[med-svn] r12293 - in trunk/packages/concavity/trunk/debian: . patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-09-28 19:39:30 +0000 (Fri, 28 Sep 2012)
New Revision: 12293

Added:
   trunk/packages/concavity/trunk/debian/concavity.examples
   trunk/packages/concavity/trunk/debian/concavity.install
   trunk/packages/concavity/trunk/debian/dirs
   trunk/packages/concavity/trunk/debian/patches/spelling
Modified:
   trunk/packages/concavity/trunk/debian/README.source
   trunk/packages/concavity/trunk/debian/control
   trunk/packages/concavity/trunk/debian/patches/series
Log:
fixed lintian warnings

Modified: trunk/packages/concavity/trunk/debian/README.source
===================================================================
--- trunk/packages/concavity/trunk/debian/README.source	2012-09-28 15:59:19 UTC (rev 12292)
+++ trunk/packages/concavity/trunk/debian/README.source	2012-09-28 19:39:30 UTC (rev 12293)
@@ -13,8 +13,7 @@
 
 Static linking to GAPS library
 ------------------------------
-These are the files in pkg/. In a personal communication the author (Thomas Funkhouser <funk at CS.Princeton.EDU>) did not endorse the separate packaging of this library, although the license would allow this. 
-His argument is:
-'The problem is that gaps is truly a research-oriented code base.  It is highly dynamic, it is partially implemented (some functionality is very fleshed out and other is not at all depending on the needs of our research), and it is not easy to learn (there is no user manual).  [...]  If other people used the gaps, then they would surely stumble across aspects of the code they don't understand and/or aren't implemented and/or don't work.  Unfortunately, I am not in a position to answer questions or to fix/complete the parts of the code not relevant to our research.'
+These are the files in pkg/. In a personal communication the author (Thomas Funkhouser <funk at CS.Princeton.EDU>) did not endorse the separate packaging of this library, although the license would allow this.
+His argument is roughly that GAPS is handled very dynamically by its developers and its versions are not expected to be compatible.
 
 # vim:et:ts=2:

Added: trunk/packages/concavity/trunk/debian/concavity.examples
===================================================================
--- trunk/packages/concavity/trunk/debian/concavity.examples	                        (rev 0)
+++ trunk/packages/concavity/trunk/debian/concavity.examples	2012-09-28 19:39:30 UTC (rev 12293)
@@ -0,0 +1 @@
+examples/*

Added: trunk/packages/concavity/trunk/debian/concavity.install
===================================================================
--- trunk/packages/concavity/trunk/debian/concavity.install	                        (rev 0)
+++ trunk/packages/concavity/trunk/debian/concavity.install	2012-09-28 19:39:30 UTC (rev 12293)
@@ -0,0 +1 @@
+bin/x86_64/concavity usr/bin

Modified: trunk/packages/concavity/trunk/debian/control
===================================================================
--- trunk/packages/concavity/trunk/debian/control	2012-09-28 15:59:19 UTC (rev 12292)
+++ trunk/packages/concavity/trunk/debian/control	2012-09-28 19:39:30 UTC (rev 12293)
@@ -4,7 +4,7 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>
 Build-Depends: debhelper (>= 8.0.0)
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Homepage: http://compbio.cs.princeton.edu/concavity/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/concavity/trunk/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/concavity/trunk/
@@ -13,6 +13,7 @@
 Package: concavity
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: pymol
 Description: predictor of protein ligand binding sites from structure and conservation
  ConCavity predicts protein ligand binding sites by combining evolutionary
  sequence conservation and 3D structure.
@@ -35,9 +36,10 @@
  Conservation and 3D Structure. PLoS Comput Biol, 5(12).'.
 
 Package: concavity-dbg
+Section: debug
 Architecture: any
 Depends: concavity (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
-Description: predictor of protein ligand binding sites from structure and conservation (debug)
+Description: predictor of protein ligand binding sites (debug)
  ConCavity predicts protein ligand binding sites by combining evolutionary
  sequence conservation and 3D structure.
  .

Added: trunk/packages/concavity/trunk/debian/dirs
===================================================================
--- trunk/packages/concavity/trunk/debian/dirs	                        (rev 0)
+++ trunk/packages/concavity/trunk/debian/dirs	2012-09-28 19:39:30 UTC (rev 12293)
@@ -0,0 +1 @@
+usr/bin

Modified: trunk/packages/concavity/trunk/debian/patches/series
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/series	2012-09-28 15:59:19 UTC (rev 12292)
+++ trunk/packages/concavity/trunk/debian/patches/series	2012-09-28 19:39:30 UTC (rev 12293)
@@ -4,3 +4,4 @@
 CFLAGSasf
 compiler_errors
 noopengllink
+spelling

Added: trunk/packages/concavity/trunk/debian/patches/spelling
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/spelling	                        (rev 0)
+++ trunk/packages/concavity/trunk/debian/patches/spelling	2012-09-28 19:39:30 UTC (rev 12293)
@@ -0,0 +1,11 @@
+--- a/apps/concavity/pocket_extraction.C
++++ b/apps/concavity/pocket_extraction.C
+@@ -1028,7 +1028,7 @@
+     printf("  Minimum cavity radius = %g\n", min_cavity_radius);
+     printf("  Minimum cavity volume = %g\n", min_cavity_volume);
+     printf("  Max cavities = %d\n", max_cavities);
+-    printf("  Grid treshold = %g\n", threshold_range.Mid());
++    printf("  Grid threshold = %g\n", threshold_range.Mid());
+     printf("  Cardinality = %d\n", mask->Cardinality());
+     printf("  Volume = %g\n", mask->Volume());
+     RNInterval grid_range = mask->Range();