[med-svn] [Git][med-team/trnascan-se][master] Update changelog

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch master at Debian Med / trnascan-se


Commits:
05be319f by Afif Elghraoui at 2018-02-19T17:26:44-05:00
Update changelog

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -9,8 +9,11 @@ trnascan-se (2.0.0-1) UNRELEASED; urgency=medium
   [ Afif Elghraoui ]
   * debian/watch: update to new URL
   * New upstream version 2.0.0
+  * Standards-Version 4.1.3
+  * debhelper compat 11
+  * d/rules: clean up and remove dh_installchangelogs
 
- -- Afif Elghraoui   Mon, 19 Feb 2018 17:16:29 -0500
+ -- Afif Elghraoui   Mon, 19 Feb 2018 17:26:27 -0500
 
 trnascan-se (1.3.1-1) unstable; urgency=medium
 



View it on GitLab: 
https://salsa.debian.org/med-team/trnascan-se/commit/05be319f6c58589470935e0d5159ae94639b19aa

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[med-svn] [Git][med-team/trnascan-se][master] 3 commits: Standards-Version 4.1.3

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch master at Debian Med / trnascan-se


Commits:
96cc42d4 by Afif Elghraoui at 2018-02-19T17:24:14-05:00
Standards-Version 4.1.3

- - - - -
71c9eedc by Afif Elghraoui at 2018-02-19T17:25:14-05:00
debhelper compat 11

- - - - -
dace1810 by Afif Elghraoui at 2018-02-19T17:25:41-05:00
d/rules: clean up and remove dh_installchangelogs

That changelog file isnt there anymore.

- - - - -


3 changed files:

- debian/compat
- debian/control
- debian/rules


Changes:

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


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -3,8 +3,8 @@ Section: non-free/science
 Priority: optional
 Maintainer: Debian Med Packaging Team 

 Uploaders: Afif Elghraoui 
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.8
+Build-Depends: debhelper (>= 11)
+Standards-Version: 4.1.3
 Homepage: http://lowelab.ucsc.edu/tRNAscan-SE
 Vcs-Git: https://anonscm.debian.org/git/debian-med/trnascan-se.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trnascan-se.git


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -1,14 +1,6 @@
 #!/usr/bin/make -f
 
-#DH_VERBOSE = 1
-
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/default.mk
-
 CFLAGS := $(CPPFLAGS) $(CFLAGS)
 
 %:
-   dh $@ --parallel
-
-override_dh_installchangelogs:
-   dh_installchangelogs Release.history
+   dh $@



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[med-svn] [Git][med-team/trnascan-se] Pushed new tag upstream/2.0.0

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed new tag upstream/2.0.0 at Debian Med / trnascan-se

---
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[med-svn] [Git][med-team/trnascan-se][master] 5 commits: debian/watch: update to new URL

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch master at Debian Med / trnascan-se


Commits:
7537bfe4 by Afif Elghraoui at 2018-02-19T17:11:07-05:00
debian/watch: update to new URL

- - - - -
5844a2c7 by Afif Elghraoui at 2018-02-19T17:12:34-05:00
Revert New upstream version 1.23

This reverts commit dc9d5b7eea6a47c5537aa75b88d77e81ea7b3b57.

1.23 was actually older than 1.3.1; upsteam wasnt using proper
monotic versions. Reverting this merge so that we can properly see
the differences between the latest and previous releases.

- - - - -
b12160d8 by Afif Elghraoui at 2018-02-19T17:14:07-05:00
New upstream version 2.0.0
- - - - -
401fd847 by Afif Elghraoui at 2018-02-19T17:14:09-05:00
Merge tag upstream/2.0.0

Upstream version 2.0.0

- - - - -
dc5a63cb by Afif Elghraoui at 2018-02-19T17:17:08-05:00
Update changelog

- - - - -


30 changed files:

- COPYING
- − Cove/COPYING
- − Cove/DEMO
- − Cove/Demos/7SL-euk.cm
- − Cove/Demos/7SL-euk.fa
- − Cove/Demos/K11H3frag.fa
- − Cove/Demos/fig5.fa
- − Cove/Demos/fig5.slx
- − Cove/Demos/sim100.fa
- − Cove/Demos/sim100.slx
- − Cove/Demos/sim65.fa
- − Cove/Demos/sim65.slx
- − Cove/Demos/test100.fa
- − Cove/Demos/test100.slx
- − Cove/Demos/trna1415.slx
- − Cove/Demos/yeast-phe.fa
- − Cove/Guide.tex
- − Demo/C28G1.fa
- − Demo/DQ6060.fa
- + Demo/Example1-tRNAs.bed
- + Demo/Example1-tRNAs.iso
- + Demo/Example1-tRNAs.out
- + Demo/Example1-tRNAs.ss
- + Demo/Example1-tRNAs.stats
- Demo/F22B7.fa → Demo/Example1.fa
- + Demo/Example2-tRNAs.iso
- + Demo/Example2-tRNAs.out
- + Demo/Example2-tRNAs.ss
- + Demo/Example2-tRNAs.stats
- + Demo/Example2.fa


The diff was not included because it is too large.


View it on GitLab: 
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---
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[med-svn] [Git][med-team/trnascan-se][upstream] New upstream version 2.0.0

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch upstream at Debian Med / trnascan-se


Commits:
b12160d8 by Afif Elghraoui at 2018-02-19T17:14:07-05:00
New upstream version 2.0.0
- - - - -


29 changed files:

- − Archaea-BHB-noncan.cm
- COPYING
- − Cove/COPYING
- − Cove/DEMO
- − Cove/Demos/7SL-euk.cm
- − Cove/Demos/7SL-euk.fa
- − Cove/Demos/K11H3frag.fa
- − Cove/Demos/fig5.fa
- − Cove/Demos/fig5.slx
- − Cove/Demos/sim100.fa
- − Cove/Demos/sim100.slx
- − Cove/Demos/sim65.fa
- − Cove/Demos/sim65.slx
- − Cove/Demos/test100.fa
- − Cove/Demos/test100.slx
- − Cove/Demos/trna1415.slx
- − Cove/Demos/yeast-phe.fa
- − Cove/Guide.tex
- − Demo/C28G1.fa
- − Demo/DQ6060.fa
- + Demo/Example1-tRNAs.bed
- + Demo/Example1-tRNAs.iso
- + Demo/Example1-tRNAs.out
- + Demo/Example1-tRNAs.ss
- + Demo/Example1-tRNAs.stats
- Demo/F22B7.fa → Demo/Example1.fa
- + Demo/Example2-tRNAs.iso
- + Demo/Example2-tRNAs.out
- + Demo/Example2-tRNAs.ss


The diff was not included because it is too large.


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[med-svn] [Git][med-team/trnascan-se][pristine-tar] pristine-tar data for trnascan-se_2.0.0.orig.tar.gz

2018-02-19 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch pristine-tar at Debian Med / trnascan-se


Commits:
aa11a88d by Afif Elghraoui at 2018-02-19T17:14:09-05:00
pristine-tar data for trnascan-se_2.0.0.orig.tar.gz

- - - - -


2 changed files:

- + trnascan-se_2.0.0.orig.tar.gz.delta
- + trnascan-se_2.0.0.orig.tar.gz.id


Changes:

=
trnascan-se_2.0.0.orig.tar.gz.delta
=
Binary files /dev/null and b/trnascan-se_2.0.0.orig.tar.gz.delta differ


=
trnascan-se_2.0.0.orig.tar.gz.id
=
--- /dev/null
+++ b/trnascan-se_2.0.0.orig.tar.gz.id
@@ -0,0 +1 @@
+242a07a8e31ce38c108cd8d3d614db99268e7825



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[med-svn] [Git][med-team/macs] Pushed new tag debian/2.1.1.20160309-2

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag debian/2.1.1.20160309-2 at Debian Med / macs

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[med-svn] [Git][med-team/macs][master] 4 commits: Using a singular e-mail address from Katerina Kalou (as used in other cases)

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / macs


Commits:
aa16b5c7 by Andreas Tille at 2018-02-19T19:41:03+01:00
Using a singular e-mail address from Katerina Kalou (as used in other cases)

- - - - -
ecbb1eff by Andreas Tille at 2018-02-19T19:42:42+01:00
Merge two changelog entries - both saying UNRELEASED

- - - - -
641f4ff5 by Andreas Tille at 2018-02-19T19:43:29+01:00
Upload to unstable

- - - - -
333c9cf8 by Andreas Tille at 2018-02-19T19:46:52+01:00
typo

- - - - -


2 changed files:

- debian/changelog
- debian/patches/spelling


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,8 @@
-macs (2.1.1.20160309-3) UNRELEASED; urgency=medium
+macs (2.1.1.20160309-2) unstable; urgency=medium
 
   * Team upload.
-  * Add autopkgtest (Closes: #879622)
-
- -- kate   Mon, 19 Feb 2018 20:00:45 +0200
-
-macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * debian/upstream/metadata:
  - UTF-8 notation of names rather than TeX syntax
  - added eprint
@@ -16,7 +12,10 @@ macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
   * hardening=+all
   * debhelper 11
 
- -- Andreas Tille   Wed, 10 Aug 2016 08:15:22 +0200
+  [ Katerina Kalou ]
+  * Add autopkgtest (Closes: #879622)
+
+ -- Katerina Kalou   Mon, 19 Feb 2018 20:00:45 +0200
 
 macs (2.1.1.20160309-1) unstable; urgency=medium
 


=
debian/patches/spelling
=
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,5 +1,5 @@
 From: Michael R. Crusoe 
-Subject: Fix spelling erorr
+Subject: Fix spelling error
 Forwarded: https://github.com/taoliu/MACS/pull/129
 
 --- macs.orig/MACS2/Pileup.pyx



View it on GitLab: 
https://salsa.debian.org/med-team/macs/compare/2e5e4e83ac380aeb1351fa42df888cca79348b82...333c9cf8a6e17df9efd21c44413380d0b62f4f42

---
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[med-svn] [Git][med-team/macs][master] Adding the changelog entry and closing the bug

2018-02-19 Thread Aikaterini Kalou 
Aikaterini Kalou pushed to branch master at Debian Med / macs


Commits:
2e5e4e83 by kkalou-guest at 2018-02-19T20:01:42+02:00
Adding the changelog entry and closing the bug

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+macs (2.1.1.20160309-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add autopkgtest (Closes: #879622)
+
+ -- kate   Mon, 19 Feb 2018 20:00:45 +0200
+
 macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
 
   * debian/upstream/metadata:



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[med-svn] [Git][med-team/beads] Pushed new tag debian/1.1.18+dfsg-1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag debian/1.1.18+dfsg-1 at Debian Med / beads

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[med-svn] [Git][med-team/beads] Pushed new tag upstream/1.1.18

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/1.1.18 at Debian Med / beads

---
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[med-svn] [Git][med-team/beads][pristine-tar] 2 commits: pristine-tar data for beads_1.1.18.orig.tar.gz

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / beads


Commits:
0fcac776 by Andreas Tille at 2018-02-19T13:24:09+01:00
pristine-tar data for beads_1.1.18.orig.tar.gz

- - - - -
2c514958 by Andreas Tille at 2018-02-19T13:26:59+01:00
pristine-tar data for beads_1.1.18+dfsg.orig.tar.xz

- - - - -


4 changed files:

- + beads_1.1.18+dfsg.orig.tar.xz.delta
- + beads_1.1.18+dfsg.orig.tar.xz.id
- + beads_1.1.18.orig.tar.gz.delta
- + beads_1.1.18.orig.tar.gz.id


Changes:

=
beads_1.1.18+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/beads_1.1.18+dfsg.orig.tar.xz.delta differ


=
beads_1.1.18+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/beads_1.1.18+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+05d65bc9a359f5b1cf11ee62a63bc72d5668623e


=
beads_1.1.18.orig.tar.gz.delta
=
Binary files /dev/null and b/beads_1.1.18.orig.tar.gz.delta differ


=
beads_1.1.18.orig.tar.gz.id
=
--- /dev/null
+++ b/beads_1.1.18.orig.tar.gz.id
@@ -0,0 +1 @@
+ccb67095d137853697daa1c6f44057a1682683a6



View it on GitLab: 
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---
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[med-svn] [Git][med-team/beads] Pushed new tag upstream/1.1.18+dfsg

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/1.1.18+dfsg at Debian Med / beads

---
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[med-svn] [Git][med-team/beads][master] 7 commits: Versioned Build-Depends: libodsstream-qt5-dev (>= 0.4.13-2)

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / beads


Commits:
26af4067 by Andreas Tille at 2018-02-19T13:22:23+01:00
Versioned Build-Depends: libodsstream-qt5-dev (= 0.4.13-2)

- - - - -
cd0f5a9f by Andreas Tille at 2018-02-19T13:24:07+01:00
New upstream version 1.1.18
- - - - -
ba168f67 by Andreas Tille at 2018-02-19T13:24:09+01:00
Update upstream source from tag upstream/1.1.18

Update to upstream version 1.1.18
with Debian dir 9f8df97db3d77b32a47f21d97b07ffb3023f6c4d
- - - - -
e58227d1 by Andreas Tille at 2018-02-19T13:24:58+01:00
Another new upstream version

- - - - -
232a717c by Andreas Tille at 2018-02-19T13:26:58+01:00
New upstream version 1.1.18+dfsg
- - - - -
f840155f by Andreas Tille at 2018-02-19T13:26:59+01:00
Update upstream source from tag upstream/1.1.18+dfsg

Update to upstream version 1.1.18+dfsg
with Debian dir 84474c039bff7e889bece7b49f14b08829cf6864
- - - - -
5a9c0894 by Andreas Tille at 2018-02-19T14:59:36+01:00
Drop unused lintian override, upload to unstable

- - - - -


8 changed files:

- − .gitignore
- .kdev4/beads.kdev4
- CMakeLists.txt
- debian/changelog
- debian/control
- − debian/source/lintian-overrides
- src/CMakeLists.txt
- src/config.h


Changes:

=
.gitignore deleted
=
--- a/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.project
-build
-src/config.h


=
.kdev4/beads.kdev4
=
--- a/.kdev4/beads.kdev4
+++ b/.kdev4/beads.kdev4
@@ -4,20 +4,14 @@ 
BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x
 [CMake]
 Build Directory Count=1
 Current Build Directory Index=0
-ProjectRootRelative=./
 
 [CMake][CMake Build Directory 0]
-Build Directory Path=file:///home/langella/developpement/git/beads/build
-Build Type=
-CMake Binary=file:///usr/bin/cmake
+Build Directory Path=/home/olivier/eclipse/git/beads/build
+Build Type=Debug
+CMake Binary=/usr/bin/cmake
 Environment Profile=
 Extra Arguments=
-Install Directory=file:///usr/local
-
-[Defines And Includes][Compiler]
-Name=GCC
-Path=gcc
-Type=GCC
+Install Directory=
 
 [Project]
 VersionControlSupport=kdevgit


=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -75,7 +75,7 @@ SET(CMAKE_CXX_FLAGS_DEBUG "-g -s")
 SET(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
 SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
 
-SET (BEADS_VERSION "1.1.17")
+SET (BEADS_VERSION "1.1.18")
 
 SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
 SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -111,6 +111,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"moc_.*cxx"
"/devel_archives/"
"/build/"
+   "/buildw64/"
"/cbuild/"
"/figures/"
".*.so"
@@ -127,6 +128,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"CPackConfig.cmake"
"CPackSourceConfig.cmake"
"install_manifest.txt"
+   ".gitignore"
"/CMakeFiles/"
"/_CPack_Packages/"
"/Debug/"


=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,13 +1,14 @@
-beads (1.1.17+dfsg-1) UNRELEASED; urgency=medium
+beads (1.1.18+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Watch file now reports new upstream URLs (not fit for proper download
 yet since some more sophisticated name mangling is needed)
   * Standards-Version: 4.1.3
   * debhelper 11
-  * Build-Depends: libodsstream-qt5-dev
+  * Build-Depends: libodsstream-qt5-dev (>= 0.4.13-2)
+  * Drop unused lintian override
 
- -- Andreas Tille   Mon, 12 Feb 2018 10:22:39 +0100
+ -- Andreas Tille   Mon, 19 Feb 2018 13:27:11 +0100
 
 beads (1.1.13+dfsg-2) unstable; urgency=medium
 


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11),
cmake,
qtbase5-dev,
qttools5-dev,
-   libodsstream-qt5-dev,
+   libodsstream-qt5-dev (>= 0.4.13-2),
cimg-dev
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/beads.git


=
debian/source/lintian-overrides deleted
=
--- a/debian/source/lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-# UPstream provides only http no https
-beads source: debian-watch-uses-insecure-uri line 4


=
src/CMakeLists.txt
=
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,7 +6,25 @@ list( APPEND CMAKE_MODULE_PATH
 )
 
 set (CImg_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/src/cimg")
-find_package( CImg REQUIRED )
+
+if (DEBIAN_PACKAGE)
+#  CImg_FOUND - system has CImg lib
+set (CImg_FOUND 1)
+#  CImg_INCLUDE_DIRS - the

[med-svn] [Git][med-team/beads][upstream] 2 commits: New upstream version 1.1.18

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch upstream at Debian Med / beads


Commits:
cd0f5a9f by Andreas Tille at 2018-02-19T13:24:07+01:00
New upstream version 1.1.18
- - - - -
232a717c by Andreas Tille at 2018-02-19T13:26:58+01:00
New upstream version 1.1.18+dfsg
- - - - -


9 changed files:

- − .gitignore
- .kdev4/beads.kdev4
- CMakeLists.txt
- debian/beads.install
- debian/changelog
- debian/control
- debian/rules
- src/CMakeLists.txt
- src/config.h


Changes:

=
.gitignore deleted
=
--- a/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.project
-build
-src/config.h


=
.kdev4/beads.kdev4
=
--- a/.kdev4/beads.kdev4
+++ b/.kdev4/beads.kdev4
@@ -4,20 +4,14 @@ 
BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x
 [CMake]
 Build Directory Count=1
 Current Build Directory Index=0
-ProjectRootRelative=./
 
 [CMake][CMake Build Directory 0]
-Build Directory Path=file:///home/langella/developpement/git/beads/build
-Build Type=
-CMake Binary=file:///usr/bin/cmake
+Build Directory Path=/home/olivier/eclipse/git/beads/build
+Build Type=Debug
+CMake Binary=/usr/bin/cmake
 Environment Profile=
 Extra Arguments=
-Install Directory=file:///usr/local
-
-[Defines And Includes][Compiler]
-Name=GCC
-Path=gcc
-Type=GCC
+Install Directory=
 
 [Project]
 VersionControlSupport=kdevgit


=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -75,7 +75,7 @@ SET(CMAKE_CXX_FLAGS_DEBUG "-g -s")
 SET(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
 SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
 
-SET (BEADS_VERSION "1.1.17")
+SET (BEADS_VERSION "1.1.18")
 
 SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
 SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -111,6 +111,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"moc_.*cxx"
"/devel_archives/"
"/build/"
+   "/buildw64/"
"/cbuild/"
"/figures/"
".*.so"
@@ -127,6 +128,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"CPackConfig.cmake"
"CPackSourceConfig.cmake"
"install_manifest.txt"
+   ".gitignore"
"/CMakeFiles/"
"/_CPack_Packages/"
"/Debug/"


=
debian/beads.install
=
--- a/debian/beads.install
+++ b/debian/beads.install
@@ -1 +1 @@
-/usr/*
+usr/*


=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+beads (1.1.17-2) stretch; urgency=medium
+
+  * better debian package
+
+ -- Olivier Langella   Fri, 16 Feb 2018 06:57:23 
+0100
+
 beads (1.1.17-1) stretch; urgency=medium
 
   * move to QT5


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -27,4 +27,6 @@ Depends: ${shlibs:Depends},
  libodsstream-qt5-0
 Pre-Depends: ${misc:Pre-Depends}
 Description: 2-DE electrophoresis gel image spot detection
- 2-DE electrophoresis gel image spot detection
+ BEADS is a program for spot detection on 2-D gel images. It is based on
+ an analogy with beads flowing uphill on the surface of the gel image and
+ on the analysis of their paths (Langella & Zivy, 2008).


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -3,13 +3,15 @@
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
+export DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+
 export DESTDIR=$(CURDIR)/debian/tmp
 
 %:
dh $@ --buildsystem=cmake --parallel
 
 override_dh_auto_configure:
-   dh_auto_configure -- -DCMAKE_INSTALL_PREFIX=/usr 
-DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=1
+   dh_auto_configure -- -DLIB_SUFFIX="/$(DEB_HOST_MULTIARCH)" 
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=1 
-DDEBIAN_PACKAGE=1

 override_dh_auto_install:
dh_auto_install -- DESTDIR=$(DESTDIR)


=
src/CMakeLists.txt
=
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,7 +6,25 @@ list( APPEND CMAKE_MODULE_PATH
 )
 
 set (CImg_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/src/cimg")
-find_package( CImg REQUIRED )
+
+if (DEBIAN_PACKAGE)
+#  CImg_FOUND - system has CImg lib
+set (CImg_FOUND 1)
+#  CImg_INCLUDE_DIRS - the CImg include directory
+set (CImg_INCLUDE_DIR "/usr/include")
+#  CImg_SYSTEM_LIBS - external libraries that CImg uses
+set (CImg_SYSTEM_LIBS "/usr/lib${LIB_SUFFIX}/libz.so"
+"/usr/lib${LIB_SUFFIX}/libpng16.so"
+"/usr/lib${LIB_SUFFIX}/libjpeg.so"
+"/usr/lib${LIB_SUFFIX}/libtiff.so")
+#  CImg_SYSTEM_LIBS_DIR - external library directories
+set (CImg_SYSTEM_LIBS_DIR "")
+#  CImg_CFLAGS -

[med-svn] [Git][med-team/tnseq-transit] Pushed new tag upstream/2.1.1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/2.1.1 at Debian Med / tnseq-transit

---
View it on GitLab: 
https://salsa.debian.org/med-team/tnseq-transit/tree/upstream/2.1.1
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[med-svn] [Git][med-team/tnseq-transit][upstream] New upstream version 2.1.1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch upstream at Debian Med / tnseq-transit


Commits:
a2b7d313 by Andreas Tille at 2018-02-19T11:35:38+01:00
New upstream version 2.1.1
- - - - -


30 changed files:

- .gitignore
- + .travis.yml
- CHANGELOG.md
- README.md
- VERSION
- setup.py
- src/pytpp/__main__.py
- src/pytpp/tpp_gui.py
- src/pytpp/tpp_tools.py
- src/pytransit/__init__.py
- src/pytransit/__main__.py
- src/pytransit/analysis/__init__.py
- src/pytransit/analysis/base.py
- src/pytransit/analysis/binomial.py
- src/pytransit/analysis/example.py
- src/pytransit/analysis/griffin.py
- src/pytransit/analysis/gumbel.py
- src/pytransit/analysis/hmm.py
- + src/pytransit/analysis/norm.py
- src/pytransit/analysis/rankproduct.py
- src/pytransit/analysis/resampling.py
- src/pytransit/analysis/tn5gaps.py
- + src/pytransit/doc/images/transit_logo.png
- + src/pytransit/doc/images/transit_quality_control_histogram.png
- + src/pytransit/doc/images/transit_quality_control_qqplot.png
- + src/pytransit/doc/images/transit_quality_control_ranked.png
- + src/pytransit/doc/images/transit_quality_control_window.png
- + src/pytransit/doc/images/transit_tutorial_norm_options.png
- src/pytransit/doc/source/_images/TPP-screenshot.png
- src/pytransit/doc/source/_images/tutorial_glyc_ctrl.png


The diff was not included because it is too large.


View it on GitLab: 
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[med-svn] [Git][med-team/tnseq-transit][master] 6 commits: New upstream version 2.1.1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / tnseq-transit


Commits:
a2b7d313 by Andreas Tille at 2018-02-19T11:35:38+01:00
New upstream version 2.1.1
- - - - -
4954ac80 by Andreas Tille at 2018-02-19T11:37:57+01:00
Update upstream source from tag upstream/2.1.1

Update to upstream version 2.1.1
with Debian dir 87a409af61b7c98e2ccddf0dfb450431af47820e
- - - - -
92da34ea by Andreas Tille at 2018-02-19T11:39:28+01:00
New upstream version

- - - - -
4eb439b5 by Andreas Tille at 2018-02-19T11:39:38+01:00
Standards-Version: 4.1.3

- - - - -
0c4d667a by Andreas Tille at 2018-02-19T11:40:02+01:00
debhelper 11

- - - - -
acd4235c by Andreas Tille at 2018-02-19T11:43:37+01:00
do not parse d/changelog, upload to unstable

- - - - -


30 changed files:

- .gitignore
- + .travis.yml
- CHANGELOG.md
- README.md
- VERSION
- debian/changelog
- debian/compat
- debian/control
- debian/rules
- setup.py
- src/pytpp/__main__.py
- src/pytpp/tpp_gui.py
- src/pytpp/tpp_tools.py
- src/pytransit/__init__.py
- src/pytransit/__main__.py
- src/pytransit/analysis/__init__.py
- src/pytransit/analysis/base.py
- src/pytransit/analysis/binomial.py
- src/pytransit/analysis/example.py
- src/pytransit/analysis/griffin.py
- src/pytransit/analysis/gumbel.py
- src/pytransit/analysis/hmm.py
- + src/pytransit/analysis/norm.py
- src/pytransit/analysis/rankproduct.py
- src/pytransit/analysis/resampling.py
- src/pytransit/analysis/tn5gaps.py
- + src/pytransit/doc/images/transit_logo.png
- + src/pytransit/doc/images/transit_quality_control_histogram.png
- + src/pytransit/doc/images/transit_quality_control_qqplot.png
- + src/pytransit/doc/images/transit_quality_control_ranked.png


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/tnseq-transit/compare/858941269f9bbf41ff0fc3483a1d80b2417510f0...acd4235c0b4d27b383db28b25d3aab73b963b556

---
View it on GitLab: 
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[med-svn] [Git][med-team/tnseq-transit] Pushed new tag debian/2.1.1-1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag debian/2.1.1-1 at Debian Med / tnseq-transit

---
View it on GitLab: 
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[med-svn] [Git][med-team/tnseq-transit][pristine-tar] pristine-tar data for tnseq-transit_2.1.1.orig.tar.gz

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / tnseq-transit


Commits:
9776d2ee by Andreas Tille at 2018-02-19T11:37:57+01:00
pristine-tar data for tnseq-transit_2.1.1.orig.tar.gz

- - - - -


2 changed files:

- + tnseq-transit_2.1.1.orig.tar.gz.delta
- + tnseq-transit_2.1.1.orig.tar.gz.id


Changes:

=
tnseq-transit_2.1.1.orig.tar.gz.delta
=
Binary files /dev/null and b/tnseq-transit_2.1.1.orig.tar.gz.delta differ


=
tnseq-transit_2.1.1.orig.tar.gz.id
=
--- /dev/null
+++ b/tnseq-transit_2.1.1.orig.tar.gz.id
@@ -0,0 +1 @@
+19780d47ef03daeb28f8e666e0f02288f30b8f53



View it on GitLab: 
https://salsa.debian.org/med-team/tnseq-transit/commit/9776d2ee63c0923d58182da846ead443757011ed

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[med-svn] [Git][med-team/python-pysam][master] 4 commits: Add Python 2.7 compatibility symlink for libchtslib.so

2018-02-19 Thread Graham Inggs 
Graham Inggs pushed to branch master at Debian Med / python-pysam


Commits:
78a7073d by Graham Inggs at 2018-02-19T11:58:59+02:00
Add Python 2.7 compatibility symlink for libchtslib.so

- - - - -
a9441105 by Graham Inggs at 2018-02-19T12:01:24+02:00
Update Vcs-* URIs for move to salsa.debian.org

- - - - -
d0c3e89a by Graham Inggs at 2018-02-19T12:11:09+02:00
Remove trailing whitespace from debian/changelog

- - - - -
aba2ff4f by Graham Inggs at 2018-02-19T12:11:53+02:00
Prepare for upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/python-pysam.links


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+python-pysam (0.14+ds-2) unstable; urgency=medium
+
+  * Team upload
+  * Add Python 2.7 compatibility symlink for libchtslib.so (Closes: #890748)
+  * Update Vcs-* URIs for move to salsa.debian.org
+  * Remove trailing whitespace from debian/changelog
+
+ -- Graham Inggs   Mon, 19 Feb 2018 10:11:17 +
+
 python-pysam (0.14+ds-1) unstable; urgency=medium
 
   * New upstream version
@@ -219,7 +228,7 @@ python-pysam (0.8.3+ds1-1) experimental; urgency=medium
   * provide python3-pysam
 
   [ Charles Plessy ]
-  * Requires Python 2.7 or higher. 
+  * Requires Python 2.7 or higher.
 
   [ Andreas Tille ]
   * Link against htslib


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -22,8 +22,8 @@ Build-Depends: debhelper (>= 11~),
python-pytest ,
python3-pytest 
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-pysam.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-pysam.git
+Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
+Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
 Homepage: http://pysam.readthedocs.org/en/latest
 X-Python-Version: >= 2.7
 X-Python3-Version: >= 3.2


=
debian/python-pysam.links
=
--- a/debian/python-pysam.links
+++ b/debian/python-pysam.links
@@ -1,3 +1,4 @@
 #!/usr/bin/dh-exec
 /usr/lib/python2.7/dist-packages/pysam/libcsamtools.${DEB_HOST_GNU_TYPE}.so 
/usr/lib/python2.7/dist-packages/pysam/libcsamtools.so
 /usr/lib/python2.7/dist-packages/pysam/libcbcftools.${DEB_HOST_GNU_TYPE}.so 
/usr/lib/python2.7/dist-packages/pysam/libcbcftools.so
+/usr/lib/python2.7/dist-packages/pysam/libchtslib.${DEB_HOST_GNU_TYPE}.so 
/usr/lib/python2.7/dist-packages/pysam/libchtslib.so



View it on GitLab: 
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---
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[med-svn] [Git][med-team/tnseq-transit] Pushed new branch debian/jessie-backports

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new branch debian/jessie-backports at Debian Med / 
tnseq-transit

---
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[med-svn] [Git][med-team/swarm-cluster] Pushed new tag debian/2.2.2+dfsg-1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag debian/2.2.2+dfsg-1 at Debian Med / swarm-cluster

---
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[med-svn] [Git][med-team/swarm-cluster] Pushed new tag upstream/2.2.2+dfsg

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/2.2.2+dfsg at Debian Med / swarm-cluster

---
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[med-svn] [Git][med-team/swarm-cluster][pristine-tar] pristine-tar data for swarm-cluster_2.2.2+dfsg.orig.tar.xz

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / swarm-cluster


Commits:
dba8de08 by Andreas Tille at 2018-02-19T11:04:07+01:00
pristine-tar data for swarm-cluster_2.2.2+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + swarm-cluster_2.2.2+dfsg.orig.tar.xz.delta
- + swarm-cluster_2.2.2+dfsg.orig.tar.xz.id


Changes:

=
swarm-cluster_2.2.2+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/swarm-cluster_2.2.2+dfsg.orig.tar.xz.delta differ


=
swarm-cluster_2.2.2+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/swarm-cluster_2.2.2+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+f95af47e8777dad644bccb7d5e714dc8c0d6bcca



View it on GitLab: 
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[med-svn] [Git][med-team/seqan2][master] Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.

2018-02-19 Thread Michael R. Crusoe 
Michael R. Crusoe pushed to branch master at Debian Med / seqan2


Commits:
8dee2cd3 by Michael R. Crusoe at 2018-02-19T02:15:23-08:00
Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.

- - - - -


8 changed files:

- debian/changelog
- debian/clean
- debian/control
- + debian/libseqan2-dev.docs
- − debian/libseqan2-dev.install
- debian/rules
- debian/tests/control
- debian/tests/run-tests


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+seqan2 (2.4.0+dfsg-8) unstable; urgency=medium
+
+  * Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.
+  * Use seperate build directory for the -dev package so we can run cmake with
+-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+
+ -- Michael R. Crusoe   Mon, 19 Feb 2018 02:15:18 
-0800
+
 seqan2 (2.4.0+dfsg-7) unstable; urgency=medium
 
   * Split override_dh_install into -arch and -indep


=
debian/clean
=
--- a/debian/clean
+++ b/debian/clean
@@ -1,2 +1,3 @@
 fakehome/
 debian/files
+build/


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -6,9 +6,9 @@ Uploaders: Andreas Tille ,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
-   python
-Build-Depends-Arch: cmake,
-zlib1g-dev,
+   python,
+   cmake
+Build-Depends-Arch: zlib1g-dev,
 libbz2-dev,
 libbam-dev,
 libboost-dev,


=
debian/libseqan2-dev.docs
=
--- /dev/null
+++ b/debian/libseqan2-dev.docs
@@ -0,0 +1 @@
+README.rst


=
debian/libseqan2-dev.install deleted
=
--- a/debian/libseqan2-dev.install
+++ /dev/null
@@ -1,3 +0,0 @@
-include/seqan  usr/include
-util/cmake/seqan-config.cmake  usr/share/cmake/seqan
-seqan-2.pc usr/share/pkgconfig


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -44,11 +44,13 @@ pkgdev=libseqan2-dev
 
 override_dh_auto_configure-arch:
export DEB_BUILD_ARCH=${DEB_BUILD_ARCH} ; \
-   dh_auto_configure -- \
+   dh_auto_configure --arch -- \
-DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \
-DSEQAN_DISABLE_VERSION_CHECK=YES
 
-override_dh_auto_configure-indep: ;
+override_dh_auto_configure-indep:
+   dh_auto_configure --indep -B build -- \
+   -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1
 
 override_dh_auto_build-arch:
dh_auto_build --arch ${MAX_PARALLEL}
@@ -58,16 +60,13 @@ override_dh_auto_build-arch:
# Seems there is no sphinx module bibtex - thus deactivating creation 
of html manual
# cd manual && make html
 
-override_dh_auto_build-indep:
-   sed -e "s=@CMAKE_INSTALL_PREFIX@=/usr=g" \
-   -e "s/@SEQAN_VERSION_STRING@/$(DEB_VERSION_UPSTREAM_REVISION)/g" \
-   -e "s/@CMAKE_PROJECT_NAME@/seqan/g" \
-   -e "s=@CMAKE_INSTALL_FULL_INCLUDEDIR@=/usr/include=g" \
-   util/pkgconfig/seqan.pc.in > seqan-2.pc
+override_dh_auto_install-indep:
+   dh_auto_install --indep -B build --destdir=$(CURDIR)/debian/$(pkgdev)/
+   rm -Rf $(CURDIR)/debian/$(pkgdev)/usr/share/doc/seqan
 
 override_dh_install-indep:
dh_install --indep
-   # Delete additional LICENSE files
+   # Delete additional LICENSE and compiled Python files
if [ -d $(CURDIR)/debian/$(pkgdev) ] ; then \
find $(CURDIR)/debian/$(pkgdev) -type f -name LICENSE -delete ; \
find $(CURDIR)/debian/$(pkgdev) -type f -name "*.pyc" -delete ; \
@@ -90,36 +89,26 @@ override_dh_auto_clean:
mv $${header} `echo $$header | sed 's?orig/??'` ; \
  done ; \
fi
-   rm -rf orig seqan-2.pc
+   rm -rf orig
 
 override_dh_installman-arch:
-   dh_link -a
+   dh_link --arch
if [ -d $(CURDIR)/debian/$(pkgapps)/usr/bin ] ; then \
find $(CURDIR)/debian/$(pkgapps)/usr/bin -type l -xtype l 
-delete ; \
fi
$(CURDIR)/debian/generate_manpages
-   #for bin in `ls $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin` ; do \
-   #if [ -x $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/`basename 
$${bin}` ] ; then \
-   #ln -s ../lib/seqan/bin/`basename $${bin}` 
$(CURDIR)/debian/$(pkgapps)/usr/bin/`basename $${bin}` ; \
-   #fi ; \
-   #if echo $${bin} | grep -q '\.sh$$' ; then \
-   #ln -s ../lib/seqan/bin/$${bin} 
$(CURDIR)/debian/$(pkgapps)/usr/bin/`basename $${bin} .sh` ; \
-   #fi ; \
-   #done
-   # we generate only

[med-svn] [Git][med-team/seqan2] Pushed new tag debian/2.4.0+dfsg-8

2018-02-19 Thread Michael R. Crusoe 
Michael R. Crusoe pushed new tag debian/2.4.0+dfsg-8 at Debian Med / seqan2

---
View it on GitLab: 
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[med-svn] [Git][med-team/python-dendropy] Pushed new tag debian/4.3.0+dfsg-1

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag debian/4.3.0+dfsg-1 at Debian Med / python-dendropy

---
View it on GitLab: 
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[med-svn] [Git][med-team/python-dendropy] Pushed new tag upstream/4.3.0+dfsg

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/4.3.0+dfsg at Debian Med / python-dendropy

---
View it on GitLab: 
https://salsa.debian.org/med-team/python-dendropy/tree/upstream/4.3.0+dfsg
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[med-svn] [Git][med-team/python-dendropy][pristine-tar] pristine-tar data for python-dendropy_4.3.0+dfsg.orig.tar.xz

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / python-dendropy


Commits:
3658a707 by Andreas Tille at 2018-02-18T20:17:30+01:00
pristine-tar data for python-dendropy_4.3.0+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + python-dendropy_4.3.0+dfsg.orig.tar.xz.delta
- + python-dendropy_4.3.0+dfsg.orig.tar.xz.id


Changes:

=
python-dendropy_4.3.0+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/python-dendropy_4.3.0+dfsg.orig.tar.xz.delta differ


=
python-dendropy_4.3.0+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/python-dendropy_4.3.0+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+b7f0a5cd5e234a92b68abc798919a574cc692135



View it on GitLab: 
https://salsa.debian.org/med-team/python-dendropy/commit/3658a707995ea37c5053108bc04e6a5dea3a50c8

---
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[med-svn] [Git][med-team/macs][master] Rather use unchanged (==gzipped) example data and precisely describe how these were obtained

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / macs


Commits:
770bb8d5 by Andreas Tille at 2018-02-19T09:46:35+01:00
Rather use unchanged (==gzipped) example data and precisely describe how these 
were obtained

- - - - -


6 changed files:

- debian/README.test
- − debian/examples/aluY.chr1.bed
- + debian/examples/aluY.chr1.bed.gz
- − debian/examples/gerp.chr1.bed
- + debian/examples/gerp.chr1.bed.gz
- + debian/source/include-binaries


Changes:

=
debian/README.test
=
--- a/debian/README.test
+++ b/debian/README.test
@@ -7,6 +7,12 @@ This package can be tested by executing
 
 in order to confirm its integrity.
 
-Note: The sample data are recovered from https://github.com/arq5x/  They are 
both ‘.BED’ 
-file extensions. However the macs package install instructions is
-using the ‘BAM’ extension format. If anyone has any recommendation on where to 
find sample data in this format it will be much appreciated :)
+Note: The sample data are obtained via
+
+wget -q 
https://github.com/arq5x/bedtools2/blob/master/data/aluY.chr1.bed.gz?raw=true 
-O debian/examples/aluY.chr1.bed.gz
+wget -q 
https://github.com/arq5x/bedtools2/blob/master/data/gerp.chr1.bed.gz?raw=true 
-O debian/examples/gerp.chr1.bed.gz
+
+They are both ‘.BED’ file extensions. However the macs package install
+instructions is using the ‘BAM’ extension format. If anyone has any
+recommendation on where to find sample data in this format it will be
+much appreciated :)


=
debian/examples/aluY.chr1.bed deleted
=
The diff for this file was not included because it is too large.

=
debian/examples/aluY.chr1.bed.gz
=
Binary files /dev/null and b/debian/examples/aluY.chr1.bed.gz differ


=
debian/examples/gerp.chr1.bed deleted
=
The diff for this file was not included because it is too large.

=
debian/examples/gerp.chr1.bed.gz
=
Binary files /dev/null and b/debian/examples/gerp.chr1.bed.gz differ


=
debian/source/include-binaries
=
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1,2 @@
+debian/examples/aluY.chr1.bed.gz
+debian/examples/gerp.chr1.bed.gz



View it on GitLab: 
https://salsa.debian.org/med-team/macs/commit/770bb8d52b583cf8e85ad0b37c853624d5a3dbc9

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[med-svn] [Git][med-team/macs][master] 9 commits: README.test needs to be in debian/ dir, spelling changes, add README.test +…

2018-02-19 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / macs


Commits:
f4b9f1ed by Andreas Tille at 2018-02-19T08:35:24+01:00
README.test needs to be in debian/ dir, spelling changes, add README.test + 
run-unit-test to package doc dir

- - - - -
bddd3cf3 by Andreas Tille at 2018-02-19T08:56:33+01:00
Example data were compressed in the packaging process and thus need to be 
uncompressed

- - - - -
2a8f764f by Andreas Tille at 2018-02-19T09:01:05+01:00
d/rules: Do not parse d/changelog

- - - - -
783a8c88 by Andreas Tille at 2018-02-19T09:02:05+01:00
Remove Tim Booth and H. Soon Gweon from Uploaders

- - - - -
bc3d2390 by Andreas Tille at 2018-02-19T09:02:22+01:00
Standards-Version: 4.1.3

- - - - -
37d04ce7 by Andreas Tille at 2018-02-19T09:02:50+01:00
hardening=+all

- - - - -
99791913 by Andreas Tille at 2018-02-19T09:03:11+01:00
debhelper 11

- - - - -
b9684156 by Andreas Tille at 2018-02-19T09:22:28+01:00
There is no dir examples/ neither are there and *.tree files - do 
not attempt to install non-existing files which breaks higher debhelper compat 
level

- - - - -
7c3b8d96 by Andreas Tille at 2018-02-19T09:23:42+01:00
There is no such package macs-example-data declared in debian/control thus this 
file is superflous

- - - - -


9 changed files:

- README.test → debian/README.test
- debian/changelog
- debian/compat
- debian/control
- debian/docs
- − debian/macs-example-data.install
- debian/macs.examples
- debian/rules
- debian/tests/run-unit-test


Changes:

=
README.test → debian/README.test
=
--- a/README.test
+++ b/debian/README.test
@@ -1,4 +1,4 @@
-otes on how this package can be tested.
+Notes on how this package can be tested.
 
 
 This package can be tested by executing
@@ -7,6 +7,6 @@ This package can be tested by executing
 
 in order to confirm its integrity.
 
-Notes : the sample data are recovered from; https://github.com/arq5x/  They 
are both ‘.BED’ 
+Note: The sample data are recovered from https://github.com/arq5x/  They are 
both ‘.BED’ 
 file extensions. However the macs package install instructions is
 using the ‘BAM’ extension format. If anyone has any recommendation on where to 
find sample data in this format it will be much appreciated :)


=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,11 @@ macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
   * debian/upstream/metadata:
  - UTF-8 notation of names rather than TeX syntax
  - added eprint
+  * d/rules: Do not parse d/changelog
+  * Remove Tim Booth and H. Soon Gweon from Uploaders
+  * Standards-Version: 4.1.3
+  * hardening=+all
+  * debhelper 11
 
  -- Andreas Tille   Wed, 10 Aug 2016 08:15:22 +0200
 


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


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,17 @@
 Source: macs
 Maintainer: Debian Med Packaging Team 

 Uploaders: Michael R. Crusoe ,
-   Tim Booth ,
-   H. Soon Gweon ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
dh-python,
python-all-dev,
python-numpy,
python-setuptools,
help2man,
cython
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/macs.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/macs.git
 Homepage: http://github.com/taoliu/MACS/


=
debian/docs
=
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,3 @@
 README.rst
+debian/README.test
+debian/tests/run-unit-test
\ No newline at end of file


=
debian/macs-example-data.install deleted
=
--- a/debian/macs-example-data.install
+++ /dev/null
@@ -1,4 +0,0 @@
-debian/examples/aluY.chr1.bed usr/share/doc/macs/examples
-debian/examples/gerp.chr1.bed  usr/share/doc/macs/examples
-debian/README.test usr/share/doc/macs
-debian/tests/run-unit-test usr/share/doc/macs


=
debian/macs.examples
=
--- a/debian/macs.examples
+++ b/debian/macs.examples
@@ -1,3 +1 @@
-examples/*
 debian/examples/*
-release/common/*.tree


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -1,9 +1,10 @@
 #!/usr/bin/make -f
 
 export PYBUILD_NAME=MACS2
-export