[med-svn] [Git][med-team/libbpp-core][master] 3 commits: Update years

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / libbpp-core


Commits:
f988840a by Andreas Tille at 2018-04-07T09:01:56+02:00
Update years

- - - - -
12e2c494 by Andreas Tille at 2018-04-07T11:50:53+02:00
Provide symbols file only for amd64

- - - - -
b77136c0 by Andreas Tille at 2018-04-07T11:58:48+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-core (2.4.0-3) unstable; urgency=medium
+
+  * Provide symbols file only for amd64
+
+ -- Andreas Tille   Sat, 07 Apr 2018 11:50:58 +0200
+
 libbpp-core (2.4.0-2) unstable; urgency=medium
 
   * Provide full license text of CeCILL license


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,14 +4,14 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-core/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 
 Files: debian/*
-Copyright: 2014 Julien Yann Dutheil 
-Bio++ Development Team
-   2016 Andreas Tille 
+Copyright: 2014-2018 Julien Yann Dutheil 
+ Bio++ Development Team
+   2016-2018 Andreas Tille 
 License: GPL-2+
 
 Files: src/Bpp/Numeric/Matrix/EigenValue.h


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-core/compare/cc18852b0287f5c93c1be27c0cf9713b17fec4c6...b77136c03cc6fcb79fc53d80e07d685bfe5262d0

---
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[med-svn] [Git][med-team/libbpp-core] Pushed new tag debian/2.4.0-3

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed new tag debian/2.4.0-3 at Debian Med / libbpp-core

---
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[med-svn] [Git][med-team/berkeley-express][master] 13 commits: point to GitHub after upstream has added release tags

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / berkeley-express


Commits:
a9db6a95 by Andreas Tille at 2018-04-07T08:20:53+02:00
point to GitHub after upstream has added release tags

- - - - -
73726db7 by Andreas Tille at 2018-04-07T08:21:18+02:00
New upstream version 1.5.2
- - - - -
04aba20e by Andreas Tille at 2018-04-07T08:24:42+02:00
Update upstream source from tag upstream/1.5.2

Update to upstream version 1.5.2
with Debian dir 3c28bc74bf8ebc0711fee266514daa0da3055eb0
- - - - -
0178249b by Andreas Tille at 2018-04-07T08:25:44+02:00
New upstream version

- - - - -
fca463f1 by Andreas Tille at 2018-04-07T08:28:39+02:00
Point Vcs fields to salsa.debian.org (the URL is also normalized to the package 
name as per cme and general considerations)

- - - - -
4d0e9104 by Andreas Tille at 2018-04-07T08:29:37+02:00
debhelper 11

- - - - -
e6ba0dff by Andreas Tille at 2018-04-07T08:38:01+02:00
Adapt patches

- - - - -
20151611 by Andreas Tille at 2018-04-07T08:58:25+02:00
Detection of libbamtools does not work properly - needs to be investigated in 
bamtools

- - - - -
1c93835c by Andreas Tille at 2018-04-07T11:41:05+02:00
express-doc.pdf is not in upstream source any more

- - - - -
e93c9d14 by Andreas Tille at 2018-04-07T11:57:32+02:00
Exclude binaries and other unneeded files

- - - - -
df9edba9 by Andreas Tille at 2018-04-07T11:57:53+02:00
New upstream version 1.5.2+dfsg
- - - - -
6f530420 by Andreas Tille at 2018-04-07T11:58:28+02:00
Update upstream source from tag upstream/1.5.2+dfsg

Update to upstream version 1.5.2+dfsg
with Debian dir bf3dad4c63ea1c4c56b5d0e01de197afccaf13c6
- - - - -
fb534e26 by Andreas Tille at 2018-04-07T12:02:20+02:00
provide html documentation

- - - - -


30 changed files:

- + .gitignore
- CMakeLists.txt
- + Doxyfile
- + README.devel.org
- − debian/berkeley-express-doc.doc-base
- debian/berkeley-express-doc.docs
- debian/berkeley-express.install
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/patches/correct-debug-flags.patch
- debian/patches/drop-zlib
- debian/patches/fix-bamtools-path
- debian/rules
- debian/watch
- − express-doc.pdf
- + html/css/googlesearch.css
- + html/css/mf54_content.css
- + html/css/mf54_grid.css
- + html/css/mf54_reset.css
- + html/downloads/express-0.9.0/express-0.9.0-linux_x86_64.tgz
- + html/downloads/express-0.9.0/express-0.9.0-macosx_x86_64.tgz
- + html/downloads/express-0.9.0/express-0.9.0-src.tgz
- + html/downloads/express-0.9.1/express-0.9.1-linux_x86_64.tgz
- + html/downloads/express-0.9.1/express-0.9.1-macosx_x86_64.tgz
- + html/downloads/express-0.9.1/express-0.9.1-src.tgz
- + html/downloads/express-0.9.2/express-0.9.2-linux_x86_64.tgz
- + html/downloads/express-0.9.2/express-0.9.2-macosx_x86_64.tgz
- + html/downloads/express-0.9.2/express-0.9.2-src.tgz


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/berkeley-express/compare/7aa7b3799a674654d2a2cffd0cccbdd23a568e7f...fb534e2646f6c6d1b0c42ba2f637bf0d84767595

---
View it on GitLab: 
https://salsa.debian.org/med-team/berkeley-express/compare/7aa7b3799a674654d2a2cffd0cccbdd23a568e7f...fb534e2646f6c6d1b0c42ba2f637bf0d84767595
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[med-svn] [Git][med-team/libbpp-qt][pristine-tar] pristine-tar data for libbpp-qt_2.4.0.orig.tar.gz

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-qt


Commits:
9bfbc64c by Julien Y. Dutheil at 2018-04-07T07:38:52+02:00
pristine-tar data for libbpp-qt_2.4.0.orig.tar.gz

- - - - -


2 changed files:

- + libbpp-qt_2.4.0.orig.tar.gz.delta
- + libbpp-qt_2.4.0.orig.tar.gz.id


Changes:

=
libbpp-qt_2.4.0.orig.tar.gz.delta
=
Binary files /dev/null and b/libbpp-qt_2.4.0.orig.tar.gz.delta differ


=
libbpp-qt_2.4.0.orig.tar.gz.id
=
--- /dev/null
+++ b/libbpp-qt_2.4.0.orig.tar.gz.id
@@ -0,0 +1 @@
+c7391650f052c58887612c937e7ddb9d0656ed1c



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-qt/commit/9bfbc64c025761f5f968038be128efe470cd6280

---
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[med-svn] [Git][med-team/berkeley-express][upstream] 2 commits: New upstream version 1.5.2

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed to branch upstream at Debian Med / berkeley-express


Commits:
73726db7 by Andreas Tille at 2018-04-07T08:21:18+02:00
New upstream version 1.5.2
- - - - -
df9edba9 by Andreas Tille at 2018-04-07T11:57:53+02:00
New upstream version 1.5.2+dfsg
- - - - -


30 changed files:

- + .gitignore
- CMakeLists.txt
- + Doxyfile
- + README.devel.org
- − express-doc.pdf
- + html/css/googlesearch.css
- + html/css/mf54_content.css
- + html/css/mf54_grid.css
- + html/css/mf54_reset.css
- + html/downloads/express-0.9.0/express-0.9.0-linux_x86_64.tgz
- + html/downloads/express-0.9.0/express-0.9.0-macosx_x86_64.tgz
- + html/downloads/express-0.9.0/express-0.9.0-src.tgz
- + html/downloads/express-0.9.1/express-0.9.1-linux_x86_64.tgz
- + html/downloads/express-0.9.1/express-0.9.1-macosx_x86_64.tgz
- + html/downloads/express-0.9.1/express-0.9.1-src.tgz
- + html/downloads/express-0.9.2/express-0.9.2-linux_x86_64.tgz
- + html/downloads/express-0.9.2/express-0.9.2-macosx_x86_64.tgz
- + html/downloads/express-0.9.2/express-0.9.2-src.tgz
- + html/downloads/express-0.9.3/express-0.9.3-linux_x86_64.tgz
- + html/downloads/express-0.9.3/express-0.9.3-macosx_x86_64.tgz
- + html/downloads/express-0.9.3/express-0.9.3-src.tgz
- + html/downloads/express-0.9.3/express-0.9.3-win32_x86_64.zip
- + html/downloads/express-0.9.4/express-0.9.4-linux_x86_64.tgz
- + html/downloads/express-0.9.4/express-0.9.4-macosx_x86_64.tgz
- + html/downloads/express-0.9.4/express-0.9.4-src.tgz
- + html/downloads/express-0.9.4/express-0.9.4-win32_x86_64.zip
- + html/downloads/express-0.9.5/express-0.9.5-linux_x86_64.tgz
- + html/downloads/express-0.9.5/express-0.9.5-macosx_x86_64.tgz
- + html/downloads/express-0.9.5/express-0.9.5-src.tgz
- + html/downloads/express-0.9.5/express-0.9.5-win32_x86_64.zip


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/berkeley-express/compare/85eeccb324e8a71a4fdb4f8f57a4865e25de8a0c...df9edba9a8dcac367fdcd6d97ab928811060d926

---
View it on GitLab: 
https://salsa.debian.org/med-team/berkeley-express/compare/85eeccb324e8a71a4fdb4f8f57a4865e25de8a0c...df9edba9a8dcac367fdcd6d97ab928811060d926
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[med-svn] [Git][med-team/berkeley-express][pristine-tar] 2 commits: pristine-tar data for berkeley-express_1.5.2.orig.tar.gz

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / berkeley-express


Commits:
ed569466 by Andreas Tille at 2018-04-07T08:24:42+02:00
pristine-tar data for berkeley-express_1.5.2.orig.tar.gz

- - - - -
44e17586 by Andreas Tille at 2018-04-07T11:58:28+02:00
pristine-tar data for berkeley-express_1.5.2+dfsg.orig.tar.xz

- - - - -


4 changed files:

- + berkeley-express_1.5.2+dfsg.orig.tar.xz.delta
- + berkeley-express_1.5.2+dfsg.orig.tar.xz.id
- + berkeley-express_1.5.2.orig.tar.gz.delta
- + berkeley-express_1.5.2.orig.tar.gz.id


Changes:

=
berkeley-express_1.5.2+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/berkeley-express_1.5.2+dfsg.orig.tar.xz.delta 
differ


=
berkeley-express_1.5.2+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/berkeley-express_1.5.2+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+1d393c93aa9d8a7f3b6ecd49c5ae3a2189e9fa84


=
berkeley-express_1.5.2.orig.tar.gz.delta
=
Binary files /dev/null and b/berkeley-express_1.5.2.orig.tar.gz.delta differ


=
berkeley-express_1.5.2.orig.tar.gz.id
=
--- /dev/null
+++ b/berkeley-express_1.5.2.orig.tar.gz.id
@@ -0,0 +1 @@
+5b8bf0f483a0e9a51866b84ad93d367fd771a36a



View it on GitLab: 
https://salsa.debian.org/med-team/berkeley-express/compare/5033a671393844b689542d596a9d2606efb96992...44e17586466faa6aac0d106b31556a69ca45ffdc

---
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[med-svn] [Git][med-team/berkeley-express] Pushed new tag upstream/1.5.2

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/1.5.2 at Debian Med / berkeley-express

---
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[med-svn] [Git][med-team/community/package_template][master] Hint to https://github.com/FedericoCeratto/debian-package-init/blob/master/deb_create_watch.py

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / community / 
package_template


Commits:
cd816451 by Andreas Tille at 2018-04-07T08:06:14+02:00
Hint to 
https://github.com/FedericoCeratto/debian-package-init/blob/master/deb_create_watch.py

- - - - -


1 changed file:

- debian/watch


Changes:

=
debian/watch
=
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,6 @@
+# alternatively to this template you might like to try
+#   
https://github.com/FedericoCeratto/debian-package-init/blob/master/deb_create_watch.py
+
 version=4
 
 # Uncomment to examine a Webpage



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[med-svn] [Git][med-team/libbpp-qt] Pushed new tag upstream/2.4.0

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-qt

---
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[med-svn] [Git][med-team/berkeley-express] Pushed new tag upstream/1.5.2+dfsg

2018-04-07 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/1.5.2+dfsg at Debian Med / 
berkeley-express

---
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[med-svn] [Git][med-team/libbpp-popgen][master] Symbol files for amd64 only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen


Commits:
e4cb4464 by Julien Y. Dutheil at 2018-04-07T21:49:41+02:00
Symbol files for amd64 only.

Fixed date in copyright file.

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-popgen (2.4.0-3) UNRELEASED; urgency=medium
+
+  * Provide symbols file only for amd64
+
+ -- Julien Dutheil   Sat, 07 Apr 2018 21:48:53 
+0200
+
 libbpp-popgen (2.4.0-2) UNRELEASED; urgency=medium
 
   * Provide full license text of CeCILL license


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-popgen/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -7,6 +7,23 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-popgen/commit/e4cb446416a332522166566a97d0b8b39055374e

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[med-svn] [Git][med-team/libbpp-seq][master] Symbols file for amd64 only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq


Commits:
9f467c88 by Julien Y. Dutheil at 2018-04-07T20:38:36+02:00
Symbols file for amd64 only.

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-seq (2.4.0-3) UNRELEASED; urgency=medium
+
+  * Provide symbols file only for amd64
+
+ -- Julien Dutheil   Sat, 07 Apr 2018 20:37:13 
+0200
+
 libbpp-seq (2.4.0-2) UNRELEASED; urgency=medium
 
   * Provide full license text of CeCILL license


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,9 +9,24 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
-   # Broken header, don't install (if we do, the postinst will pull it
-   # into generic include files)
dh_install
d-shlibmove --commit \
--multiarch \



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-seq/commit/9f467c88bd4d867c96caf18552b11142daa21a37

---
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[med-svn] [Git][med-team/libbpp-seq][master] Fixed changelog.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq


Commits:
fe0ca09c by Julien Y. Dutheil at 2018-04-07T21:57:55+02:00
Fixed changelog.

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,9 @@
-libbpp-seq (2.4.0-3) UNRELEASED; urgency=medium
-
-  * Provide symbols file only for amd64
-
- -- Julien Dutheil   Sat, 07 Apr 2018 20:37:13 
+0200
-
 libbpp-seq (2.4.0-2) UNRELEASED; urgency=medium
 
+  [ Julien Dutheil ]
+  * Provide symbols file only for amd64
+  
+  [ Andreas Tille ]
   * Provide full license text of CeCILL license
 
  -- Andreas Tille   Fri, 06 Apr 2018 07:51:07 +0200



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-seq/commit/fe0ca09c12c33f971eacc1364e01da1eb0cc29af

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[med-svn] [Git][med-team/libbpp-popgen][master] Fixed changelog.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen


Commits:
6466a41e by Julien Y. Dutheil at 2018-04-07T21:58:49+02:00
Fixed changelog.

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,9 @@
-libbpp-popgen (2.4.0-3) UNRELEASED; urgency=medium
-
-  * Provide symbols file only for amd64
-
- -- Julien Dutheil   Sat, 07 Apr 2018 21:48:53 
+0200
-
 libbpp-popgen (2.4.0-2) UNRELEASED; urgency=medium
 
+  [ Julien Dutheil ]
+  * Provide symbols file only for amd64
+  
+  [ Andreas Tille ]
   * Provide full license text of CeCILL license
 
  -- Andreas Tille   Fri, 06 Apr 2018 07:55:34 +0200



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-popgen/commit/6466a41e5c1a63cad951ef4315fdffe60e082896

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[med-svn] [Git][med-team/libbpp-phyl][master] Symbols for amd64 arch only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl


Commits:
1b47abd0 by Julien Y. Dutheil at 2018-04-07T21:45:42+02:00
Symbols for amd64 arch only.

Fixed dates in copyright file.

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-phyl (2.4.0-3) UNRELEASED; urgency=medium
+
+  * Provide symbols file only for amd64
+
+ -- Julien Dutheil   Sat, 07 Apr 2018 21:35:24 
+0200
+
 libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium
 
   * Provide full license text of CeCILL license


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-phyl/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



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[med-svn] [Git][med-team/libbpp-phyl][master] Fixed changelog.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl


Commits:
75daa418 by Julien Y. Dutheil at 2018-04-07T21:57:05+02:00
Fixed changelog.

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,9 @@
-libbpp-phyl (2.4.0-3) UNRELEASED; urgency=medium
-
-  * Provide symbols file only for amd64
-
- -- Julien Dutheil   Sat, 07 Apr 2018 21:35:24 
+0200
-
 libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium
 
+  [ Julien Dutheil ]
+  * Provide symbols file only for amd64
+  
+  [ Andreas Tille ]
   * Provide full license text of CeCILL license
 
  -- Andreas Tille   Fri, 06 Apr 2018 07:53:20 +0200



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https://salsa.debian.org/med-team/libbpp-phyl/commit/75daa418a0ccac25c0c9d35297f567589a88c3a6

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[med-svn] [Git][med-team/libbpp-raa][master] Symbol files for amd64 arch only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-raa


Commits:
5e61f327 by Julien Y. Dutheil at 2018-04-07T21:55:52+02:00
Symbol files for amd64 arch only.

Fixed dates in copyright file.

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,9 @@
 libbpp-raa (2.4.0-2) UNRELEASED; urgency=medium
 
+  [ Julien Dutheil ]
+  * Provide symbols file only for amd64
+
+  [ Andreas Tille ]
   * Provide full license text of CeCILL license
 
  -- Andreas Tille   Fri, 06 Apr 2018 07:57:17 +0200


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-raa/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -6,6 +6,22 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
dh $@
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
 
 override_dh_install:
dh_install



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[med-svn] [Git][med-team/libbpp-seq-omics][master] Symbols for amd64 arch only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics


Commits:
8d9fc21e by Julien Y. Dutheil at 2018-04-07T22:18:36+02:00
Symbols for amd64 arch only.

Fixed dates in copyright file.

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
-libbpp-seq-omics (2.4.0-3) UNRELEASED; urgency=medium
+libbpp-seq-omics (2.4.0-2) UNRELEASED; urgency=medium
 
   [ Julien Dutheil ]
+  * Provide symbols file only for amd64
   * Versioned Build-Depends: d-shlibs (>= 0.82)
 
   [ Andreas Tille ]


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-seq-omics/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



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---
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[med-svn] [Git][med-team/gff2ps][master] Updated RRID in d/u/metadata

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / gff2ps


Commits:
bb9a13f7 by Steffen Möller at 2018-04-07T14:07:32+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,20 @@
 Reference:
-  Author: J. F. Abril and R. Guigó
-  Title: "gff2ps: visualizing genomic annotations."
-  Journal: Bioinformatics
-  Year: 2000
-  Volume: 16
-  Number: 8
-  Pages: 743-744
-  DOI: 10.1093/bioinformatics/16.8.743
-  PMID: 11099262
-  URL: http://bioinformatics.oxfordjournals.org/content/16/8/743.abstract
-  eprint: 
http://bioinformatics.oxfordjournals.org/content/16/8/743.full.pdf+html
+ Author: J. F. Abril and R. Guigó
+ Title: "gff2ps: visualizing genomic annotations."
+ Journal: Bioinformatics
+ Year: 2000
+ Volume: 16
+ Number: 8
+ Pages: 743-744
+ DOI: 10.1093/bioinformatics/16.8.743
+ PMID: 11099262
+ URL: http://bioinformatics.oxfordjournals.org/content/16/8/743.abstract
+ eprint: >
+  http://bioinformatics.oxfordjournals.org/content/16/8/743.full.pdf+html
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_17140
+ - Name: SciCrunch
+   Entry: SCR_000462
+ - Name: bio.tools
+   Entry: gff2ps
\ No newline at end of file



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[med-svn] [Git][med-team/raccoon][master] Updated RRID in d/u/metadata

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / raccoon


Commits:
e58ef230 by Steffen Möller at 2018-04-07T15:04:59+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,21 @@
 Reference:
-  Author: Sandro Cosconati and Stefano Forli and Alex L Perryman and Rodney 
Harris and David S Goodsell and Arthur J Olson
-  Title: "Virtual screening with AutoDock: theory and practice"
-  Journal: Expert Opinion on Drug Discovery
-  Year: 2010
-  Volume: 5
-  Number: 6
-  Pages: 597–607
-  DOI: 10.1517/17460441.2010.484460
-  PMID: 21532931
-  URL: http://informahealthcare.com/doi/abs/10.1517/17460441.2010.484460
-  eprint: http://informahealthcare.com/doi/pdfplus/10.1517/17460441.2010.484460
+ Author: >
+  Sandro Cosconati and Stefano Forli and Alex L. Perryman and Rodney Harris and
+  David S. Goodsell and Arthur J. Olson
+ Title: "Virtual screening with AutoDock: theory and practice"
+ Journal: Expert Opinion on Drug Discovery
+ Year: 2010
+ Volume: 5
+ Number: 6
+ Pages: 597–607
+ DOI: 10.1517/17460441.2010.484460
+ PMID: 21532931
+ URL: http://informahealthcare.com/doi/abs/10.1517/17460441.2010.484460
+ ePrint: http://informahealthcare.com/doi/pdfplus/10.1517/17460441.2010.484460
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_21300
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA



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[med-svn] [Git][med-team/clonalorigin][master] Updated RRID in d/u/metadata

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / clonalorigin


Commits:
bea9875a by Steffen Möller at 2018-04-07T13:44:17+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,23 @@
+Name: ClonalOrigin
 Reference:
-  Author: Xavier Didelot and Daniel Lawson and Aaron Darling and Daniel Falush
-  Title: Inference of Homologous Recombination in Bacteria Using Whole-Genome 
Sequences
-  Journal: Genetics
-  Year: 2010
-  Volume: 186
-  Number: 4
-  Pages: 1435-1449
-  DOI: 10.1534/genetics.110.120121
-  PMID: 20923983
-  URL: http://www.genetics.org/content/186/4/1435.abstract
-  eprint: http://www.genetics.org/content/186/4/1435.full.pdf+html
+ - Author: >
+Xavier Didelot and Daniel Lawson and Aaron Darling and Daniel Falush
+   Title: >
+Inference of Homologous Recombination in Bacteria Using
+Whole-Genome Sequences
+   Journal: Genetics
+   Year: 2010
+   Volume: 186
+   Number: 4
+   Pages: 1435-1449
+   DOI: 10.1534/genetics.110.120121
+   PMID: 20923983
+   URL: http://www.genetics.org/content/186/4/1435.abstract
+   eprint: http://www.genetics.org/content/186/4/1435.full.pdf+html
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_18881
+ - Name: bio.tools
+   Entry: ClonalOrigin
+ - Name: SciCrunch
+   Entry: SCR_016061



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[med-svn] [Git][med-team/logol][master] Added new d/u/metadata file

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / logol


Commits:
77c6e10d by Steffen Möller at 2018-04-07T20:21:42+00:00
Added new d/u/metadata file

RRIDs only.
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_20118
+ - Name: bio.tools
+   Entry: logol
+ - Name: SciCrunch
+   Entry: NA



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https://salsa.debian.org/med-team/logol/commit/77c6e10da3686ec4c3bf7d8975dd05a7f29b3a16

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[med-svn] [Git][med-team/bcbio][master] Added new d/u/metadata file

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
04fae2cc by Steffen Möller at 2018-04-07T21:40:17+00:00
Added new d/u/metadata file
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_01121
+ - Name: bio.tools
+   Entry: bcbio-nextgen
+ - Name: SciCrunch
+   Entry: NA



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https://salsa.debian.org/med-team/bcbio/commit/04fae2cc47566fc50fffd2f3a17dc7f8577f9725

---
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[med-svn] [Git][med-team/logol][master] Update control

2018-04-07 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / logol


Commits:
9cb2907b by Steffen Möller at 2018-04-07T22:27:11+00:00
Update control
- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -56,8 +56,8 @@ Depends: ${shlibs:Depends},
 Suggests: ruby-cassiopee (>=0.1.12)
 Description: Pattern matching tool using Logol language
  Logol is a pattern matching tool using the Logol language.
- It searches with a specific grammar a pattern in small
- or large sequence (dna, rna, protein). It provides complete
+ It searches with a specific grammar for a pattern in small
+ or large sequences (DNA, RNA, protein). It provides complete
  result matching with the original grammar in the results.
 
 Package: logol-bin
@@ -72,5 +72,5 @@ Description: Pattern matching tool using Logol language
  .
  Logol is a pattern matching tool using the Logol language.
  It searches with a specific grammar a pattern in small
- or large sequence (dna, rna, protein). It provides complete
+ or large sequences (DNA, RNA, protein). It provides complete
  result matching with the original grammar in the results.



View it on GitLab: 
https://salsa.debian.org/med-team/logol/commit/9cb2907b673bc38c5c0e5e06b97f7a552d8eadfc

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[med-svn] [Git][med-team/libbpp-phyl-omics][master] Symbols for amd64 arch only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl-omics


Commits:
30462412 by Julien Y. Dutheil at 2018-04-07T22:22:13+02:00
Symbols for amd64 arch only.

Also restored CMakeList.txt file.
Updated dates in copyright file.

- - - - -


4 changed files:

- CMakeLists.txt
- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
 project (bpp-phyl-omics CXX)
 
 # Compile options
-#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
+set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
 
 IF(NOT CMAKE_BUILD_TYPE)
   SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING


=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,9 @@
 libbpp-phyl-omics (2.4.0-2) UNRELEASED; urgency=medium
 
+  [ Julien Dutheil ]
+  * Provide symbols file only for amd64
+  
+  [ Andreas Tille ]
   * Provide full license text of CeCILL license
 
  -- Andreas Tille   Fri, 06 Apr 2018 07:54:46 +0200


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil 

 Source: https://github.com/BioPP/bpp-phyl-omics/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/304624126151f5cecd0b43f5928a70aab0dd09c1

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[med-svn] [Git][med-team/libbpp-qt][master] Symbols for amd64 arch only.

2018-04-07 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-qt


Commits:
7be1b21e by Julien Y. Dutheil at 2018-04-07T22:27:00+02:00
Symbols for amd64 arch only.

Updated dates in copyright file.

- - - - -


3 changed files:

- debian/changelog
- debian/copyright
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ libbpp-qt (2.4.0-1) UNRELEASED; urgency=medium
   * Provide full license text of CeCILL license
 
   [ Julien Y. Dutheil ]
+  * Provide symbols file only for amd64
   * New upstream version
   * Removed unnecessary override
 


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,10 +1,10 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Qt
+Upstream-Name: Bpp-Qt
 Upstream-Contact: Julien Yann Dutheil 
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-qt/
 
 Files: *
-Copyright: 2010-2016 Julien Yann Dutheil 
+Copyright: 2010-2018 Julien Yann Dutheil 
  Bio++ Development Team
 License: CeCILL
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
 %:
dh $@
 
+override_dh_makeshlibs:
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "Architecture amd64 is the only one where a symbols file is 
provided"
+else
+   echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided"
+   mkdir -p debian/hidesymbols
+   mv debian/*.symbols debian/hidesymbols
+endif
+   dh_makeshlibs
+ifeq ($(DEB_BUILD_ARCH),amd64)
+   echo "dh_makeshlibs for architecture amd64 including symbols done"
+else
+   # restore original debian/ dir to enable building twice in a row
+   mv debian/hidesymbols/*.symbols debian
+   rmdir debian/hidesymbols
+endif
+
 override_dh_install:
dh_install
d-shlibmove --commit \



View it on GitLab: 
https://salsa.debian.org/med-team/libbpp-qt/commit/7be1b21e92bfbd2a64302b488b2f3ff9d2375767

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https://salsa.debian.org/med-team/libbpp-qt/commit/7be1b21e92bfbd2a64302b488b2f3ff9d2375767
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