add missing -lz to pkg-config for linking with zlib
+Closes: #893192
+
+ -- Andreas Tille   Sat, 17 Mar 2018 10:51:57 +0100
+
 libseqlib (1.1.1+dfsg-4) unstable; urgency=medium
 
   * Make sure also private headers of htslib will be installed and usable


=
debian/patches/pkg-config.patch
=
--- a/debian/patches/pkg-config.patch
+++ b/debian/patches/pkg-config.patch
@@ -13,7 +13,7 @@ Description: Add pkg-config file
 +Name: libseqlib
 +Version: @VERSION@
 +Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence 
data
-+Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw
++Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw -lz
 +Cflags: -I${includedir}
 +
 --- a/Makefile.am


=
debian/patches/use_private_htslib_headers.patch
=
--- a/debian/patches/use_private_htslib_headers.patch
+++ b/debian/patches/use_private_htslib_headers.patch
@@ -21,7 +21,7 @@ Description: Hack around improper use of private files of 
htslib
 @@ -7,5 +7,5 @@ Name: libseqlib
  Version: @VERSION@
  Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence 
data
- Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw
+ Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw -lz
 -Cflags: -I${includedir}
 +Cflags: -I${includedir} -I/usr/include/htslib
  



View it on GitLab: 
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---
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[med-svn] [Git][med-team/libseqlib] Pushed new tag debian/1.1.1+dfsg-5

[Andreas Tille]

Andreas Tille pushed new tag debian/1.1.1+dfsg-5 at Debian Med / libseqlib

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[med-svn] [Git][med-team/artemis][pristine-tar] pristine-tar data for artemis_17.0.1+dfsg.orig.tar.gz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / artemis


Commits:
20d747f5 by Andreas Tille at 2018-03-17T10:57:46+01:00
pristine-tar data for artemis_17.0.1+dfsg.orig.tar.gz

- - - - -


2 changed files:

- + artemis_17.0.1+dfsg.orig.tar.gz.delta
- + artemis_17.0.1+dfsg.orig.tar.gz.id


Changes:

=
artemis_17.0.1+dfsg.orig.tar.gz.delta
=
Binary files /dev/null and b/artemis_17.0.1+dfsg.orig.tar.gz.delta differ


=
artemis_17.0.1+dfsg.orig.tar.gz.id
=
--- /dev/null
+++ b/artemis_17.0.1+dfsg.orig.tar.gz.id
@@ -0,0 +1 @@
+9c9b7dcf80e0c6c7ce3d7fc3533f9f0bff8a9384



View it on GitLab: 
https://salsa.debian.org/med-team/artemis/commit/20d747f56464aa4d428ecd18c03d7c49e5b451cd

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[med-svn] [Git][med-team/artemis] Pushed new tag upstream/17.0.1+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/17.0.1+dfsg at Debian Med / artemis

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[med-svn] [Git][med-team/artemis][upstream] New upstream version 17.0.1+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / artemis


Commits:
f19ab489 by Andreas Tille at 2018-03-17T10:53:04+01:00
New upstream version 17.0.1+dfsg
- - - - -


30 changed files:

- .classpath
- .gitignore
- .travis.yml
- AUTHORS
- ChangeLog
- INSTALL
- LICENSE
- Makefile
- README.md
- act
- − act.command
- art
- art.bat
- + bamview
- build.xml
- − corba/apollo.idl
- − corba/ensembl.idl
- − corba/nsdb.idl
- − corba/nsdb_write.idl
- − corba/seqdb.idl
- − corba/types.idl
- dnaplotter
- docs/act_start_chapter.sgml
- docs/chado/GMOD2009SummerSchool.shtml
- docs/start_chapter.sgml
- − etc/gene_builder
- etc/log4j.properties
- etc/options
- etc/run_fasta.sanger
- etc/run_fasta.sanger.linux


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/artemis/commit/f19ab4890d54528c506a3b3830750f7e7d84e935

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[med-svn] [Git][med-team/artemis][master] 5 commits: New upstream version 17.0.1+dfsg

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / artemis


Commits:
f19ab489 by Andreas Tille at 2018-03-17T10:53:04+01:00
New upstream version 17.0.1+dfsg
- - - - -
20e0398b by Andreas Tille at 2018-03-17T10:57:47+01:00
Update upstream source from tag upstream/17.0.1+dfsg

Update to upstream version 17.0.1+dfsg
with Debian dir 71664fc05095745172e6c5856bd2e98a3feb1bb9
- - - - -
ea9e8ae8 by Andreas Tille at 2018-03-17T11:40:02+01:00
New upstream version, adapted patches

- - - - -
a018b558 by Andreas Tille at 2018-03-17T11:41:28+01:00
Standards-Version: 4.1.3

- - - - -
fb81f14e by Andreas Tille at 2018-03-17T11:59:28+01:00
New upstream version should fix #893184 according to upstream changelog - but 
there are other build issues

- - - - -


27 changed files:

- .classpath
- .gitignore
- .travis.yml
- AUTHORS
- ChangeLog
- INSTALL
- LICENSE
- Makefile
- README.md
- act
- − act.command
- art
- art.bat
- + bamview
- build.xml
- − corba/apollo.idl
- − corba/ensembl.idl
- − corba/nsdb.idl
- − corba/nsdb_write.idl
- − corba/seqdb.idl
- − corba/types.idl
- debian/changelog
- debian/control
- debian/patches/class-path.patch
- − debian/patches/htsjdk-api-change.patch
- debian/patches/jar-rules.patch
- − debian/patches/picard-api-change.patch


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/artemis/compare/3f77074466c0c81cd71bd23646ed55dab15e50d8...fb81f14e605091517388bc832d16a86404017a75

---
View it on GitLab: 
https://salsa.debian.org/med-team/artemis/compare/3f77074466c0c81cd71bd23646ed55dab15e50d8...fb81f14e605091517388bc832d16a86404017a75
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[med-svn] [Git][med-team/phyutility] Pushed new tag debian/2.7.3+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/2.7.3+dfsg-1 at Debian Med / phyutility

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https://salsa.debian.org/med-team/phyutility/tree/debian/2.7.3+dfsg-1
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[med-svn] [Git][med-team/phyutility][pristine-tar] pristine-tar data for phyutility_2.7.3+dfsg.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / phyutility


Commits:
ae2733e4 by Andreas Tille at 2018-03-17T08:27:25+01:00
pristine-tar data for phyutility_2.7.3+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + phyutility_2.7.3+dfsg.orig.tar.xz.delta
- + phyutility_2.7.3+dfsg.orig.tar.xz.id


Changes:

=
phyutility_2.7.3+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/phyutility_2.7.3+dfsg.orig.tar.xz.delta differ


=
phyutility_2.7.3+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/phyutility_2.7.3+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+622c0535a5a0bf6fea719f0ff5d76066fd558fef



View it on GitLab: 
https://salsa.debian.org/med-team/phyutility/commit/ae2733e4498ff29be98a00bca60a275c9539be00

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[med-svn] [Git][med-team/phyutility][master] 9 commits: Stick to Java 8 compatibility level to avoid conflicts with org.xml.sax classes…

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / phyutility


Commits:
71b56994 by Andreas Tille at 2018-03-17T08:15:48+01:00
Stick to Java 8 compatibility level to avoid conflicts with org.xml.sax classes 
that should be removed

- - - - -
ad0921bd by Andreas Tille at 2018-03-17T08:16:22+01:00
cme fix dpkg-control

- - - - -
f385a465 by Andreas Tille at 2018-03-17T08:16:47+01:00
debhelper 11

- - - - -
e3552af9 by Andreas Tille at 2018-03-17T08:27:07+01:00
Repack upstream tarball to get rid of useless binary without source

- - - - -
98179530 by Andreas Tille at 2018-03-17T08:27:23+01:00
New upstream version 2.7.3+dfsg
- - - - -
d3f3c15d by Andreas Tille at 2018-03-17T08:27:25+01:00
Update upstream source from tag upstream/2.7.3+dfsg

Update to upstream version 2.7.3+dfsg
with Debian dir bcde0f679032194d5c0cb256074097f711f0102f
- - - - -
820d65ae by Andreas Tille at 2018-03-17T08:29:55+01:00
DEP5 fixes

- - - - -
1c79ae22 by Andreas Tille at 2018-03-17T08:35:20+01:00
Fix spelling

- - - - -
4902220f by Andreas Tille at 2018-03-17T08:37:40+01:00
Upload to unstable

- - - - -


9 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/patches/series
- + debian/patches/stick_to_java_8_until_xml.sax_is_removed.patch
- debian/phyutility.1
- debian/watch
- − src/jade/lib/libmatrixExp.so


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,18 @@
+phyutility (2.7.3+dfsg-1) unstable; urgency=medium
+
+  [ Emmanuel Bourg ]
+  * Stick to Java 8 compatibility level to avoid conflicts with org.xml.sax
+classes that should be removed
+Closes: #874155
+
+  [ Andreas Tille ]
+  * cme fix dpkg-control
+  * debhelper 11
+  * Repack upstream tarball to get rid of useless binary without source
+  * DEP5 fixes
+
+ -- Andreas Tille   Sat, 17 Mar 2018 08:30:04 +0100
+
 phyutility (2.7.3-1) unstable; urgency=medium
 
   * Initial release. (Closes: #741900)


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -4,13 +4,13 @@ Uploaders: Andreas Tille ,
Stephen Smith 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
javahelper,
default-jdk,
ant
-Standards-Version: 3.9.5
-Vcs-Git: git://anonscm.debian.org/debian-med/phyutility.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/phyutility.git
+Standards-Version: 4.1.3
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phyutility.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/phyutility.git
 Homepage: http://github.com/blackrim/phyutility
 
 Package: phyutility


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,7 @@ Format: 
http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: phyutility
 Upstream-Contact: Stephen Smith 
 Source: https://github.com/blackrim/phyutility/
+Files-Excluded: */*.so
 
 Files: *
 Copyright: © 2007-2014 Stephen Smith 
@@ -24,11 +25,11 @@ Copyright: © 2002-2006 Marc A. Suchard
© 2002-2006 Stephen Smith 
 License: LGPL-2.1
 
-Files: src/jade/drb/*
+Files: src/phyutility/drb/*
 Copyright: © 2004-2014 The Apache Software Foundation
-License: Apache 2.0
+License: Apache-2.0
 
-Files: src/jade/data/
+Files: src/jade/data/*
 Copyright: © 1999-2001 PAL Development Core Team
 License: LGPL-2.1
 
@@ -79,7 +80,7 @@ License: LGPL-2.1
  Public License version 3 can be found in
  "/usr/share/common-licenses/LGPL-2.1".
 
-License: Apache 2.0
+License: Apache-2.0
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at


=
debian/patches/series
=
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+stick_to_java_8_until_xml.sax_is_removed.patch


=
debian/patches/stick_to_java_8_until_xml.sax_is_removed.patch
=
--- /dev/null
+++ b/debian/patches/stick_to_java_8_until_xml.sax_is_removed.patch
@@ -0,0 +1,18 @@
+Author: Emmanuel Bourg 
+Last-Update: Mon, 12 Mar 2018 22:42:50 +0100
+Bug-Debian: https://bugs.debian.org/874155
+Description:
+ The org.xml.sax classes should be removed from the package. Until that
+ happens, the build failure can be solved with this patch:
+
+--- a/build.xml
 b/build.xml
+@@ 

[med-svn] [Git][med-team/phyutility][upstream] New upstream version 2.7.3+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / phyutility


Commits:
98179530 by Andreas Tille at 2018-03-17T08:27:23+01:00
New upstream version 2.7.3+dfsg
- - - - -


1 changed file:

- − src/jade/lib/libmatrixExp.so


Changes:

=
src/jade/lib/libmatrixExp.so deleted
=
Binary files a/src/jade/lib/libmatrixExp.so and /dev/null differ



View it on GitLab: 
https://salsa.debian.org/med-team/phyutility/commit/9817953000fdbdae9c2851911cb9f3da0df6774d

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[med-svn] [Git][med-team/phyutility] Pushed new tag upstream/2.7.3+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/2.7.3+dfsg at Debian Med / phyutility

---
View it on GitLab: 
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[med-svn] [Git][med-team/libdsol1-java][master] New upstream version

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / libdsol1-java


Commits:
d6bb3dc4 by Andreas Tille at 2018-03-17T06:36:21+01:00
New upstream version

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-libdsol1-java (1.6.10-1) UNRELEASED; urgency=medium
+libdsol1-java (2.1.0-1) UNRELEASED; urgency=medium
 
   * Initial upload to Debian (Closes: #???)
   * debhelper 10



View it on GitLab: 
https://salsa.debian.org/med-team/libdsol1-java/commit/d6bb3dc47fba1eb51c22cca09a239e8cbf01cf24

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[med-svn] [Git][med-team/tide][master] Add links

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / tide


Commits:
82e35d77 by Andreas Tille at 2018-03-17T06:25:53+01:00
Add links

- - - - -


1 changed file:

- + debian/links


Changes:

=
debian/links
=
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,3 @@
+/usr/lib/tide/index/usr/bin/tide-index
+/usr/lib/tide/results  /usr/bin/tide-results
+/usr/lib/tide/search   /usr/bin/tide-search



View it on GitLab: 
https://salsa.debian.org/med-team/tide/commit/82e35d77153c766e043f55b2c9f89b482c11cbe4

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