[med-svn] r11937 - trunk/packages/vxl/trunk/debian/patches
Author: malat
Date: 2012-07-28 23:04:00 + (Sat, 28 Jul 2012)
New Revision: 11937
Added:
trunk/packages/vxl/trunk/debian/patches/fixingupstream.patch
Modified:
trunk/packages/vxl/trunk/debian/patches/series
Log:
Fix upstream cmake issues
Added: trunk/packages/vxl/trunk/debian/patches/fixingupstream.patch
===
--- trunk/packages/vxl/trunk/debian/patches/fixingupstream.patch
(rev 0)
+++ trunk/packages/vxl/trunk/debian/patches/fixingupstream.patch
2012-07-28 23:04:00 UTC (rev 11937)
@@ -0,0 +1,516 @@
+Description:
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ vxl (1.17.0-1) UNRELEASED; urgency=low
+ .
+ * New upstream
+Author: Mathieu Malaterre
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: ,
+Bug:
+Bug-Debian: http://bugs.debian.org/
+Bug-Ubuntu: https://launchpad.net/bugs/
+Forwarded:
+Reviewed-By:
+Last-Update:
+
+--- vxl-1.17.0.orig/core/vpgl/CMakeLists.txt
vxl-1.17.0/core/vpgl/CMakeLists.txt
+@@ -32,6 +32,7 @@ SET( vpgl_sources
+ AUX_SOURCE_DIRECTORY(Templates vpgl_sources)
+
+ ADD_LIBRARY(vpgl ${vpgl_sources})
++SET_TARGET_PROPERTIES(vpgl PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+ TARGET_LINK_LIBRARIES(vpgl vnl_algo vnl vgl_algo vgl vul vsl vbl)
+
+ IF( BUILD_TESTING )
+--- vxl-1.17.0.orig/core/vpgl/io/CMakeLists.txt
vxl-1.17.0/core/vpgl/io/CMakeLists.txt
+@@ -13,7 +13,7 @@ SET(vpgl_io_sources
+ AUX_SOURCE_DIRECTORY(Templates vpgl_io_sources)
+
+ ADD_LIBRARY(vpgl_io ${vpgl_io_sources})
+-
++SET_TARGET_PROPERTIES(vpgl_io PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+ TARGET_LINK_LIBRARIES(vpgl_io vsl vpgl vnl vgl vgl_algo vgl_io vnl_io vbl_io)
+
+ INSTALL_TARGETS(/lib vpgl_io)
+--- vxl-1.17.0.orig/core/vpgl/file_formats/CMakeLists.txt
vxl-1.17.0/core/vpgl/file_formats/CMakeLists.txt
+@@ -21,7 +21,7 @@ IF(TIFF_FOUND)
+ ENDIF(TIFF_FOUND)
+
+ ADD_LIBRARY(vpgl_file_formats ${vpgl_file_formats_sources})
+-
++SET_TARGET_PROPERTIES(vpgl_file_formats PROPERTIES ${VNL_LIBRARY_PROPERTIES})
+ TARGET_LINK_LIBRARIES(vpgl_file_formats vpgl vil vnl)
+
+ IF( BUILD_TESTING )
+--- vxl-1.17.0.orig/core/vpgl/algo/CMakeLists.txt
vxl-1.17.0/core/vpgl/algo/CMakeLists.txt
+@@ -29,10 +29,10 @@ SET( vpgl_algo_sources
+ AUX_SOURCE_DIRECTORY(Templates vpgl_algo_sources)
+
+ ADD_LIBRARY(vpgl_algo ${vpgl_algo_sources})
+-
++message(${V3P_NETLIB_LIBRARY_PROPERTIES})
++SET_TARGET_PROPERTIES(vpgl_algo PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+ TARGET_LINK_LIBRARIES(vpgl_algo vpgl vpgl_file_formats vgl_algo vnl_algo vnl
vgl vil vul vbl)
+
+-
+ IF( BUILD_TESTING )
+ SUBDIRS(tests)
+ ENDIF( BUILD_TESTING )
+--- vxl-1.17.0.orig/core/vpgl/xio/CMakeLists.txt
vxl-1.17.0/core/vpgl/xio/CMakeLists.txt
+@@ -6,6 +6,7 @@ SET(vpgl_xio_sources
+
+ ADD_LIBRARY(vpgl_xio ${vpgl_xio_sources} )
+ TARGET_LINK_LIBRARIES( vpgl_xio vpgl vsl )
++SET_TARGET_PROPERTIES(vpgl_xio PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+
+ INSTALL_TARGETS(/lib vpgl_xio)
+ INSTALL_NOBASE_HEADER_FILES(/include/vxl/core/vpgl/xio ${vpgl_xio_sources})
+--- vxl-1.17.0.orig/core/vgl/xio/CMakeLists.txt
vxl-1.17.0/core/vgl/xio/CMakeLists.txt
+@@ -10,6 +10,7 @@ SET(vgl_xio_sources
+ AUX_SOURCE_DIRECTORY(Templates vgl_xio_sources)
+
+ ADD_LIBRARY(vgl_xio ${vgl_xio_sources})
++SET_TARGET_PROPERTIES(vgl_xio PROPERTIES ${VNL_LIBRARY_PROPERTIES})
+ IF(NOT WIN32)
+ SET_TARGET_PROPERTIES(vgl_xio PROPERTIES COMPILE_FLAGS "-fPIC")
+ ENDIF(NOT WIN32)
+--- vxl-1.17.0.orig/core/vpl/CMakeLists.txt
vxl-1.17.0/core/vpl/CMakeLists.txt
+@@ -13,6 +13,7 @@ SET( vpl_sources
+ )
+
+ ADD_LIBRARY(vpl ${vpl_sources})
++SET_TARGET_PROPERTIES(vpl PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+ IF(NOT WIN32)
+ SET_TARGET_PROPERTIES(vpl PROPERTIES COMPILE_FLAGS "-fPIC")
+ ENDIF(NOT WIN32)
+--- vxl-1.17.0.orig/contrib/rpl/rrel/CMakeLists.txt
vxl-1.17.0/contrib/rpl/rrel/CMakeLists.txt
+@@ -44,6 +44,7 @@ SET(rrel_sources
+ AUX_SOURCE_DIRECTORY(Templates rrel_sources)
+
+ ADD_LIBRARY(rrel ${rrel_sources})
++SET_TARGET_PROPERTIES(rrel PROPERTIES ${V3P_NETLIB_LIBRARY_PROPERTIES})
+
+ INSTALL_TARGETS(/lib rrel)
+ INSTALL_NOBASE_HEADER_FILES(/include/vxl/contrib/rpl/rrel ${rrel_sources})
+--- vxl-1.17.0.orig/contrib/brl/bseg/bvxm/grid/CMakeLists.txt
vxl-1.17.0/contrib/brl/bseg/bvxm/grid/CMakeLists.txt
+@@ -27,7 +27,9 @@ SET(bvxm_grid_sources
+ AUX_SOURCE_DIRECTORY(Templates bvxm_grid_sources)
+
+ ADD_LIBRARY( bvxm_grid ${bvxm_grid_sources})
+-
++SET_TARGET_PROPERTIES(bvxm_grid PROPE
[med-svn] r11936 - trunk/packages/vxl/trunk/debian
Author: malat
Date: 2012-07-28 20:06:46 + (Sat, 28 Jul 2012)
New Revision: 11936
Modified:
trunk/packages/vxl/trunk/debian/control
trunk/packages/vxl/trunk/debian/rules
Log:
Update version
Modified: trunk/packages/vxl/trunk/debian/control
===
--- trunk/packages/vxl/trunk/debian/control 2012-07-28 20:04:01 UTC (rev
11935)
+++ trunk/packages/vxl/trunk/debian/control 2012-07-28 20:06:46 UTC (rev
11936)
@@ -16,7 +16,7 @@
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vxl/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/vxl/trunk/
-Package: libvxl1.14
+Package: libvxl1.17
Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
@@ -30,7 +30,7 @@
Package: libvxl1-dev
Section: libdevel
Architecture: any
-Depends: ${misc:Depends}, libvxl1.14 (= ${binary:Version})
+Depends: ${misc:Depends}, libvxl1.17 (= ${binary:Version})
Provides: libvxl-dev
Description: C++ Libraries for Computer Vision Research
VXL (the Vision-something-Libraries) is a collection of C++ libraries
Modified: trunk/packages/vxl/trunk/debian/rules
===
--- trunk/packages/vxl/trunk/debian/rules 2012-07-28 20:04:01 UTC (rev
11935)
+++ trunk/packages/vxl/trunk/debian/rules 2012-07-28 20:06:46 UTC (rev
11936)
@@ -48,10 +48,6 @@
dh $@ --buildsystem=cmake --parallel --with python2
override_dh_auto_configure:
- # remove duplicate from bprb_parameters+unsigned_int-.cxx
- rm -f
$(CURDIR)/contrib/brl/bpro/bprb/Templates/bprb_parameters+unsigned-.cxx
- # remove duplicate from
bvxm_voxel_grid+bsta_num_obs+bsta_mixture_fixed+bsta_num_obs+bsta_gauss_f1-.3---.cxx
- rm -f
$(CURDIR)/contrib/brl/bseg/bvxm/grid/Templates/bvxm_voxel_grid+bsta_num_obs+bsta_mixture_fixed+bsta_num_obs+bsta_gaussian_sphere+float.1--.3---.cxx
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
override_dh_lintian:
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[med-svn] r11934 - in trunk/packages/python-biom-format/trunk/debian: . patches
Author: tille
Date: 2012-07-28 19:21:29 + (Sat, 28 Jul 2012)
New Revision: 11934
Added:
trunk/packages/python-biom-format/trunk/debian/patches/
trunk/packages/python-biom-format/trunk/debian/patches/enable_cython_beta.patch
trunk/packages/python-biom-format/trunk/debian/patches/series
Modified:
trunk/packages/python-biom-format/trunk/debian/changelog
trunk/packages/python-biom-format/trunk/debian/control
trunk/packages/python-biom-format/trunk/debian/rules
Log:
Enable building with Cython 0.17.beta1
Modified: trunk/packages/python-biom-format/trunk/debian/changelog
===
--- trunk/packages/python-biom-format/trunk/debian/changelog2012-07-28
18:59:14 UTC (rev 11933)
+++ trunk/packages/python-biom-format/trunk/debian/changelog2012-07-28
19:21:29 UTC (rev 11934)
@@ -2,4 +2,4 @@
* Initial release (Closes: #682242)
- -- Andreas Tille Fri, 20 Jul 2012 11:21:44 +0200
+ -- Andreas Tille Sat, 28 Jul 2012 20:59:32 +0200
Modified: trunk/packages/python-biom-format/trunk/debian/control
===
--- trunk/packages/python-biom-format/trunk/debian/control 2012-07-28
18:59:14 UTC (rev 11933)
+++ trunk/packages/python-biom-format/trunk/debian/control 2012-07-28
19:21:29 UTC (rev 11934)
@@ -11,8 +11,8 @@
Vcs-Svn:
svn://svn.debian.org/debian-med/trunk/packages/python-biom-format/trunk/
Package: python-biom-format
-Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}
+Architecture: any
+Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends}
Description: Biological Observation Matrix (BIOM) format
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation
Added:
trunk/packages/python-biom-format/trunk/debian/patches/enable_cython_beta.patch
===
---
trunk/packages/python-biom-format/trunk/debian/patches/enable_cython_beta.patch
(rev 0)
+++
trunk/packages/python-biom-format/trunk/debian/patches/enable_cython_beta.patch
2012-07-28 19:21:29 UTC (rev 11934)
@@ -0,0 +1,23 @@
+Author: Andreas Tille
+Date: Sat, 28 Jul 2012 20:59:32 +0200
+Description: Enable building also with beta versions of Cython
+
+--- biom-format-1.0.0.orig/setup.py
biom-format-1.0.0/setup.py
+@@ -5,6 +5,7 @@
+ from os.path import join, split
+ from os import getcwd
+ from glob import glob
++from re import sub
+
+ __author__ = "Daniel McDonald"
+ __copyright__ = "Copyright 2012, The BIOM Format"
+@@ -25,7 +26,7 @@
+ import Cython
+ from Cython.Distutils import build_ext
+
+-cy_version = tuple(map(int, Cython.__version__.split('.')))
++cy_version = tuple(map(int, sub('beta', '0.',
Cython.__version__).split('.')))
+ if cy_version >= (0, 14, 1):
+ cython_present = True
+ else:
Added: trunk/packages/python-biom-format/trunk/debian/patches/series
===
--- trunk/packages/python-biom-format/trunk/debian/patches/series
(rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/patches/series
2012-07-28 19:21:29 UTC (rev 11934)
@@ -0,0 +1 @@
+enable_cython_beta.patch
Modified: trunk/packages/python-biom-format/trunk/debian/rules
===
--- trunk/packages/python-biom-format/trunk/debian/rules2012-07-28
18:59:14 UTC (rev 11933)
+++ trunk/packages/python-biom-format/trunk/debian/rules2012-07-28
19:21:29 UTC (rev 11934)
@@ -3,7 +3,7 @@
# DH_VERBOSE := 1
%:
- dh $@ --with python2
+ dh $@ --with python2 # ,sphinxdoc
override_dh_auto_clean:
dh_auto_clean
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[med-svn] r11933 - in trunk/packages/vxl/trunk/debian: . patches
Author: malat
Date: 2012-07-28 18:59:14 + (Sat, 28 Jul 2012)
New Revision: 11933
Modified:
trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
trunk/packages/vxl/trunk/debian/rules
trunk/packages/vxl/trunk/debian/watch
Log:
Prefer UNIX eol tarball
Modified: trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
===
--- trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
2012-07-28 18:52:58 UTC (rev 11932)
+++ trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
2012-07-28 18:59:14 UTC (rev 11933)
@@ -23,42 +23,50 @@
Reviewed-By:
Last-Update:
vxl-1.17.0.orig/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
-+++ vxl-1.17.0/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
+Index: vxl-1.17.0/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
+===
+--- vxl-1.17.0.orig/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
2010-09-26 08:37:58.0 +0200
vxl-1.17.0/contrib/brl/b3p/shapelib/tests/CMakeLists.txt 2012-07-28
20:58:45.335213478 +0200
@@ -1,2 +1,2 @@
- ADD_EXECUTABLE(shapelib_test_include test_include.cxx )
--TARGET_LINK_LIBRARIES( shapelib_test_include shapelib )
-+TARGET_LINK_LIBRARIES( shapelib_test_include shp )
vxl-1.17.0.orig/contrib/brl/bbas/baio/baio_unix.cxx
-+++ vxl-1.17.0/contrib/brl/bbas/baio/baio_unix.cxx
+ ADD_EXECUTABLE(shapelib_test_include test_include.cxx )
+-TARGET_LINK_LIBRARIES( shapelib_test_include shapelib )
++TARGET_LINK_LIBRARIES( shapelib_test_include shp )
+Index: vxl-1.17.0/contrib/brl/bbas/baio/baio_unix.cxx
+===
+--- vxl-1.17.0.orig/contrib/brl/bbas/baio/baio_unix.cxx2010-11-22
17:11:21.0 +0100
vxl-1.17.0/contrib/brl/bbas/baio/baio_unix.cxx 2012-07-28
20:58:45.339213477 +0200
@@ -11,7 +11,7 @@
- #include //for aio_read
- //#include// for open (not really necessary
- #include //includes bzero
--
-+#include
-
- //: baio_info struct: wrapper for status variables
- struct baio_info {
vxl-1.17.0.orig/contrib/brl/bbas/bwm/algo/CMakeLists.txt
-+++ vxl-1.17.0/contrib/brl/bbas/bwm/algo/CMakeLists.txt
-@@ -32,7 +32,7 @@ ENDIF(ECW_FOUND)
-
- ADD_LIBRARY(bwm_algo ${bwm_algo_sources})
-
--TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shapelib )
-+TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shp )
-
- IF( BUILD_TESTING )
- SUBDIRS(tests)
vxl-1.17.0.orig/vcl/vcl_config_compiler.h.in
-+++ vxl-1.17.0/vcl/vcl_config_compiler.h.in
+ #include //for aio_read
+ //#include// for open (not really necessary
+ #include //includes bzero
+-
++#include
+
+ //: baio_info struct: wrapper for status variables
+ struct baio_info {
+Index: vxl-1.17.0/contrib/brl/bbas/bwm/algo/CMakeLists.txt
+===
+--- vxl-1.17.0.orig/contrib/brl/bbas/bwm/algo/CMakeLists.txt 2012-05-31
21:59:20.0 +0200
vxl-1.17.0/contrib/brl/bbas/bwm/algo/CMakeLists.txt2012-07-28
20:58:45.339213477 +0200
+@@ -32,7 +32,7 @@
+
+ ADD_LIBRARY(bwm_algo ${bwm_algo_sources})
+
+-TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shapelib )
++TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shp )
+
+ IF( BUILD_TESTING )
+ SUBDIRS(tests)
+Index: vxl-1.17.0/vcl/vcl_config_compiler.h.in
+===
+--- vxl-1.17.0.orig/vcl/vcl_config_compiler.h.in 2012-03-16
16:26:54.0 +0100
vxl-1.17.0/vcl/vcl_config_compiler.h.in2012-07-28 20:58:45.339213477
+0200
@@ -145,7 +145,7 @@
- // define VCL_CAN_STATIC_CONST_INIT_FLOAT to either 0 or 1.
-
- //#define VCL_CAN_STATIC_CONST_INIT_FLOAT 1 /* allowed */
--//#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
-+#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
- #ifndef VCL_CAN_STATIC_CONST_INIT_FLOAT
- # define VCL_CAN_STATIC_CONST_INIT_FLOAT @VCL_STATIC_CONST_INIT_FLOAT@
- #endif
+ // define VCL_CAN_STATIC_CONST_INIT_FLOAT to either 0 or 1.
+
+ //#define VCL_CAN_STATIC_CONST_INIT_FLOAT 1 /* allowed */
+-//#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
++#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
+ #ifndef VCL_CAN_STATIC_CONST_INIT_FLOAT
+ # define VCL_CAN_STATIC_CONST_INIT_FLOAT @VCL_STATIC_CONST_INIT_FLOAT@
+ #endif
Modified: trunk/packages/vxl/trunk/debian/rules
===
--- trunk
[med-svn] r11932 - in trunk/packages/vxl/trunk/debian: . patches
Author: malat
Date: 2012-07-28 18:52:58 + (Sat, 28 Jul 2012)
New Revision: 11932
Added:
trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
Modified:
trunk/packages/vxl/trunk/debian/changelog
trunk/packages/vxl/trunk/debian/patches/series
trunk/packages/vxl/trunk/debian/rules
Log:
First pass at getting vxl 1.17 to compile
Modified: trunk/packages/vxl/trunk/debian/changelog
===
--- trunk/packages/vxl/trunk/debian/changelog 2012-07-28 16:51:38 UTC (rev
11931)
+++ trunk/packages/vxl/trunk/debian/changelog 2012-07-28 18:52:58 UTC (rev
11932)
@@ -1,3 +1,9 @@
+vxl (1.17.0-1) UNRELEASED; urgency=low
+
+ * New upstream
+
+ -- Mathieu Malaterre Sat, 28 Jul 2012 19:43:10 +0200
+
vxl (1.14.0-18) unstable; urgency=low
* Fix compilation with gcc 4.7. Closes: #674350
Added: trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
===
--- trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
(rev 0)
+++ trunk/packages/vxl/trunk/debian/patches/fixcompilation2.patch
2012-07-28 18:52:58 UTC (rev 11932)
@@ -0,0 +1,64 @@
+Description:
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ vxl (1.17.0-1) UNRELEASED; urgency=low
+ .
+ * New upstream
+Author: Mathieu Malaterre
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: ,
+Bug:
+Bug-Debian: http://bugs.debian.org/
+Bug-Ubuntu: https://launchpad.net/bugs/
+Forwarded:
+Reviewed-By:
+Last-Update:
+
+--- vxl-1.17.0.orig/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
vxl-1.17.0/contrib/brl/b3p/shapelib/tests/CMakeLists.txt
+@@ -1,2 +1,2 @@
+ ADD_EXECUTABLE(shapelib_test_include test_include.cxx )
+-TARGET_LINK_LIBRARIES( shapelib_test_include shapelib )
++TARGET_LINK_LIBRARIES( shapelib_test_include shp )
+--- vxl-1.17.0.orig/contrib/brl/bbas/baio/baio_unix.cxx
vxl-1.17.0/contrib/brl/bbas/baio/baio_unix.cxx
+@@ -11,7 +11,7 @@
+ #include //for aio_read
+ //#include// for open (not really necessary
+ #include //includes bzero
+-
++#include
+
+ //: baio_info struct: wrapper for status variables
+ struct baio_info {
+--- vxl-1.17.0.orig/contrib/brl/bbas/bwm/algo/CMakeLists.txt
vxl-1.17.0/contrib/brl/bbas/bwm/algo/CMakeLists.txt
+@@ -32,7 +32,7 @@ ENDIF(ECW_FOUND)
+
+ ADD_LIBRARY(bwm_algo ${bwm_algo_sources})
+
+-TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shapelib )
++TARGET_LINK_LIBRARIES( bwm_algo sdet vtol vil vil_algo vgl vgl_algo vnl
vnl_algo vsol vpgl vpgl_algo vpgl_file_formats bgui brip vdgl bsta vgui vul vcl
shp )
+
+ IF( BUILD_TESTING )
+ SUBDIRS(tests)
+--- vxl-1.17.0.orig/vcl/vcl_config_compiler.h.in
vxl-1.17.0/vcl/vcl_config_compiler.h.in
+@@ -145,7 +145,7 @@
+ // define VCL_CAN_STATIC_CONST_INIT_FLOAT to either 0 or 1.
+
+ //#define VCL_CAN_STATIC_CONST_INIT_FLOAT 1 /* allowed */
+-//#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
++#define VCL_CAN_STATIC_CONST_INIT_FLOAT 0 /* not allowed */
+ #ifndef VCL_CAN_STATIC_CONST_INIT_FLOAT
+ # define VCL_CAN_STATIC_CONST_INIT_FLOAT @VCL_STATIC_CONST_INIT_FLOAT@
+ #endif
Modified: trunk/packages/vxl/trunk/debian/patches/series
===
--- trunk/packages/vxl/trunk/debian/patches/series 2012-07-28 16:51:38 UTC
(rev 11931)
+++ trunk/packages/vxl/trunk/debian/patches/series 2012-07-28 18:52:58 UTC
(rev 11932)
@@ -1,15 +1 @@
-vxl.soname.patch
-video4linux.patch
-opencl_unix.patch
-sse2.patch
-renamelibs.patch
-fixcomp.patch
-fix_alphacomp.patch
-install_doxygen.patch
-libav_trunk.patch
-ffmpeg_C99.patch
-removedoxyen.patch
-png15.patch
-dcmtkgcc47.patch
-vnl_r28976.patch
-gcc47other.patch
+fixcompilation2.patch
Modified: trunk/packages/vxl/trunk/debian/rules
===
--- trunk/packages/vxl/trunk/debian/rules 2012-07-28 16:51:38 UTC (rev
11931)
+++ trunk/packages/vxl/trunk/debian/rules 2012-07-28 18:52:58 UTC (rev
11932)
@@ -69,4 +69,4 @@
override_dh_auto_test:
get-orig-source:
- uscan --verbose --force-download --repack
+ uscan --verbose --force-download --rename --repack
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[med-svn] r11931 - trunk/packages/gassst/trunk/debian
Author: malat
Date: 2012-07-28 16:51:38 + (Sat, 28 Jul 2012)
New Revision: 11931
Modified:
trunk/packages/gassst/trunk/debian/changelog
trunk/packages/gassst/trunk/debian/control
Log:
Upload to fix FTBFS on non-SSE arch
Modified: trunk/packages/gassst/trunk/debian/changelog
===
--- trunk/packages/gassst/trunk/debian/changelog2012-07-28 16:51:08 UTC
(rev 11930)
+++ trunk/packages/gassst/trunk/debian/changelog2012-07-28 16:51:38 UTC
(rev 11931)
@@ -1,3 +1,10 @@
+gassst (1.28-2) unstable; urgency=low
+
+ * Team upload.
+ * Arch: i386 amd64 because code rely on SSE2/SSE3. Closes: #680433
+
+ -- Mathieu Malaterre Sat, 28 Jul 2012 18:48:00 +0200
+
gassst (1.28-1) unstable; urgency=low
* Initial release (Closes: #654603)
Modified: trunk/packages/gassst/trunk/debian/control
===
--- trunk/packages/gassst/trunk/debian/control 2012-07-28 16:51:08 UTC (rev
11930)
+++ trunk/packages/gassst/trunk/debian/control 2012-07-28 16:51:38 UTC (rev
11931)
@@ -11,7 +11,7 @@
Homepage: http://www.irisa.fr/symbiose/projects/gassst/
Package: gassst
-Architecture: any
+Architecture: amd64 i386
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Global alignment short sequence search tool
GASSST finds global alignments of short DNA sequences against large DNA banks.
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[med-svn] r11930 - in trunk/packages/gassst/tags: . 1.28-2/debian
Author: malat
Date: 2012-07-28 16:51:08 + (Sat, 28 Jul 2012)
New Revision: 11930
Added:
trunk/packages/gassst/tags/1.28-2/
Modified:
trunk/packages/gassst/tags/1.28-2/debian/changelog
trunk/packages/gassst/tags/1.28-2/debian/control
Log:
[svn-buildpackage] Tagging gassst 1.28-2
Modified: trunk/packages/gassst/tags/1.28-2/debian/changelog
===
--- trunk/packages/gassst/trunk/debian/changelog2012-07-28 15:49:02 UTC
(rev 11929)
+++ trunk/packages/gassst/tags/1.28-2/debian/changelog 2012-07-28 16:51:08 UTC
(rev 11930)
@@ -1,3 +1,10 @@
+gassst (1.28-2) unstable; urgency=low
+
+ * Team upload.
+ * Arch: i386 amd64 because code rely on SSE2/SSE3. Closes: #680433
+
+ -- Mathieu Malaterre Sat, 28 Jul 2012 18:48:00 +0200
+
gassst (1.28-1) unstable; urgency=low
* Initial release (Closes: #654603)
Modified: trunk/packages/gassst/tags/1.28-2/debian/control
===
--- trunk/packages/gassst/trunk/debian/control 2012-07-28 15:49:02 UTC (rev
11929)
+++ trunk/packages/gassst/tags/1.28-2/debian/control2012-07-28 16:51:08 UTC
(rev 11930)
@@ -11,7 +11,7 @@
Homepage: http://www.irisa.fr/symbiose/projects/gassst/
Package: gassst
-Architecture: any
+Architecture: amd64 i386
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Global alignment short sequence search tool
GASSST finds global alignments of short DNA sequences against large DNA banks.
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[med-svn] r11929 - trunk/packages/insighttoolkit/tags
Author: malat Date: 2012-07-28 15:49:02 + (Sat, 28 Jul 2012) New Revision: 11929 Added: trunk/packages/insighttoolkit/tags/3.20.1+git20120521-3/ Log: [svn-buildpackage] Tagging insighttoolkit 3.20.1+git20120521-3 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11928 - in trunk/packages/insighttoolkit/branches/3.20.1/debian: . patches
Author: malat Date: 2012-07-28 15:11:28 + (Sat, 28 Jul 2012) New Revision: 11928 Added: trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/nan-i386.patch Modified: trunk/packages/insighttoolkit/branches/3.20.1/debian/changelog trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/series Log: Need to patch itk to get plastimatch test suite to pass on gcc 4.7.0 Modified: trunk/packages/insighttoolkit/branches/3.20.1/debian/changelog === --- trunk/packages/insighttoolkit/branches/3.20.1/debian/changelog 2012-07-28 13:39:53 UTC (rev 11927) +++ trunk/packages/insighttoolkit/branches/3.20.1/debian/changelog 2012-07-28 15:11:28 UTC (rev 11928) @@ -1,3 +1,10 @@ +insighttoolkit (3.20.1+git20120521-3) unstable; urgency=low + + * Fix a sanity check yielding false negatives. Closes: #682805 ++ debian/patches/nan-i386.patch + + -- Mathieu Malaterre Sat, 28 Jul 2012 17:10:41 +0200 + insighttoolkit (3.20.1+git20120521-2) unstable; urgency=low * Fix gcc 4.7.1 build failure of wrapitk-python. Closes: #667417 Added: trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/nan-i386.patch === --- trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/nan-i386.patch (rev 0) +++ trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/nan-i386.patch 2012-07-28 15:11:28 UTC (rev 11928) @@ -0,0 +1,26 @@ +Description: Fix test failures due to NrrdIO on i386 + Fix a bunch of failing tests, all because NrrdIO was doing some run + time checks on NaN. The run-time check is already skipped on Apple + builds and with Visual Studio. So now we add GCC version >= 4.7. +Author: Paul Novotny +Applied-Upstream: http://itk.org/gitweb?p=ITK.git;a=commit;h=21da36bc995 + +Index: insighttoolkit-3.20.1+git20120521/Utilities/NrrdIO/sane.c +=== +--- insighttoolkit-3.20.1+git20120521.orig/Utilities/NrrdIO/sane.c 2012-05-03 18:11:41.0 +0200 insighttoolkit-3.20.1+git20120521/Utilities/NrrdIO/sane.c 2012-07-28 17:04:31.319720796 +0200 +@@ -107,9 +107,12 @@ + + 1) APPLE builds due to a cross-compilation problem, and + 2) Visual Studio builds for version newer than 2005 (not included) +- when building in 32bits. */ ++ when building in 32bits. ++ 3) GCC 4.7 Builds when building in 32bits */ + +-#if defined(__APPLE__) || ( defined(_MSC_VER) && _MSC_VER >= 1400 ) ++ ++#if defined(__APPLE__) || ( defined(_MSC_VER) && _MSC_VER >= 1400 ) || \ ++ ( defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7 ))) + /* don't compare airFP_SNAN */ + #else + && airFP_SNAN == airFPClass_f(AIR_SNAN) Modified: trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/series === --- trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/series 2012-07-28 13:39:53 UTC (rev 11927) +++ trunk/packages/insighttoolkit/branches/3.20.1/debian/patches/series 2012-07-28 15:11:28 UTC (rev 11928) @@ -13,3 +13,4 @@ openjpegmath.patch ITKNrrdIOmath.patch bug667417.patch +nan-i386.patch ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11927 - trunk/packages/openslide-python/trunk/debian
Author: malat Date: 2012-07-28 13:39:53 + (Sat, 28 Jul 2012) New Revision: 11927 Removed: trunk/packages/openslide-python/trunk/debian/examples Modified: trunk/packages/openslide-python/trunk/debian/copyright Log: Fix d/copyright bits Modified: trunk/packages/openslide-python/trunk/debian/copyright === --- trunk/packages/openslide-python/trunk/debian/copyright 2012-07-28 13:29:41 UTC (rev 11926) +++ trunk/packages/openslide-python/trunk/debian/copyright 2012-07-28 13:39:53 UTC (rev 11927) @@ -6,6 +6,27 @@ Copyright: © 2010-2011 Carnegie Mellon University License: LGPL-2.1 +Files: examples/deepzoom/static/jquery.js +Copyright: © 2009-2011 John Resig +License: MIT + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + . + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. + Files: examples/deepzoom/static/OpenSeadragon.js Copyright: © Copyright (c) 2010, OpenSeadragon, © 2010, CodePlex Foundation Deleted: trunk/packages/openslide-python/trunk/debian/examples === --- trunk/packages/openslide-python/trunk/debian/examples 2012-07-28 13:29:41 UTC (rev 11926) +++ trunk/packages/openslide-python/trunk/debian/examples 2012-07-28 13:39:53 UTC (rev 11927) @@ -1 +0,0 @@ -examples/* ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11926 - trunk/packages/openslide-python/trunk/debian
Author: malat Date: 2012-07-28 13:29:41 + (Sat, 28 Jul 2012) New Revision: 11926 Modified: trunk/packages/openslide-python/trunk/debian/changelog trunk/packages/openslide-python/trunk/debian/control trunk/packages/openslide-python/trunk/debian/copyright trunk/packages/openslide-python/trunk/debian/docs trunk/packages/openslide-python/trunk/debian/rules Log: remaining issues Modified: trunk/packages/openslide-python/trunk/debian/changelog === --- trunk/packages/openslide-python/trunk/debian/changelog 2012-07-28 09:55:24 UTC (rev 11925) +++ trunk/packages/openslide-python/trunk/debian/changelog 2012-07-28 13:29:41 UTC (rev 11926) @@ -1,5 +1,5 @@ -openslide-python (0.2.0-1) unstable; urgency=low +openslide-python (0.3.0-1) unstable; urgency=low - * Initial release (Closes: #) + * Initial release (Closes: #683077) - -- Mathieu Malaterre Thu, 01 Sep 2011 17:18:40 +0200 + -- Mathieu Malaterre Sat, 28 Jul 2012 15:22:36 +0200 Modified: trunk/packages/openslide-python/trunk/debian/control === --- trunk/packages/openslide-python/trunk/debian/control2012-07-28 09:55:24 UTC (rev 11925) +++ trunk/packages/openslide-python/trunk/debian/control2012-07-28 13:29:41 UTC (rev 11926) @@ -3,9 +3,9 @@ Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes -Uploaders: Mathieu Malaterre +Uploaders: Mathieu Malaterre Build-Depends: debhelper (>= 7.0.50~), python-all-dev (>= 2.6.6-3) -Standards-Version: 3.9.2 +Standards-Version: 3.9.3 X-Python-Version: >=2.6 Homepage: http://openslide.org Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/openslide-python/trunk/ Modified: trunk/packages/openslide-python/trunk/debian/copyright === --- trunk/packages/openslide-python/trunk/debian/copyright 2012-07-28 09:55:24 UTC (rev 11925) +++ trunk/packages/openslide-python/trunk/debian/copyright 2012-07-28 13:29:41 UTC (rev 11926) @@ -12,7 +12,7 @@ License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - + . - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - Redistributions in binary form must reproduce the above copyright notice, @@ -21,7 +21,7 @@ - Neither the name of OpenSeadragon nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. - + . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE Modified: trunk/packages/openslide-python/trunk/debian/docs === --- trunk/packages/openslide-python/trunk/debian/docs 2012-07-28 09:55:24 UTC (rev 11925) +++ trunk/packages/openslide-python/trunk/debian/docs 2012-07-28 13:29:41 UTC (rev 11926) @@ -1,2 +1 @@ README.txt -TODO.txt Modified: trunk/packages/openslide-python/trunk/debian/rules === --- trunk/packages/openslide-python/trunk/debian/rules 2012-07-28 09:55:24 UTC (rev 11925) +++ trunk/packages/openslide-python/trunk/debian/rules 2012-07-28 13:29:41 UTC (rev 11926) @@ -1,10 +1,13 @@ #!/usr/bin/make -f # Uncomment this to turn on verbose mode. -export DH_VERBOSE=1 +#export DH_VERBOSE=1 %: dh $@ --with python2 --buildsystem=python_distutils -override_dh_auto_clean: - # bla +override_dh_installexamples: + dh_installexamples -Xjquery.js examples/* + +get-orig-source: + uscan --verbose --force-download --rename ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11925 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-28 09:55:24 + (Sat, 28 Jul 2012) New Revision: 11925 Modified: trunk/packages/genometools/trunk/debian/genometools-common.install trunk/packages/genometools/trunk/debian/rules Log: make sure that cgilua is not installed Modified: trunk/packages/genometools/trunk/debian/genometools-common.install === --- trunk/packages/genometools/trunk/debian/genometools-common.install 2012-07-28 09:38:09 UTC (rev 11924) +++ trunk/packages/genometools/trunk/debian/genometools-common.install 2012-07-28 09:55:24 UTC (rev 11925) @@ -1,3 +1,16 @@ -usr/bin/gtdata usr/share/genometools/ +usr/bin/gtdata/doc usr/share/genometools/gtdata +usr/bin/gtdata/obo_files usr/share/genometools/gtdata +usr/bin/gtdata/sketch usr/share/genometools/gtdata +usr/bin/gtdata/trans usr/share/genometools/gtdata +usr/bin/gtdata/modules/fileutils.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtdoclib.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtdoclib usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtmodulehelper.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/stringext.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/warning.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/external/md5.lua usr/share/genometools/gtdata/modules/external +usr/bin/gtdata/modules/external/re.lua usr/share/genometools/gtdata/modules/external - Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:38:09 UTC (rev 11924) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:55:24 UTC (rev 11925) @@ -18,13 +18,13 @@ $(MAKE) cleanup override_dh_auto_build: - dh_auto_build -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no + dh_auto_build --parallel -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no override_dh_auto_test: #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: - dh_auto_install --exclude=cgilua -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr + dh_auto_install -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=genometools-dbg ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11924 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-28 09:38:09 + (Sat, 28 Jul 2012) New Revision: 11924 Modified: trunk/packages/genometools/trunk/debian/changelog trunk/packages/genometools/trunk/debian/copyright trunk/packages/genometools/trunk/debian/rules Log: address issues raised by ftpmaster Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/changelog 2012-07-28 09:38:09 UTC (rev 11924) @@ -1,4 +1,4 @@ -genometools (1.4.1-1) UNRELEASED; urgency=low +genometools (1.4.1-1) unstable; urgency=low * Initial release (Closes: #657923) * the GFF3 parser now handles children which are defined before their parents Modified: trunk/packages/genometools/trunk/debian/copyright === --- trunk/packages/genometools/trunk/debian/copyright 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/copyright 2012-07-28 09:38:09 UTC (rev 11924) @@ -9,14 +9,19 @@ 2003-2012 Gordon Gremme 2007-2012 Sascha Steinbiss 2004-2012 Stefan Bienert + 2010-2011 Joachim Bonnet 2007 David Ellinghaus + 2008 Johannes Fischer 2009-2012 Giorgio Gonnella 2007-2008 Thomas Jahns 2007 Malte Mader 2009 Brent Pedersen 2007 Christin Schaerfer 2007 David Schmitz-Huebsch + 2003-2005 Michael E Sparks + 2009 Zhihao Tang 2010-2012 Dirk Willrodt + 2004-2012 Center for Bioinformatics, University of Hamburg License: Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:38:09 UTC (rev 11924) @@ -24,10 +24,10 @@ #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: - dh_auto_install -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr + dh_auto_install --exclude=cgilua -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=genometools-dbg override_dh_installdocs: - dh_installdocs --exclude=license.template + dh_installdocs --exclude=license.template --exclude=lgpl.txt ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
