[med-svn] [r-cran-ape] 01/01: Update d/changelog

2015-12-06 Thread Dylan Aïssi 
This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository r-cran-ape.

commit e17e358ba86679df436ddbf694b5cd4618960f14
Author: Dylan Aïssi 
Date:   Sun Dec 6 16:22:35 2015 +0100

Update d/changelog
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 69669a8..47fee71 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+r-cran-ape (3.4-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+
+ -- Dylan Aïssi   Sun, 06 Dec 2015 16:20:20 +0100
+
 r-cran-ape (3.3-1) unstable; urgency=low
 
   * New upstream release.

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[med-svn] [r-cran-ape] branch master updated (09deb23 -> e17e358)

2015-12-06 Thread Dylan Aïssi 
This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to branch master
in repository r-cran-ape.

  from  09deb23   Merge tag 'upstream/3.4'
   new  e17e358   Update d/changelog

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

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[med-svn] r20655 - trunk/packages/altree/trunk/debian

2015-12-06 Thread Vincent Danjean 
Author: vdanjean
Date: 2015-12-06 14:23:58 + (Sun, 06 Dec 2015)
New Revision: 20655

Modified:
   trunk/packages/altree/trunk/debian/changelog
   trunk/packages/altree/trunk/debian/control
Log:
[debian/control] Update build dependencies for GSL 2, change libgsl0-dev to
libgsl-dev. Thanks Bas Couwenberg  (Closes: #807173)

Modified: trunk/packages/altree/trunk/debian/changelog
===
--- trunk/packages/altree/trunk/debian/changelog2015-12-05 23:00:06 UTC 
(rev 20654)
+++ trunk/packages/altree/trunk/debian/changelog2015-12-06 14:23:58 UTC 
(rev 20655)
@@ -1,3 +1,10 @@
+altree (1.3.1-3) UNRELEASED; urgency=medium
+
+  * [debian/control] Update build dependencies for GSL 2, change libgsl0-dev to
+libgsl-dev. Thanks Bas Couwenberg  (Closes: #807173)
+
+ -- Vincent Danjean   Sun, 06 Dec 2015 15:22:44 +0100
+
 altree (1.3.1-2) unstable; urgency=medium
 
   * Fix "FTBFS with clang instead of gcc" 

Modified: trunk/packages/altree/trunk/debian/control
===
--- trunk/packages/altree/trunk/debian/control  2015-12-05 23:00:06 UTC (rev 
20654)
+++ trunk/packages/altree/trunk/debian/control  2015-12-06 14:23:58 UTC (rev 
20655)
@@ -8,7 +8,7 @@
 Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript,
  texlive-lang-french, texlive-latex-extra, texlive-latex-recommended,
  texlive-fonts-recommended,
- libmath-tamuanova-perl, libgsl0-dev, libatlas-base-dev,
+ libmath-tamuanova-perl, libgsl-dev, libatlas-base-dev,
  libtest-deep-perl
 Standards-Version: 3.9.5
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/altree/trunk/


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[med-svn] [python-skbio] 01/01: Package is actually not yet released

2015-12-06 Thread Andreas Tille 
This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-skbio.

commit 3a0186d05e06601255eaa9ce6072de874e6460ad
Author: Andreas Tille 
Date:   Sun Dec 6 09:05:46 2015 +0100

Package is actually not yet released
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index d7c9248..3687f17 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-python-skbio (0.4.0-4) unstable; urgency=medium
+python-skbio (0.4.0-4) UNRELEASED; urgency=medium
 
   * Build documentation and create new python-skbio-doc package (Closes:
 #806594)

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[med-svn] [bart] 01/01: add to build-depends and recommends

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to branch master
in repository bart.

commit 846496ab91ffdb82c7a13c79a095c358219598c2
Author: Martin Uecker 
Date:   Sun Dec 6 12:02:44 2015 +0100

add to build-depends and recommends
---
 debian/control | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 60ce4e6..f68af2f 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Martin Uecker 
 Section: science
 Priority: optional
 Standards-Version: 3.9.5
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9), libfftw3-dev, libgsl0-dev, liblapack-dev, 
libpng-dev
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bart.git
 Vcs-Git: git://anonscm.debian.org/debian-med/bart.git
 Homepage: https://mrirecon.github.io/bart/
@@ -12,6 +12,7 @@ Homepage: https://mrirecon.github.io/bart/
 Package: bart
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: octave
 Description: tools for computational magnetic resonance imaging
  The Berkeley Advanced Reconstruction Toolbox (BART) is a free and
  open-source image-reconstruction framework for Computational Magnetic

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[med-svn] [bart] branch master updated (afd08db -> 846496a)

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a change to branch master
in repository bart.

  from  afd08db   Add Vcs fields and homepage
   new  846496a   add to build-depends and recommends

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/control | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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[med-svn] r20660 - trunk/packages/ampliconnoise/trunk/debian

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 20:26:09 + (Sun, 06 Dec 2015)
New Revision: 20660

Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
Log:
Close bug


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===
--- trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:24:24 UTC 
(rev 20659)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:26:09 UTC 
(rev 20660)
@@ -2,6 +2,7 @@
 
   [ Bas Couwenberg ]
   * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
+Closes: #804246
 
   [ Andreas Tille ]
   * cme fix dpkg-control


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[med-svn] [fastqc] tag debian/0.11.4+dfsg-1 created (now 8e19dba)

2015-12-06 Thread Andreas Tille 
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tille pushed a change to tag debian/0.11.4+dfsg-1
in repository fastqc.

at  8e19dba   (commit)
No new revisions were added by this update.

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[med-svn] [fastqc] 01/02: replace debian/menu by debian/fastqc.desktop

2015-12-06 Thread Andreas Tille 
This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository fastqc.

commit 266955fd44435c5be11ab25dfd5df012d9a892a5
Author: Andreas Tille 
Date:   Sun Dec 6 20:02:59 2015 +0100

replace debian/menu by debian/fastqc.desktop
---
 debian/changelog  |  1 +
 debian/fastqc.desktop | 13 +
 debian/install|  6 --
 debian/menu   |  2 --
 4 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 636a667..ad4e076 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ fastqc (0.11.4+dfsg-1) UNRELEASED; urgency=medium
   * deban/watch: fix version mangling
   * New Build-Depends: ant, libsis-hdf5-java
   * DEP5 issue solved by proper sequence of paragraphs
+  * replace debian/menu by debian/fastqc.desktop
 
  -- Andreas Tille   Tue, 03 Nov 2015 14:37:28 +0100
 
diff --git a/debian/fastqc.desktop b/debian/fastqc.desktop
new file mode 100644
index 000..eae1f48
--- /dev/null
+++ b/debian/fastqc.desktop
@@ -0,0 +1,13 @@
+[Desktop Entry]
+Comment=quality control for high throughput sequence data
+Exec=fastqc
+GenericName[en_US]=FastQC quality control
+GenericName=FastQC quality control
+Icon=fastqc_icon
+Name[en_US]=FastQC quality control
+Name=FastQC quality control
+Categories=Science;Biology;
+StartupNotify=false
+Terminal=false
+Type=Application
+Keywords=genomics
diff --git a/debian/install b/debian/install
index 3a04635..101f343 100644
--- a/debian/install
+++ b/debian/install
@@ -1,2 +1,4 @@
-fastqc usr/bin
-Help   usr/share/fastqc
\ No newline at end of file
+fastqc usr/bin
+Help   usr/share/fastqc
+debian/*.desktop   usr/share/applications
+Templates/Icons/fastqc_icon.pngusr/share/icons/hicolor/32x32/apps/
\ No newline at end of file
diff --git a/debian/menu b/debian/menu
deleted file mode 100644
index efe2e38..000
--- a/debian/menu
+++ /dev/null
@@ -1,2 +0,0 @@
-?package(fastqc):needs="X11" section="Applications/Science/Biology"\
-  title="fastqc" command="/usr/bin/fastqc"

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[med-svn] r20663 - trunk/packages/gwyddion/trunk/debian

2015-12-06 Thread Jan Beyer 
Author: beathovn-guest
Date: 2015-12-06 21:13:17 + (Sun, 06 Dec 2015)
New Revision: 20663

Modified:
   trunk/packages/gwyddion/trunk/debian/changelog
Log:
new upstream version 2.43 released. First Debian revision -1. no particular 
changes needed.


Modified: trunk/packages/gwyddion/trunk/debian/changelog
===
--- trunk/packages/gwyddion/trunk/debian/changelog  2015-12-06 21:04:45 UTC 
(rev 20662)
+++ trunk/packages/gwyddion/trunk/debian/changelog  2015-12-06 21:13:17 UTC 
(rev 20663)
@@ -1,3 +1,9 @@
+gwyddion (2.43-1) unstable; urgency=medium
+
+  * New upstream release
+
+ -- Jan Beyer   Sun, 06 Dec 2015 21:44:42 +0100
+
 gwyddion (2.42-1) unstable; urgency=medium
 
   * New upstream release


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[med-svn] [pbalign] branch debian/jessie-backports created (now c555a02)

2015-12-06 Thread Afif Elghraoui 
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afif-guest pushed a change to branch debian/jessie-backports
in repository pbalign.

at  c555a02   pbalign (0.2.0-1~bpo8+1) jessie-backports; urgency=medium

This branch includes the following new commits:

   new  c555a02   pbalign (0.2.0-1~bpo8+1) jessie-backports; urgency=medium

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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[med-svn] [pbalign] 01/01: pbalign (0.2.0-1~bpo8+1) jessie-backports; urgency=medium

2015-12-06 Thread Afif Elghraoui 
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afif-guest pushed a commit to branch debian/jessie-backports
in repository pbalign.

commit c555a02c9c9317132513965dc8c2bf8abdbed7f2
Author: Afif Elghraoui 
Date:   Sun Dec 6 14:23:33 2015 -0800

pbalign (0.2.0-1~bpo8+1) jessie-backports; urgency=medium

  * Rebuild for jessie-backports.
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 45a299c..999542b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+pbalign (0.2.0-1~bpo8+1) jessie-backports; urgency=medium
+
+  * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui   Sun, 06 Dec 2015 14:04:12 -0800
+
 pbalign (0.2.0-1) unstable; urgency=low
 
   * Initial release (Closes: #797675)

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[med-svn] [bart] branch upstream updated (f2cc7f3 -> fc30b69)

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a change to branch upstream
in repository bart.

  from  f2cc7f3   fix install on Mac OS X
  adds  53b631b   added lrdecom to do multi-scale low rank decomposition
  adds  b2f5336   merge bart
  adds  1966516   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  c04a198   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  b02cdc5   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  5e9bf80   changed lrdecom to lrmatrix. added matrix completion 
ability
  adds  7ad77df   Merge pull request #15 from frankong/master
  adds  263f961   make bartview show file name
  adds  12d2968   add Sid to ACKNOWLEDGEMENTS
  adds  67660b3   make bart matlab script look for system-wide bart
  adds  ccf350d   make git-version.sh more robust
  adds  f3f6d1a   Makefile improvements
  adds  d689d04   rework main dispatch
  adds  fc30b69   fix const

No new revisions were added by this update.

Summary of changes:
 ACKNOWLEDGEMENTS |   1 +
 Makefile |  26 +++--
 bartview.py  |   1 +
 git-version.sh   |   4 +-
 matlab/bart.m|  18 +++-
 rules/box.mk |   2 -
 src/bart.c   |  10 +-
 src/bbox.c   |   1 +
 src/lrmatrix.c   | 320 +++
 src/main.c   |   8 ++
 src/main.h   |  12 +++
 src/nlinv.c  |   2 +-
 12 files changed, 378 insertions(+), 27 deletions(-)
 create mode 100644 src/lrmatrix.c
 create mode 100644 src/main.c
 create mode 100644 src/main.h

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[med-svn] [bart] 01/03: standards version

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to branch master
in repository bart.

commit 0febf1cbdbb73f28985ba179bef3cf9cc1038c46
Author: Martin Uecker 
Date:   Mon Dec 7 00:32:53 2015 +0100

standards version
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index f68af2f..8d16f72 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team 

 Section: science
 Priority: optional
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
 Build-Depends: debhelper (>= 9), libfftw3-dev, libgsl0-dev, liblapack-dev, 
libpng-dev
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bart.git
 Vcs-Git: git://anonscm.debian.org/debian-med/bart.git

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[med-svn] [bart] 02/03: ignore autogen. files

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to branch master
in repository bart.

commit bd25f464371279737d80fc19569fe5ebe253a3e4
Author: Martin Uecker 
Date:   Mon Dec 7 00:33:04 2015 +0100

ignore autogen. files
---
 debian/source/options | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/source/options b/debian/source/options
index c9bbbcc..61b41e4 100644
--- a/debian/source/options
+++ b/debian/source/options
@@ -1,2 +1,2 @@
 # Don't store changes on autogenerated files
-extend-diff-ignore = "(^|/)(version.inc)$"
+extend-diff-ignore = "(^|/)(version.(inc|txt)|commands.txt)$"

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[med-svn] [bart] branch master updated (846496a -> f120ff0)

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a change to branch master
in repository bart.

  from  846496a   add to build-depends and recommends
   new  0febf1c   standards version
   new  bd25f46   ignore autogen. files
  adds  53b631b   added lrdecom to do multi-scale low rank decomposition
  adds  b2f5336   merge bart
  adds  1966516   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  c04a198   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  b02cdc5   Merge branch 'master' of https://github.com/mrirecon/bart
  adds  5e9bf80   changed lrdecom to lrmatrix. added matrix completion 
ability
  adds  7ad77df   Merge pull request #15 from frankong/master
  adds  263f961   make bartview show file name
  adds  12d2968   add Sid to ACKNOWLEDGEMENTS
  adds  67660b3   make bart matlab script look for system-wide bart
  adds  ccf350d   make git-version.sh more robust
  adds  f3f6d1a   Makefile improvements
  adds  d689d04   rework main dispatch
  adds  fc30b69   fix const
   new  f120ff0   Merge tag 'v0.2.09d'

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 ACKNOWLEDGEMENTS  |   1 +
 Makefile  |  26 ++--
 bartview.py   |   1 +
 debian/control|   2 +-
 debian/source/options |   2 +-
 git-version.sh|   4 +-
 matlab/bart.m |  18 ++-
 rules/box.mk  |   2 -
 src/bart.c|  10 +-
 src/bbox.c|   1 +
 src/lrmatrix.c| 320 ++
 src/main.c|   8 ++
 src/main.h|  12 ++
 src/nlinv.c   |   2 +-
 14 files changed, 380 insertions(+), 29 deletions(-)
 create mode 100644 src/lrmatrix.c
 create mode 100644 src/main.c
 create mode 100644 src/main.h

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[med-svn] [bart] 03/03: Merge tag 'v0.2.09d'

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to branch master
in repository bart.

commit f120ff0bdd1b5137c21eaa81437f07e59e974c56
Merge: bd25f46 fc30b69
Author: Martin Uecker 
Date:   Mon Dec 7 00:33:39 2015 +0100

Merge tag 'v0.2.09d'

Debian-med package 0.2.09

 ACKNOWLEDGEMENTS |   1 +
 Makefile |  26 +++--
 bartview.py  |   1 +
 git-version.sh   |   4 +-
 matlab/bart.m|  18 +++-
 rules/box.mk |   2 -
 src/bart.c   |  10 +-
 src/bbox.c   |   1 +
 src/lrmatrix.c   | 320 +++
 src/main.c   |   8 ++
 src/main.h   |  12 +++
 src/nlinv.c  |   2 +-
 12 files changed, 378 insertions(+), 27 deletions(-)

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[med-svn] r20658 - trunk/packages/ampliconnoise/trunk/debian

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 20:21:43 + (Sun, 06 Dec 2015)
New Revision: 20658

Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/control
Log:
Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===
--- trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 19:45:10 UTC 
(rev 20657)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:21:43 UTC 
(rev 20658)
@@ -1,3 +1,10 @@
+ampliconnoise (1.29-2.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
+
+ -- Bas Couwenberg   Sun, 22 Nov 2015 00:31:23 +0100
+
 ampliconnoise (1.29-2) unstable; urgency=low
 
   [ Arthur Marble ]

Modified: trunk/packages/ampliconnoise/trunk/debian/control
===
--- trunk/packages/ampliconnoise/trunk/debian/control   2015-12-06 19:45:10 UTC 
(rev 20657)
+++ trunk/packages/ampliconnoise/trunk/debian/control   2015-12-06 20:21:43 UTC 
(rev 20658)
@@ -5,7 +5,7 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-   libgsl0-dev,
+   libgsl-dev,
libopenmpi-dev
 Standards-Version: 3.9.5
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ampliconnoise/trunk/


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[med-svn] [python-pbconsensuscore] branch master updated (a097a44 -> df7e226)

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a change to branch master
in repository python-pbconsensuscore.

  from  a097a44   python-pbconsensuscore (1.0.1-1) unstable; urgency=low
   new  df7e226   Add lintian override for spurious unknown architecture 
warning

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Summary of changes:
 debian/changelog| 6 ++
 debian/source/lintian-overrides | 2 ++
 2 files changed, 8 insertions(+)
 create mode 100644 debian/source/lintian-overrides

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[med-svn] [python-pbconsensuscore] 01/01: Add lintian override for spurious unknown architecture warning

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository python-pbconsensuscore.

commit df7e2269b12dc49554464e56923663ae3d0e11ef
Author: Afif Elghraoui 
Date:   Sun Dec 6 14:09:47 2015 -0800

Add lintian override for spurious unknown architecture warning
---
 debian/changelog| 6 ++
 debian/source/lintian-overrides | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index cb37c28..7ebe0b9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-pbconsensuscore (1.0.1-2) UNRELEASED; urgency=low
+
+  * Add lintian override for "unknown architecture x32" warning.
+
+ -- Afif Elghraoui   Sun, 06 Dec 2015 14:08:21 -0800
+
 python-pbconsensuscore (1.0.1-1) unstable; urgency=low
 
   * Run build-time tests
diff --git a/debian/source/lintian-overrides b/debian/source/lintian-overrides
new file mode 100644
index 000..164c686
--- /dev/null
+++ b/debian/source/lintian-overrides
@@ -0,0 +1,2 @@
+# x32 should be a known architecture, right?
+unknown-architecture any-x32

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[med-svn] r20657 - trunk/packages/adun.app/tags

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 19:45:10 + (Sun, 06 Dec 2015)
New Revision: 20657

Added:
   trunk/packages/adun.app/tags/0.81-8/
Removed:
   trunk/packages/adun.app/tags/0.81-2/
   trunk/packages/adun.app/tags/0.81-4/
   trunk/packages/adun.app/tags/0.81-5/
Log:
Tagged 0.81-8



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[med-svn] r20656 - trunk/packages/adun.app/trunk/debian

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 19:44:18 + (Sun, 06 Dec 2015)
New Revision: 20656

Removed:
   trunk/packages/adun.app/trunk/debian/menu
Modified:
   trunk/packages/adun.app/trunk/debian/changelog
   trunk/packages/adun.app/trunk/debian/control
Log:
Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev. drop 
debian/menu file



Modified: trunk/packages/adun.app/trunk/debian/changelog
===
--- trunk/packages/adun.app/trunk/debian/changelog  2015-12-06 14:23:58 UTC 
(rev 20655)
+++ trunk/packages/adun.app/trunk/debian/changelog  2015-12-06 19:44:18 UTC 
(rev 20656)
@@ -1,3 +1,14 @@
+adun.app (0.81-8) unstable; urgency=medium
+
+  [ Bas Couwenberg ]
+  * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
+Closes: #807176
+
+  [ Andreas Tille ]
+  * drop debian/menu file
+
+ -- Andreas Tille   Sun, 06 Dec 2015 19:46:48 +0100
+
 adun.app (0.81-7) unstable; urgency=medium
 
   [ Yavor Doganov ]

Modified: trunk/packages/adun.app/trunk/debian/control
===
--- trunk/packages/adun.app/trunk/debian/control2015-12-06 14:23:58 UTC 
(rev 20655)
+++ trunk/packages/adun.app/trunk/debian/control2015-12-06 19:44:18 UTC 
(rev 20656)
@@ -9,7 +9,7 @@
libgnustep-gui-dev,
libsteptalk-dev,
libsqlclient-dev,
-   libgsl0-dev,
+   libgsl-dev,
imagemagick
 Standards-Version: 3.9.6
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/adun.app/trunk/

Deleted: trunk/packages/adun.app/trunk/debian/menu
===
--- trunk/packages/adun.app/trunk/debian/menu   2015-12-06 14:23:58 UTC (rev 
20655)
+++ trunk/packages/adun.app/trunk/debian/menu   2015-12-06 19:44:18 UTC (rev 
20656)
@@ -1,5 +0,0 @@
-?package(adun.app):needs="X11" \
-  section="Applications/Science/Biology" \
-  title="Adun" command="/usr/bin/UL" \
-  longtitle="Biomolecular Simulator" \
-  icon="/usr/share/pixmaps/adun.xpm"


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[med-svn] r20662 - trunk/packages/ampliconnoise/tags

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 21:04:45 + (Sun, 06 Dec 2015)
New Revision: 20662

Added:
   trunk/packages/ampliconnoise/tags/1.29-3/
Removed:
   trunk/packages/ampliconnoise/tags/1.24-1/
Log:
Tagged 1.29-3



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[med-svn] r20661 - trunk/packages/ampliconnoise/trunk/debian

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 21:04:09 + (Sun, 06 Dec 2015)
New Revision: 20661

Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/copyright
Log:
DEP5


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===
--- trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:26:09 UTC 
(rev 20660)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 21:04:09 UTC 
(rev 20661)
@@ -1,4 +1,4 @@
-ampliconnoise (1.29-3) UNRELEASED; urgency=medium
+ampliconnoise (1.29-3) unstable; urgency=medium
 
   [ Bas Couwenberg ]
   * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
@@ -6,8 +6,9 @@
 
   [ Andreas Tille ]
   * cme fix dpkg-control
+  * DEP5 fix
 
- -- Andreas Tille   Sun, 06 Dec 2015 21:23:19 +0100
+ -- Andreas Tille   Sun, 06 Dec 2015 21:57:05 +0100
 
 ampliconnoise (1.29-2) unstable; urgency=low
 

Modified: trunk/packages/ampliconnoise/trunk/debian/copyright
===
--- trunk/packages/ampliconnoise/trunk/debian/copyright 2015-12-06 20:26:09 UTC 
(rev 20660)
+++ trunk/packages/ampliconnoise/trunk/debian/copyright 2015-12-06 21:04:09 UTC 
(rev 20661)
@@ -15,8 +15,6 @@
 Files: debian/*
 Copyright: © Tim Booth 
 License: GPL-3
- The packaging is licensed under GPL version3
- see `/usr/share/common-licenses/GPL-3'.
 
 License: GPL-3
  This library is free software; you can redistribute it and/or
@@ -33,7 +31,5 @@
  License along with this library ('COPYING'); if not, write to the Free 
Software
  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
  .
- On Debian systems, the full text of the GNU LESSER GENERAL
- PUBLIC LICENSE can be found in the file
- `/usr/share/common-licenses/LGPL-3'.
-
+ The packaging is licensed under GPL version 3
+ see `/usr/share/common-licenses/GPL-3'.


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[med-svn] [python-pbconsensuscore] branch debian/jessie-backports updated (1e39eb6 -> 520955f)

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a change to branch debian/jessie-backports
in repository python-pbconsensuscore.

  from  1e39eb6   python-pbconsensuscore (1.0.0-1~bpo8+1) jessie-backports; 
urgency=medium
  adds  98c35cf   Run build-time tests
  adds  3b0dbd1   Limit package to x86 architectures
  adds  996cb30   Set new changelog entry
  adds  efb807b   Imported Upstream version 1.0.1
  adds  9b48678   Merge tag 'upstream/1.0.1'
  adds  e05498e   build package for all supported Python versions
  adds  a097a44   python-pbconsensuscore (1.0.1-1) unstable; urgency=low
   new  6f9046c   Merge branch 'master' into debian/jessie-backports
   new  520955f   python-pbconsensuscore (1.0.1-1~bpo8+1) jessie-backports; 
urgency=medium

The 2 revisions listed above as "new" are entirely new to this
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Summary of changes:
 CHANGELOG.md   |  4 
 debian/changelog   | 15 ++
 debian/control |  8 
 debian/rules   |  7 +++
 include/ConsensusCore/Version.hpp  |  2 +-
 setup.py   |  2 +-
 src/C++/Poa/PoaGraphImpl.cpp   |  2 +-
 src/C++/Poa/PoaGraphImpl.hpp   | 35 +++
 src/C++/Poa/PoaGraphTraversals.cpp |  2 +-
 src/C++/Poa/RangeFinder.cpp|  2 +-
 src/C++/Quiver/MutationScorer.cpp  | 27 
 src/Tests/TestPoaConsensus.cpp | 42 ++
 12 files changed, 130 insertions(+), 18 deletions(-)

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[med-svn] [python-pbconsensuscore] 01/02: Merge branch 'master' into debian/jessie-backports

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch debian/jessie-backports
in repository python-pbconsensuscore.

commit 6f9046cf7bac2c5e068f2defe5a5460472a68f1c
Merge: 1e39eb6 a097a44
Author: Afif Elghraoui 
Date:   Sun Dec 6 12:54:24 2015 -0800

Merge branch 'master' into debian/jessie-backports

 CHANGELOG.md   |  4 
 debian/changelog   |  9 
 debian/control |  8 
 debian/rules   |  7 +++
 include/ConsensusCore/Version.hpp  |  2 +-
 setup.py   |  2 +-
 src/C++/Poa/PoaGraphImpl.cpp   |  2 +-
 src/C++/Poa/PoaGraphImpl.hpp   | 35 +++
 src/C++/Poa/PoaGraphTraversals.cpp |  2 +-
 src/C++/Poa/RangeFinder.cpp|  2 +-
 src/C++/Quiver/MutationScorer.cpp  | 27 
 src/Tests/TestPoaConsensus.cpp | 42 ++
 12 files changed, 124 insertions(+), 18 deletions(-)

diff --cc debian/changelog
index 106b483,cb37c28..8418b50
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,12 +1,18 @@@
+ python-pbconsensuscore (1.0.1-1) unstable; urgency=low
+ 
+   * Run build-time tests
+   * Limit package to x86 architectures
+   * Build for all supported python versions
+   * Imported Upstream version 1.0.1
+ 
+  -- Afif Elghraoui   Tue, 24 Nov 2015 22:45:58 -0800
+ 
 +python-pbconsensuscore (1.0.0-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui   Sun, 01 Nov 2015 11:38:55 -0800
 +
  python-pbconsensuscore (1.0.0-1) unstable; urgency=low
  
* Initial release (Closes: #794450)

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[med-svn] [python-pbconsensuscore] tag debian/1.0.1-1_bpo8+1 created (now 520955f)

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a change to tag debian/1.0.1-1_bpo8+1
in repository python-pbconsensuscore.

at  520955f   (commit)
No new revisions were added by this update.

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[med-svn] [python-pbconsensuscore] 02/02: python-pbconsensuscore (1.0.1-1~bpo8+1) jessie-backports; urgency=medium

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch debian/jessie-backports
in repository python-pbconsensuscore.

commit 520955f6cab92b6654e236824afdcba72a24f632
Author: Afif Elghraoui 
Date:   Sun Dec 6 14:00:23 2015 -0800

python-pbconsensuscore (1.0.1-1~bpo8+1) jessie-backports; urgency=medium

  * Rebuild for jessie-backports.
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 8418b50..cbab506 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-pbconsensuscore (1.0.1-1~bpo8+1) jessie-backports; urgency=medium
+
+  * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui   Sun, 06 Dec 2015 12:54:48 -0800
+
 python-pbconsensuscore (1.0.1-1) unstable; urgency=low
 
   * Run build-time tests

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[med-svn] [python-htseq] 02/02: Update changelog

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository python-htseq.

commit cef58523ef7af0097bdbaae35f87f925a277ba2f
Author: Afif Elghraoui 
Date:   Sun Dec 6 13:01:42 2015 -0800

Update changelog
---
 debian/changelog | 4 
 1 file changed, 4 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 13af7f6..ad6b477 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,11 @@
 htseq (0.6.1p1-2) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Add citation data
 
+  [ Afif Elghraoui ]
+  * Add patch to allow compatibility with pysam 0.8.4
+
  -- Andreas Tille   Tue, 08 Sep 2015 13:10:00 +0200
 
 htseq (0.6.1p1-1) unstable; urgency=medium

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[med-svn] [python-htseq] branch master updated (20ddb26 -> cef5852)

2015-12-06 Thread Afif Elghraoui 
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afif-guest pushed a change to branch master
in repository python-htseq.

  from  20ddb26   Add citation data
   new  7c93b9c   Add patch to allow compatibility with pysam 0.8.4
   new  cef5852   Update changelog

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog|  4 +++
 debian/patches/series   |  1 +
 debian/patches/update-pysam-interface.patch | 53 +
 3 files changed, 58 insertions(+)
 create mode 100644 debian/patches/update-pysam-interface.patch

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[med-svn] [python-htseq] 01/02: Add patch to allow compatibility with pysam 0.8.4

2015-12-06 Thread Afif Elghraoui 
This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository python-htseq.

commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8
Author: Afif Elghraoui 
Date:   Sun Dec 6 12:45:11 2015 -0800

Add patch to allow compatibility with pysam 0.8.4
---
 debian/patches/series   |  1 +
 debian/patches/update-pysam-interface.patch | 53 +
 2 files changed, 54 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index fd4d512..c4f5cd8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ fix_version.patch
 add_sphinx_man_pages.patch
 skip_tests_with_rounding_differences.patch
 sphinx_1_3.patch
+update-pysam-interface.patch
diff --git a/debian/patches/update-pysam-interface.patch 
b/debian/patches/update-pysam-interface.patch
new file mode 100644
index 000..496a0c4
--- /dev/null
+++ b/debian/patches/update-pysam-interface.patch
@@ -0,0 +1,53 @@
+Description: Update pysam interface for 0.8.4
+ In pysam 0.8.4, interfaces that have been deprecated in
+ 0.8.1 have been removed. This patch makes the necessary
+ changes for 0.8.4 compatibility.
+Author: Afif Elghraoui 
+Forwarded: no
+Last-Update: 2015-12-06
+--- python-htseq.orig/HTSeq/__init__.py
 python-htseq/HTSeq/__init__.py
+@@ -940,14 +940,14 @@
+raise
+ 
+ def __iter__( self ):
+-sf = pysam.Samfile(self.filename, "rb")
++sf = pysam.AlignmentFile(self.filename, "rb")
+ self.record_no = 0
+ for pa in sf:
+ yield SAM_Alignment.from_pysam_AlignedRead( pa, sf )
+ self.record_no += 1
+ 
+ def fetch( self, reference = None, start = None, end = None, region = 
None ):
+-sf = pysam.Samfile(self.filename, "rb")
++sf = pysam.AlignmentFile(self.filename, "rb")
+ self.record_no = 0
+ try:
+for pa in sf.fetch( reference, start, end, region ):
+@@ -972,14 +972,14 @@
+ if not isinstance( iv, GenomicInterval ):
+raise TypeError, "Use a HTSeq.GenomicInterval to access regions 
within .bam-file!"
+ if self.sf is None:
+-   self.sf = pysam.Samfile( self.filename, "rb" )
+-   if not self.sf._hasIndex():
++   self.sf = pysam.AlignmentFile( self.filename, "rb" )
++   if not self.sf.has_index():
+   raise ValueError, "The .bam-file has no index, random-access is 
disabled!"
+ for pa in self.sf.fetch( iv.chrom, iv.start+1, iv.end ):
+ yield SAM_Alignment.from_pysam_AlignedRead( pa, self.sf )
+ 
+ def get_header_dict( self ):
+-   sf = pysam.Samfile(self.filename, "rb")
++   sf = pysam.AlignmentFile(self.filename, "rb")
+return sf.header
+ 
+
+@@ -997,7 +997,7 @@
+   self.referencelengths = referencelengths
+   self.text = text
+   self.header = header
+-  self.sf = pysam.Samfile( self.filename, mode="wb", template = 
self.template, referencenames = self.referencenames, referencelengths = 
self.referencelengths, text = self.text, header = self.header )
++  self.sf = pysam.AlignmentFile( self.filename, mode="wb", template = 
self.template, referencenames = self.referencenames, referencelengths = 
self.referencelengths, text = self.text, header = self.header )
+   
+@classmethod
+def from_BAM_Reader( cls, fn, br ):

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[med-svn] [axe-demultiplexer] branch master updated (ac8c923 -> 336bca4)

2015-12-06 Thread Kevin Murray 
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daube-guest pushed a change to branch master
in repository axe-demultiplexer.

  from  ac8c923   Add NEWS.Debian, fix cl date
   new  db66a65   Depend on GSL2 for the ongoing GSL transition
   new  336bca4   add GSL transition fix to d/changelog

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 debian/control   | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

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[med-svn] [axe-demultiplexer] 01/02: Depend on GSL2 for the ongoing GSL transition

2015-12-06 Thread Kevin Murray 
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daube-guest pushed a commit to branch master
in repository axe-demultiplexer.

commit db66a656c8bc09e3e8e43647ecf6bdfd6767aec2
Author: Kevin Murray 
Date:   Mon Dec 7 08:36:49 2015 +1100

Depend on GSL2 for the ongoing GSL transition
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 7eb0efe..847a396 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 9),
cmake,
zlib1g-dev,
libqes-dev,
-   libgsl0-dev,
+   libgsl-dev,
python-sphinx,
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/axe-demultiplexer.git
 Vcs-Git: git://anonscm.debian.org/debian-med/axe-demultiplexer.git

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[med-svn] [bart] annotated tag v0.2.09d created (now 8380311)

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a change to annotated tag v0.2.09d
in repository bart.

at  8380311   (tag)
   tagging  fc30b693ca8b8d0aafc90c082046cb33aaac32a5 (commit)
  replaces  v0.2.09
 tagged by  Martin Uecker
on  Sun Dec 6 23:57:07 2015 +0100

- Log -
Debian-med package 0.2.09
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=35iN
-END PGP SIGNATURE-

Frank Ong (12):
  added multi-scale low rank option for pics
  removed warning about locally low rank in pics
  added divergence free wavelet thresholding, locally low rank thresholding 
and wavelet thresholding options to threshold.c
  Merge branch 'master' of https://github.com/frankong/bart
  added lrdecom to do multi-scale low rank decomposition
  merge bart
  Merge branch 'master' of https://github.com/mrirecon/bart
  add .gitignore default target in Makefile, add doc/commands.txt to 
.gitignore
  Merge branch 'master' of https://github.com/mrirecon/bart
  Merge branch 'master' of https://github.com/mrirecon/bart
  changed lrdecom to lrmatrix. added matrix completion ability
  make bartview show file name

Jonathan Tamir (13):
  specify scale factor
  pics: add "-W " for warm start
  join: add option to load files based on input format (see -h for usage)
  join: remove [-p] and show example using seq tool in help
  homodyne: options to clear unacquired portion and input ref phase
  fix bug with gpu less than or equal to kernel
  add {less,greater} than or equal to prox function and corresponding 
multind/vecops functions
  add real-value prox op
  update copyright/contributions
  add some doxygen comments
  free before return statement
  actually free before return
  gitignore bbox

Martin Uecker (43):
  Merge pull request #10 from mikgroup/join-parfile
  update version.txt
  add warning for missing step size
  fixes for linking everything together
  bart with all commands (bbox for fast compilation)
  ignore priv for .coo
  avoid compilation problems
  add median filter
  fix for multiple penalties with gpu
  update URL
  add rule to autogenerate doc/commands.txt
  phantom: make k-space center consistent with rest of bart
  if we plan an in-place FFT we need to use it in-place
  use bart command in matlab wrapper
  add rule for C++ files
  add code to increase stack limit
  relax cuda fft constraints
  remove -lcuda
  Merge pull request #11 from mrirecon/md-prox-updates
  Makefile improvements
  fix for 3D CUFFT
  missing bracket
  Merge pull request #12 from sidward/master
  Merge pull request #13 from sidward/master
  Merge pull request #14 from frankong/master
  make README markdown friendly and add link for README.md
  README improvements
  add (median) filter tool
  fix for unitialized singular values for degenerate calibration matrix
  don't set debug_level
  shorten description of -W option, cosmetics
  fix warnings
  add missing const
  add install target, only build bart by default, remove commands.txt
  add manpage
  fix install on Mac OS X
  Merge pull request #15 from frankong/master
  add Sid to ACKNOWLEDGEMENTS
  make bart matlab script look for system-wide bart
  make git-version.sh more robust
  Makefile improvements
  rework main dispatch
  fix const

Siddharth (10):
  Added noise estimation cmd: estvar
  Made estvar a member of libcalib.
  Added a missing free
  Minor changes
  Minor changes
  Added soft-weighting. Still need to debug
  Soft weighting
  soft-thresholding implemented.
  Added abstract reference
  Added references

Siddharth Iyer (1):
  Forcing evecs estimate to not use orthiter fixes soft-weighting map 
estimate problem

---

This annotated tag includes the following new commits:

   new  53b631b   added lrdecom to do multi-scale low rank decomposition
   new

[med-svn] [bart] 03/14: Merge branch 'master' of https://github.com/mrirecon/bart

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 1966516020695ac634819e7fe5d9318bf2e83dfb
Merge: b2f5336 18335fc
Author: Frank Ong 
Date:   Mon Nov 30 17:04:02 2015 -0800

Merge branch 'master' of https://github.com/mrirecon/bart

 .gitignore.main|   1 +
 Makefile   |   9 +-
 doc/bart.1 |  14 ++
 doc/commands.txt   | 576 -
 src/calib/calib.c  |   4 +-
 src/calib/calmat.c |   4 +-
 src/calib/estvar.c |  16 +-
 src/calib/estvar.h |   6 +-
 src/calib/softweight.c |   6 +-
 src/calib/softweight.h |   2 +-
 src/ecalib.c   |   7 +-
 src/homodyne.c |   2 +-
 12 files changed, 46 insertions(+), 601 deletions(-)


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[med-svn] [bart] 08/14: make bartview show file name

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 263f96136fbee371c51e8869904a6ecbaf480752
Author: Frank Ong 
Date:   Thu Dec 3 13:02:04 2015 -0800

make bartview show file name
---
 bartview.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bartview.py b/bartview.py
index 5bdc672..818ab13 100755
--- a/bartview.py
+++ b/bartview.py
@@ -73,6 +73,7 @@ class BartView(object):
 self.fig = plt.figure(facecolor='black', figsize=(9,6))
 #self.fig = plt.figure(facecolor='black', figsize=(6,4))
 self.fig.subplots_adjust( left=0.0 , bottom=0.0 , right=1.0 , top=1 - 
0.25)
+self.fig.canvas.set_window_title(self.cflname)
 
 # Show image
 self.immax = np.max(abs(self.im))

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[med-svn] [bart] 01/14: added lrdecom to do multi-scale low rank decomposition

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 53b631b4359b85293784ae17e23ac115ff401a09
Author: Frank Ong 
Date:   Sun Nov 29 14:16:19 2015 -0800

added lrdecom to do multi-scale low rank decomposition
---
 Makefile  |   3 +-
 src/lrdecom.c | 300 ++
 2 files changed, 302 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 7c76031..600ccf7 100644
--- a/Makefile
+++ b/Makefile
@@ -107,7 +107,7 @@ ismrm.top ?= /usr/local/ismrmrd/
 TBASE=show slice crop resize join transpose zeros ones flip circshift extract 
repmat bitmask reshape version
 TFLP=scale conj fmac saxpy sdot spow cpyphs creal normalize cdf97 relnorm 
pattern nrmse
 TNUM=fft fftmod fftshift noise bench threshold conv rss
-TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave
+TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave lrdecom
 TCALIB=ecalib ecaltwo caldir walsh cc calmat svd estvar
 TMRI=homodyne poisson twixread fakeksp
 TSIM=phantom traj
@@ -147,6 +147,7 @@ MODULES_sake += -lsake
 MODULES_wave += -liter -lwavelet2 -llinops -lsense
 MODULES_threshold += -llowrank -llinops -lwavelet2 -liter -ldfwavelet
 MODULES_fakeksp += -lsense -llinops
+MODULES_lrdecom = -llowrank -liter -llinops
 
 -include Makefile.$(NNAME)
 -include Makefile.local
diff --git a/src/lrdecom.c b/src/lrdecom.c
new file mode 100644
index 000..ab00589
--- /dev/null
+++ b/src/lrdecom.c
@@ -0,0 +1,300 @@
+/* Copyright 2013. The Regents of the University of California.
+ * All rights reserved. Use of this source code is governed by 
+ * a educational/research license which can be found in the 
+ * LICENSE file.
+ *
+ * Authors: 
+ * 2014 Frank Ong 
+ */
+
+
+#define _GNU_SOURCE
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include "num/multind.h"
+#include "num/flpmath.h"
+#include "num/init.h"
+#include "num/ops.h"
+
+#include "linops/linop.h"
+
+#include "iter/iter.h"
+#include "iter/lsqr.h"
+#include "iter/thresh.h"
+
+#include "lowrank/lrthresh.h"
+#include "linops/sum.h"
+#include "iter/prox.h"
+#include "linops/someops.h"
+
+#include "misc/debug.h"
+#include "misc/mri.h"
+#include "misc/mmio.h"
+#include "misc/misc.h"
+
+struct s_data{
+   long size;
+};
+
+// x = (z1 + z2)/2
+
+static void sum_xupdate( const void* _data, float rho, complex float* dst, 
const complex float* src )
+{
+   UNUSED(rho);
+
+   const struct s_data* data = (const struct s_data*) _data;
+
+   for( int i = 0; i < data->size; i++)
+   dst[i] = src[i] / 2.;
+}
+
+static void sum_xupdate_free( const void* data )
+{
+   free( (void*) data);
+}
+
+
+
+static void usage(const char* name, FILE* fd)
+{
+   fprintf(fd, "Usage: %s [-options]  \n", name);
+}
+
+static void help(void)
+{
+   printf( "\n"
+   "Perform multi-scale low rank decomposition.\n"
+"-i\t\tmaximum iterations.\n"
+"-m\t\tflags to specify which dimensions are reshaped to 
matrix columns.\n"
+"-f\t\tflags to specify which dimensions to perform 
multi-scale partition.\n"
+"-j scale\tblock size scaling from one scale to the next 
one.\n"
+"-k block-size\tsmallest block size\n"
+"-N\t\tadd noise scale to account for Gaussian noise.\n"
+"-s\t\tperform low rank + sparse decomposition.\n"
+"-l block-size\tperform locally low rank soft thresholding 
with specified block size.\n"
+"-o \tsummed over all non-noise scales to create a 
denoised output.\n"
+   "\n");
+}
+
+
+int main_lrdecom(int argc, char* argv[])
+{
+   double start_time = timestamp();
+
+   bool use_gpu = false;
+
+   int maxiter = 100;
+   float rho = 0.25;
+   int blkskip = 2;
+   _Bool randshift = true;
+   unsigned long mflags = 1;
+   unsigned long flags = ~0;
+   const char* sum_str = NULL;
+   _Bool noise = false;
+
+   _Bool llr = false;
+   long llrblk = 8;
+   _Bool ls = false;
+   _Bool hogwild = false;
+   _Bool fast = true;
+   long initblk = 1;
+   int remove_mean = 0;
+
+   int c;
+   while (-1 != (c = getopt(argc, argv, "uvNi:p:m:j:k:o:hnl:sf:gHF"))) {
+   switch(c) {
+
+   case 'u':
+remove_mean = 1;
+   break;
+
+   case 'v':
+   remove_mean = 2;
+   break;
+
+   case 'H':
+   hogwild = true;
+   break;
+
+   case 'k':
+   initblk = atoi(optarg);
+   break;
+
+   case 'o':
+   sum_str = strdup(optarg);
+

[med-svn] [bart] 09/14: add Sid to ACKNOWLEDGEMENTS

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 12d29682408d756dffef50fd02ff34fb994dea18
Author: Martin Uecker 
Date:   Sun Dec 6 14:06:18 2015 +0100

add Sid to ACKNOWLEDGEMENTS
---
 ACKNOWLEDGEMENTS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ACKNOWLEDGEMENTS b/ACKNOWLEDGEMENTS
index 268286f..33f8e3c 100644
--- a/ACKNOWLEDGEMENTS
+++ b/ACKNOWLEDGEMENTS
@@ -4,6 +4,7 @@ Contributors:
 Marcus T. Alley
 Dara Bahri
 Joseph Y. Cheng
+Siddharth Iyer
 Miki Lustig
 Mark Murphy
 Frank Ong

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[med-svn] [bart] 11/14: make git-version.sh more robust

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit ccf350d1fbe9fc26bf2b6781447a6a71f9911f02
Author: Martin Uecker 
Date:   Sun Dec 6 17:39:07 2015 +0100

make git-version.sh more robust
---
 git-version.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/git-version.sh b/git-version.sh
index f23ce7b..db6693f 100755
--- a/git-version.sh
+++ b/git-version.sh
@@ -2,8 +2,8 @@
 
 if test -d ${GIT_DIR:-.git} -o -f .git
 then
-   git describe --dirty
-   git describe | cut -f1 -d'-' > version.txt
+   git describe --match "v*" --dirty
+   git describe --match "v*" | cut -f1 -d'-' > version.txt
 else
cat version.txt
 fi

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[med-svn] [bart] 04/14: Merge branch 'master' of https://github.com/mrirecon/bart

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit c04a1980693c2b2ba43ef042922e250ec80b2ec0
Merge: 1966516 4d4ef47
Author: Frank Ong 
Date:   Mon Nov 30 17:35:44 2015 -0800

Merge branch 'master' of https://github.com/mrirecon/bart

 .gitignore.main | 1 +
 Makefile| 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)


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[med-svn] [bart] 14/14: fix const

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit fc30b693ca8b8d0aafc90c082046cb33aaac32a5
Author: Martin Uecker 
Date:   Sun Dec 6 22:36:39 2015 +0100

fix const
---
 src/nlinv.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/nlinv.c b/src/nlinv.c
index ca172cb..bf1fb1b 100644
--- a/src/nlinv.c
+++ b/src/nlinv.c
@@ -46,7 +46,7 @@ static void help(void)
 
 
 
-int main_nlinv(int argc, char* const argv[])
+int main_nlinv(int argc, char* argv[])
 {
int iter = 8;
int c;

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[med-svn] [bart] 06/14: changed lrdecom to lrmatrix. added matrix completion ability

2015-12-06 Thread Martin Uecker 
This is an automated email from the git hooks/post-receive script.

uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 5e9bf804ad71c884c3a6645f900600b83f581421
Author: Frank Ong 
Date:   Tue Dec 1 22:18:20 2015 -0800

changed lrdecom to lrmatrix. added matrix completion ability
---
 Makefile  |  4 ++--
 src/{lrdecom.c => lrmatrix.c} | 28 
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 34f6ee5..9ba314c 100644
--- a/Makefile
+++ b/Makefile
@@ -109,7 +109,7 @@ ismrm.top ?= /usr/local/ismrmrd/
 TBASE=show slice crop resize join transpose zeros ones flip circshift extract 
repmat bitmask reshape version
 TFLP=scale conj fmac saxpy sdot spow cpyphs creal normalize cdf97 relnorm 
pattern nrmse
 TNUM=fft fftmod fftshift noise bench threshold conv rss filter
-TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave lrdecom
+TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave lrmatrix
 TCALIB=ecalib ecaltwo caldir walsh cc calmat svd estvar
 TMRI=homodyne poisson twixread fakeksp
 TSIM=phantom traj
@@ -149,7 +149,7 @@ MODULES_sake += -lsake
 MODULES_wave += -liter -lwavelet2 -llinops -lsense
 MODULES_threshold += -llowrank -llinops -lwavelet2 -liter -ldfwavelet
 MODULES_fakeksp += -lsense -llinops
-MODULES_lrdecom = -llowrank -liter -llinops
+MODULES_lrmatrix = -llowrank -liter -llinops
 
 -include Makefile.$(NNAME)
 -include Makefile.local
diff --git a/src/lrdecom.c b/src/lrmatrix.c
similarity index 88%
rename from src/lrdecom.c
rename to src/lrmatrix.c
index ab00589..d928252 100644
--- a/src/lrdecom.c
+++ b/src/lrmatrix.c
@@ -30,6 +30,7 @@
 
 #include "lowrank/lrthresh.h"
 #include "linops/sum.h"
+#include "linops/sampling.h"
 #include "iter/prox.h"
 #include "linops/someops.h"
 
@@ -69,21 +70,22 @@ static void usage(const char* name, FILE* fd)
 static void help(void)
 {
printf( "\n"
-   "Perform multi-scale low rank decomposition.\n"
+   "Perform (multi-scale) low rank matrix completion\n"
+"-d\t\tperform decomposition instead, ie fully sampled\n"
 "-i\t\tmaximum iterations.\n"
 "-m\t\tflags to specify which dimensions are reshaped to 
matrix columns.\n"
 "-f\t\tflags to specify which dimensions to perform 
multi-scale partition.\n"
 "-j scale\tblock size scaling from one scale to the next 
one.\n"
 "-k block-size\tsmallest block size\n"
 "-N\t\tadd noise scale to account for Gaussian noise.\n"
-"-s\t\tperform low rank + sparse decomposition.\n"
+"-s\t\tperform low rank + sparse matrix completion.\n"
 "-l block-size\tperform locally low rank soft thresholding 
with specified block size.\n"
 "-o \tsummed over all non-noise scales to create a 
denoised output.\n"
"\n");
 }
 
 
-int main_lrdecom(int argc, char* argv[])
+int main_lrmatrix(int argc, char* argv[])
 {
double start_time = timestamp();
 
@@ -97,6 +99,7 @@ int main_lrdecom(int argc, char* argv[])
unsigned long flags = ~0;
const char* sum_str = NULL;
_Bool noise = false;
+_Bool decom = false;
 
_Bool llr = false;
long llrblk = 8;
@@ -107,8 +110,11 @@ int main_lrdecom(int argc, char* argv[])
int remove_mean = 0;
 
int c;
-   while (-1 != (c = getopt(argc, argv, "uvNi:p:m:j:k:o:hnl:sf:gHF"))) {
+   while (-1 != (c = getopt(argc, argv, "uvNi:p:m:j:k:o:hnl:sf:gHFd"))) {
switch(c) {
+
+case 'd':
+decom = true;
 
case 'u':
 remove_mean = 1;
@@ -216,6 +222,13 @@ int main_lrdecom(int argc, char* argv[])
complex float* odata = create_cfl(argv[optind + 1], DIMS, odims);
md_clear( DIMS, odims, odata, sizeof(complex float) );
 
+   // Get pattern
+   complex float* pattern = NULL;
+
+if (!decom) {
+pattern = md_alloc(DIMS, idims, CFL_SIZE);
+estimate_pattern(DIMS, idims, TIME_DIM, pattern, idata);
+}
 
// Initialize algorithm
void* iconf;
@@ -233,6 +246,13 @@ int main_lrdecom(int argc, char* argv[])
// Initialize operators
 
const struct linop_s* sum_op = sum_create( odims, use_gpu );
+   const struct linop_s* sampling_op = NULL;
+if (!decom) {
+sampling_op = sampling_create(idims, idims, pattern);
+sum_op = linop_chain(sum_op, sampling_op);
+linop_free(sampling_op);
+}
+   
const struct operator_p_s* sum_prox = prox_lineq_create( sum_op, idata 
);
const struct operator_p_s* lr_prox = lrthresh_create(odims, randshift, 
mflags, (const long (*)[])blkdims, 1., noise, remove_mean, use_gpu);

[med-svn] [bart] 05/14: Merge branch 'master' of https://github.com/mrirecon/bart

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit b02cdc5705736b7a7289341a24e3d08f4eff0c8e
Merge: c04a198 f2cc7f3
Author: Frank Ong 
Date:   Tue Dec 1 22:00:24 2015 -0800

Merge branch 'master' of https://github.com/mrirecon/bart

 Makefile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)


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[med-svn] [bart] 13/14: rework main dispatch

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit d689d04667b04f7cf52791a562bc86897fb6a4c3
Author: Martin Uecker 
Date:   Sun Dec 6 22:10:18 2015 +0100

rework main dispatch
---
 Makefile | 14 --
 rules/box.mk |  2 --
 src/bart.c   | 10 +++---
 src/bbox.c   |  1 +
 src/main.c   |  8 
 src/main.h   | 12 
 6 files changed, 32 insertions(+), 15 deletions(-)

diff --git a/Makefile b/Makefile
index 6c46f2e..829e8d6 100644
--- a/Makefile
+++ b/Makefile
@@ -53,8 +53,7 @@ export TOOLBOX_PATH=$(root)
 
 DEPFILE = $(*D)/.$(*F).d
 DEPFLAG = -MMD -MF $(DEPFILE)
-#ALLDEPS = $(shell find $(srcdir) -name ".*.d")
-ALLDEPS = $(shell find $(root) -name ".*.d")
+ALLDEPS = $(shell find $(srcdir) -name ".*.d")
 
 
 # Compilation flags
@@ -332,9 +331,12 @@ all: .gitignore $(TARGETS)
 # special targets
 
 
-bbox: CPPFLAGS += -DMAIN_LIST="$(BTARGETS:%=%,) ()"
+$(XTARGETS): CPPFLAGS += -DMAIN_LIST="$(XTARGETS:%=%,) ()" -include src/main.h
 
-bart: CPPFLAGS += -DMAIN_LIST="$(YTARGETS:%=%,) ()"
+
+bbox: CPPFLAGS += -DMAIN_LIST="$(BTARGETS:%=%,) ()" -include src/main.h
+
+bart: CPPFLAGS += -DMAIN_LIST="$(YTARGETS:%=%,) ()" -include src/main.h
 
 
 ismrmrd: $(srcdir)/ismrmrd.c -lismrm -lnum -lmisc
@@ -370,8 +372,8 @@ $(BTARGETS): bbox
 
 
 .SECONDEXPANSION:
-$(ZTARGETS): % : $(srcdir)/%.c $$(MODULES_%) $(MODULES)
-   $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -Dmain_$@=main -o $@ $+ 
$(FFTW_L) $(CUDA_L) $(BLAS_L) $(GSL_L) $(PNG_L) -lm
+$(ZTARGETS): % : src/main.c $(srcdir)/%.o $$(MODULES_%) $(MODULES)
+   $(CC) $(LDFLAGS) $(CFLAGS) -Dmain_real=main_$@ -o $@ $+ $(FFTW_L) 
$(CUDA_L) $(BLAS_L) $(GSL_L) $(PNG_L) -lm
 #  rm $(srcdir)/$@.o
 
 
diff --git a/rules/box.mk b/rules/box.mk
index 2dac213..a093a30 100644
--- a/rules/box.mk
+++ b/rules/box.mk
@@ -7,7 +7,6 @@ boxobjs := $(boxsrcs:.c=.o)
 .INTERMEDIATE: $(boxobjs)
 
 lib/libbox.a: libbox.a($(boxobjs))
-lib/libbox.a: CFLAGS += -Wno-missing-prototypes
 
 
 box2srcs := $(XTARGETS:%=src/%.c)
@@ -16,7 +15,6 @@ box2objs := $(box2srcs:.c=.o)
 .INTERMEDIATE: $(box2objs)
 
 lib/libbox2.a: libbox2.a($(box2objs))
-lib/libbox2.a: CFLAGS += -Wno-missing-prototypes
 
 
 
diff --git a/src/bart.c b/src/bart.c
index 870ad09..2ff1fa9 100644
--- a/src/bart.c
+++ b/src/bart.c
@@ -15,11 +15,7 @@
 #include "misc/misc.h"
 #include "misc/cppmap.h"
 
-
-#define DECLMAIN(x) \
-extern int main_ ## x(int argc, char* argv[]);
-MAP(DECLMAIN, MAIN_LIST)
-#undef DECLMAIN
+#include "main.h"
 
 struct {
 
@@ -49,7 +45,7 @@ static void usage(void)
printf("\n");
 }
 
-int main(int argc, char* argv[])
+int main_bart(int argc, char* argv[])
 {
char* bn = basename(argv[0]);
 
@@ -61,7 +57,7 @@ int main(int argc, char* argv[])
exit(1);
}
 
-   return main(argc - 1, argv + 1);
+   return main_bart(argc - 1, argv + 1);
}
 
for (int i = 0; NULL != dispatch_table[i].name; i++) {
diff --git a/src/bbox.c b/src/bbox.c
index 8d19df0..1eb0c2e 100644
--- a/src/bbox.c
+++ b/src/bbox.c
@@ -1,3 +1,4 @@
 
+#define main_bart main_bbox
 #include "bart.c"
 
diff --git a/src/main.c b/src/main.c
new file mode 100644
index 000..ed0b846
--- /dev/null
+++ b/src/main.c
@@ -0,0 +1,8 @@
+
+extern int main_real(int argc, char** argv);
+
+int main(int argc, char** argv)
+{
+   return main_real(argc, argv);
+}
+
diff --git a/src/main.h b/src/main.h
new file mode 100644
index 000..7bd05d1
--- /dev/null
+++ b/src/main.h
@@ -0,0 +1,12 @@
+
+#include "misc/cppmap.h"
+
+
+#define DECLMAIN(x) \
+extern int main_ ## x(int argc, char* argv[]);
+MAP(DECLMAIN, MAIN_LIST)
+#undef DECLMAIN
+
+extern int main_bart(int argc, char* argv[]);
+extern int main_bbox(int argc, char* argv[]);
+

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[med-svn] [bart] 10/14: make bart matlab script look for system-wide bart

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 67660b3f36721c4955a06c9e2a6acc2e99232520
Author: Martin Uecker 
Date:   Sun Dec 6 14:06:58 2015 +0100

make bart matlab script look for system-wide bart
---
 matlab/bart.m | 18 +-
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/matlab/bart.m b/matlab/bart.m
index 638bec9..b26bed8 100644
--- a/matlab/bart.m
+++ b/matlab/bart.m
@@ -2,10 +2,18 @@ function [varargout] = bart(cmd, varargin);
 % BART Call BART command from Matlab.
 %   [A B] = bart('command', X Y) call command with inputs X Y and outputs A B
 %
-% 2014-2015 Martin Uecker 
+% 2014-2015 Martin Uecker 
 
-   if isempty(getenv('TOOLBOX_PATH'))
-   error('Environment variable TOOLBOX_PATH is not set.');
+   bart_path = getenv('TOOLBOX_PATH');
+
+   if isempty(bart_path)
+   if exist('/usr/local/bin/bart', 'file')
+   bart_path = '/usr/local/bin';
+   elseif exist('/usr/bin/bart', 'file')
+   bart_path = '/usr/bin';
+   else
+   error('Environment variable TOOLBOX_PATH is not set.');
+   end
end
 
% clear the LD_LIBRARY_PATH environment variable (to work around
@@ -39,12 +47,12 @@ function [varargout] = bart(cmd, varargin);
if ispc
% For cygwin use bash and modify paths
ERR = system(['bash.exe --login -c ', ...
-   strrep(getenv('TOOLBOX_PATH'), filesep, '/'), ...
+   strrep(bart_path, filesep, '/'), ...
'"', '/bart ', strrep(cmd, filesep, '/'), ' ', ...
strrep(in_str, filesep, '/'), ...
' ', strrep(out_str, filesep, '/'), '"']);
else
-   ERR = system([getenv('TOOLBOX_PATH'), '/bart ', cmd, ' ', 
in_str, ' ', out_str]);
+   ERR = system([bart_path, '/bart ', cmd, ' ', in_str, ' ', 
out_str]);
end
 
if ERR~=0

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[med-svn] [bart] 07/14: Merge pull request #15 from frankong/master

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit 7ad77df559281a1d8f4d2960e4f0a567b6af6372
Merge: f2cc7f3 5e9bf80
Author: Martin Uecker 
Date:   Wed Dec 2 08:58:32 2015 +0100

Merge pull request #15 from frankong/master

Low rank matrix completion

 Makefile   |   3 +-
 src/lrmatrix.c | 320 +
 2 files changed, 322 insertions(+), 1 deletion(-)

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[med-svn] [bart] 02/14: merge bart

2015-12-06 Thread Martin Uecker 
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uecker-guest pushed a commit to annotated tag v0.2.09d
in repository bart.

commit b2f5336eb223c7d7370975c1fe9ce4f50da75c31
Merge: 53b631b cb56f6f
Author: Frank Ong 
Date:   Sun Nov 29 14:27:03 2015 -0800

merge bart

 Makefile   |   2 +-
 README | 142 -
 README.md  |   1 +
 src/calib/calib.c  |   3 +-
 src/calib/calmat.c |   4 ++
 src/ecalib.c   |   1 -
 src/filter.c   | 122 +
 7 files changed, 205 insertions(+), 70 deletions(-)

diff --cc Makefile
index 600ccf7,6df9e9f..176feef
--- a/Makefile
+++ b/Makefile
@@@ -106,8 -106,8 +106,8 @@@ ismrm.top ?= /usr/local/ismrmrd
  
  TBASE=show slice crop resize join transpose zeros ones flip circshift extract 
repmat bitmask reshape version
  TFLP=scale conj fmac saxpy sdot spow cpyphs creal normalize cdf97 relnorm 
pattern nrmse
- TNUM=fft fftmod fftshift noise bench threshold conv rss
+ TNUM=fft fftmod fftshift noise bench threshold conv rss filter
 -TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave
 +TRECO=pics pocsense rsense bpsense itsense nlinv nufft rof sake wave lrdecom
  TCALIB=ecalib ecaltwo caldir walsh cc calmat svd estvar
  TMRI=homodyne poisson twixread fakeksp
  TSIM=phantom traj

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[med-svn] [libtabixpp] annotated tag upstream/0.0.20151117 created (now f95d18c)

2015-12-06 Thread Sascha Steinbiss 
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sascha-guest pushed a change to annotated tag upstream/0.0.20151117
in repository libtabixpp.

at  f95d18c   (tag)
   tagging  8af1d9f1ff7610b84993e85c293b1bc7b173026c (commit)
  replaces  upstream/0.0.20141119
 tagged by  Sascha Steinbiss
on  Sun Dec 6 12:48:03 2015 +

- Log -
Upstream version 0.0.20151117

Sascha Steinbiss (1):
  Imported Upstream version 0.0.20151117

---

No new revisions were added by this update.

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[med-svn] [libtabixpp] 01/01: pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2

2015-12-06 Thread Sascha Steinbiss 
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sascha-guest pushed a commit to branch pristine-tar
in repository libtabixpp.

commit 99b410ac85e32ae81762c7c1b429055dc750f1b2
Author: Sascha Steinbiss 
Date:   Sun Dec 6 12:48:03 2015 +

pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2
---
 libtabixpp_0.0.20151117.orig.tar.bz2.delta | Bin 0 -> 848 bytes
 libtabixpp_0.0.20151117.orig.tar.bz2.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/libtabixpp_0.0.20151117.orig.tar.bz2.delta 
b/libtabixpp_0.0.20151117.orig.tar.bz2.delta
new file mode 100644
index 000..d59dabe
Binary files /dev/null and b/libtabixpp_0.0.20151117.orig.tar.bz2.delta differ
diff --git a/libtabixpp_0.0.20151117.orig.tar.bz2.id 
b/libtabixpp_0.0.20151117.orig.tar.bz2.id
new file mode 100644
index 000..a0f390c
--- /dev/null
+++ b/libtabixpp_0.0.20151117.orig.tar.bz2.id
@@ -0,0 +1 @@
+d2a99d9d94dbad6d42cbe6c5f2d73d42b8481c7d

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[med-svn] [libtabixpp] 02/03: Merge tag 'upstream/0.0.20151117'

2015-12-06 Thread Sascha Steinbiss 
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sascha-guest pushed a commit to branch master
in repository libtabixpp.

commit e17342b6b8d98ff4e05746a863294e620caf7136
Merge: 58408e0 8af1d9f
Author: Sascha Steinbiss 
Date:   Sun Dec 6 12:48:03 2015 +

Merge tag 'upstream/0.0.20151117'

Upstream version 0.0.20151117

 .gitmodules   |   3 +
 ChangeLog | 593 --
 Makefile  |  90 ++---
 NEWS  | 126 ---
 README|   6 -
 README.md |   5 +
 TabixReader.java  | 395 
 bam_endian.h  |  42 ---
 bedidx.c  | 156 
 bgzf.c| 714 
 bgzf.h| 157 
 bgzip.c   | 206 ---
 example.gtf.gz| Bin 3778 -> 0 bytes
 example.gtf.gz.tbi| Bin 259 -> 0 bytes
 index.c   | 998 --
 khash.h   | 486 
 knetfile.c| 632 
 knetfile.h|  75 
 kseq.h| 227 
 ksort.h   | 271 --
 kstring.c | 165 -
 kstring.h |  68 
 main.c| 290 ---
 perl/MANIFEST |   8 -
 perl/Makefile.PL  |   8 -
 perl/Tabix.pm |  76 
 perl/Tabix.xs |  71 
 perl/TabixIterator.pm |  41 ---
 perl/t/01local.t  |  28 --
 perl/t/02remote.t |  28 --
 perl/typemap  |   3 -
 python/setup.py   |  55 ---
 python/tabixmodule.c  | 408 -
 python/test.py|  91 -
 tabix.1   | 132 ---
 tabix.cpp |  85 +++--
 tabix.h   | 145 
 tabix.hpp |  17 +-
 tabix.py  |  87 -
 tabix.tex | 121 --
 40 files changed, 107 insertions(+), 7002 deletions(-)

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[med-svn] [libtabixpp] 03/03: flesh out package a bit

2015-12-06 Thread Sascha Steinbiss 
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sascha-guest pushed a commit to branch master
in repository libtabixpp.

commit 457e505cc279d76a16b62fc7557a5ad3059f2133
Author: Sascha Steinbiss <sas...@steinbiss.name>
Date:   Sun Dec 6 18:59:23 2015 +

flesh out package a bit
---
 debian/README.license |  3 ++
 debian/changelog  |  4 +-
 debian/control| 32 +++
 debian/libtabixpp-dev.links   |  1 +
 debian/patches/build_with_debian_htslib.patch | 58 +++
 debian/patches/series |  1 +
 debian/rules  | 22 +++---
 7 files changed, 95 insertions(+), 26 deletions(-)

diff --git a/debian/README.license b/debian/README.license
new file mode 100644
index 000..dde526c
--- /dev/null
+++ b/debian/README.license
@@ -0,0 +1,3 @@
+This package does not yet have a license defined by upstream.
+
+ss34, 20151206
diff --git a/debian/changelog b/debian/changelog
index 5125bdd..37d71b5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-libtabixpp (0.0.20141119-1) UNRELEASED; urgency=low
+libtabixpp (0.0.20151117-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #)
 
- -- Andreas Tille <ti...@debian.org>  Sun, 01 Feb 2015 14:56:48 +0100
+ -- Sascha Steinbiss <sas...@steinbiss.name>  Sun, 06 Dec 2015 18:22:18 +
diff --git a/debian/control b/debian/control
index 309e806..4a7d1b7 100644
--- a/debian/control
+++ b/debian/control
@@ -2,24 +2,40 @@ Source: libtabixpp
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
-Uploaders: Andreas Tille <ti...@debian.org>
+Uploaders: Andreas Tille <ti...@debian.org>,
+   Sascha Steinbiss <sas...@steinbiss.name>
 Build-Depends: debhelper (>= 9),
-   python-markdown,
+   libhts-dev,
+   libhts1,
+   zlib1g,
zlib1g-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git
 Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git
 Homepage: https://github.com/ekg/tabixpp
 
-Package: libtabixpp
+Package: libtabixpp0
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
 Description: C++ wrapper to tabix indexer
  Tabix indexes files where some columns indicate sequence coordinates: name
- (usually a chromosme), start and stop. The input data file must be position
+ (usually a chromosome), start and stop. The input data file must be position
  sorted and compressed by bgzip (provided in this package), which has a gzip
- like interface. After indexing, tabix is able to quickly retrieve data lines 
by
- chromosomal coordinates. Fast data retrieval also works over network if an URI
- is given as a file name.
+ like interface. After indexing, tabix is able to quickly retrieve data lines
+ by chromosomal coordinates. Fast data retrieval also works over network if an
+ URI is given as a file name.
  .
  This package provides a C++ wrapper to the tabix indexer.
+
+Package: libtabixpp-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libtabixpp0 (= ${binary:Version})
+Description: C++ wrapper to tabix indexer (development files)
+ This package provides development headers and static libraries for libtabixpp,
+ a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular
+ files in which some columns indicate sequence coordinates.
\ No newline at end of file
diff --git a/debian/libtabixpp-dev.links b/debian/libtabixpp-dev.links
new file mode 100644
index 000..35903fa
--- /dev/null
+++ b/debian/libtabixpp-dev.links
@@ -0,0 +1 @@
+usr/lib/libtabixpp.so.0 usr/lib/libtabixpp.so
\ No newline at end of file
diff --git a/debian/patches/build_with_debian_htslib.patch 
b/debian/patches/build_with_debian_htslib.patch
new file mode 100644
index 000..9bcba7e
--- /dev/null
+++ b/debian/patches/build_with_debian_htslib.patch
@@ -0,0 +1,58 @@
+Description: Build_with_debian_htslib
+--- a/Makefile
 b/Makefile
+@@ -3,11 +3,12 @@
+ 
+ CC?=  gcc
+ CXX?= g++
+-CXXFLAGS?=-g -Wall -O2 -fPIC #-m64 #-arch ppc
++CXXFLAGS+= -fPIC
+ INCLUDES?=-Ihtslib
+ HTS_HEADERS?= htslib/htslib/bgzf.h htslib/htslib/tbx.h
+ HTS_LIB?= htslib/libhts.a
+ LIBPATH?= -L. -Lhtslib
++SONUMBER=0
+ 
+ DFLAGS=   -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ PROG= tabix++
+@@ -18,32 +19,21 @@
+ .c.o:
+   $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+ 
+-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+-  @target=`echo $@ | sed s/-recur//`; \
+-  wdir=`pwd`; \
+-  list='$(SUBDIRS)'; for subdir in $$list; do \
+-

[med-svn] [libtabixpp] branch master updated (58408e0 -> 457e505)

2015-12-06 Thread Sascha Steinbiss 
This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a change to branch master
in repository libtabixpp.

  from  58408e0   Stumbled upon this one at the end of the chain of 
dependencies of free-bayes; just fix the build for the moment
   new  8af1d9f   Imported Upstream version 0.0.20151117
   new  e17342b   Merge tag 'upstream/0.0.20151117'
   new  457e505   flesh out package a bit

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitmodules   |   3 +
 ChangeLog | 593 ---
 Makefile  |  90 +--
 NEWS  | 126 
 README|   6 -
 README.md |   5 +
 TabixReader.java  | 395 --
 bam_endian.h  |  42 --
 bedidx.c  | 156 
 bgzf.c| 714 --
 bgzf.h| 157 
 bgzip.c   | 206 --
 debian/README.license |   3 +
 debian/changelog  |   4 +-
 debian/control|  32 +-
 debian/libtabixpp-dev.links   |   1 +
 debian/patches/build_with_debian_htslib.patch |  58 ++
 debian/patches/series |   1 +
 debian/rules  |  22 +-
 example.gtf.gz| Bin 3778 -> 0 bytes
 example.gtf.gz.tbi| Bin 259 -> 0 bytes
 index.c   | 998 --
 khash.h   | 486 -
 knetfile.c| 632 
 knetfile.h|  75 --
 kseq.h| 227 --
 ksort.h   | 271 ---
 kstring.c | 165 -
 kstring.h |  68 --
 main.c| 290 
 perl/MANIFEST |   8 -
 perl/Makefile.PL  |   8 -
 perl/Tabix.pm |  76 --
 perl/Tabix.xs |  71 --
 perl/TabixIterator.pm |  41 --
 perl/t/01local.t  |  28 -
 perl/t/02remote.t |  28 -
 perl/typemap  |   3 -
 python/setup.py   |  55 --
 python/tabixmodule.c  | 408 ---
 python/test.py|  91 ---
 tabix.1   | 132 
 tabix.cpp |  85 ++-
 tabix.h   | 145 
 tabix.hpp |  17 +-
 tabix.py  |  87 ---
 tabix.tex | 121 
 47 files changed, 202 insertions(+), 7028 deletions(-)
 create mode 100644 .gitmodules
 delete mode 100644 ChangeLog
 delete mode 100644 NEWS
 delete mode 100644 README
 create mode 100644 README.md
 delete mode 100644 TabixReader.java
 delete mode 100644 bam_endian.h
 delete mode 100644 bedidx.c
 delete mode 100644 bgzf.c
 delete mode 100644 bgzf.h
 delete mode 100644 bgzip.c
 create mode 100644 debian/README.license
 create mode 100644 debian/libtabixpp-dev.links
 create mode 100644 debian/patches/build_with_debian_htslib.patch
 create mode 100644 debian/patches/series
 delete mode 100644 example.gtf.gz
 delete mode 100644 example.gtf.gz.tbi
 delete mode 100644 index.c
 delete mode 100644 khash.h
 delete mode 100644 knetfile.c
 delete mode 100644 knetfile.h
 delete mode 100644 kseq.h
 delete mode 100644 ksort.h
 delete mode 100644 kstring.c
 delete mode 100644 kstring.h
 delete mode 100644 main.c
 delete mode 100644 perl/MANIFEST
 delete mode 100644 perl/Makefile.PL
 delete mode 100644 perl/Tabix.pm
 delete mode 100644 perl/Tabix.xs
 delete mode 100644 perl/TabixIterator.pm
 delete mode 100644 perl/t/01local.t
 delete mode 100644 perl/t/02remote.t
 delete mode 100644 perl/typemap
 delete mode 100644 python/setup.py
 delete mode 100644 python/tabixmodule.c
 delete mode 100755 python/test.py
 delete mode 100644 tabix.1
 delete mode 100644 tabix.h
 delete mode 100755 tabix.py
 delete mode 100644 tabix.tex

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[med-svn] [libtabixpp] branch pristine-tar updated (eda3bce -> 99b410a)

2015-12-06 Thread Sascha Steinbiss 
This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a change to branch pristine-tar
in repository libtabixpp.

  from  eda3bce   pristine-tar data for libtabixpp_0.0.20141119.orig.tar.xz
   new  99b410a   pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 libtabixpp_0.0.20151117.orig.tar.bz2.delta | Bin 0 -> 848 bytes
 libtabixpp_0.0.20151117.orig.tar.bz2.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 libtabixpp_0.0.20151117.orig.tar.bz2.delta
 create mode 100644 libtabixpp_0.0.20151117.orig.tar.bz2.id

-- 
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[med-svn] r20659 - trunk/packages/ampliconnoise/trunk/debian

2015-12-06 Thread Andreas Tille 
Author: tille
Date: 2015-12-06 20:24:24 + (Sun, 06 Dec 2015)
New Revision: 20659

Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/control
Log:
cme fix dpkg-control


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===
--- trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:21:43 UTC 
(rev 20658)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2015-12-06 20:24:24 UTC 
(rev 20659)
@@ -1,10 +1,13 @@
-ampliconnoise (1.29-2.1) UNRELEASED; urgency=medium
+ampliconnoise (1.29-3) UNRELEASED; urgency=medium
 
-  * Non-maintainer upload.
+  [ Bas Couwenberg ]
   * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
 
- -- Bas Couwenberg   Sun, 22 Nov 2015 00:31:23 +0100
+  [ Andreas Tille ]
+  * cme fix dpkg-control
 
+ -- Andreas Tille   Sun, 06 Dec 2015 21:23:19 +0100
+
 ampliconnoise (1.29-2) unstable; urgency=low
 
   [ Arthur Marble ]

Modified: trunk/packages/ampliconnoise/trunk/debian/control
===
--- trunk/packages/ampliconnoise/trunk/debian/control   2015-12-06 20:21:43 UTC 
(rev 20658)
+++ trunk/packages/ampliconnoise/trunk/debian/control   2015-12-06 20:24:24 UTC 
(rev 20659)
@@ -7,7 +7,7 @@
 Build-Depends: debhelper (>= 9),
libgsl-dev,
libopenmpi-dev
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ampliconnoise/trunk/
 Vcs-Svn: 
svn://anonscm.debian.org/debian-med/trunk/packages/ampliconnoise/trunk/
 Homepage: http://code.google.com/p/ampliconnoise/


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