[med-svn] r18910 - trunk/packages/spades/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2015-03-04 22:25:13 +0000 (Wed, 04 Mar 2015)
New Revision: 18910

Added:
   trunk/packages/spades/trunk/debian/patches/use-debian-packaged-yaml-cpp.patch
Modified:
   trunk/packages/spades/trunk/debian/patches/series
   trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bamtools.patch
Log:
led to exclude yaml-cpp :-(


Modified: trunk/packages/spades/trunk/debian/patches/series
===================================================================
--- trunk/packages/spades/trunk/debian/patches/series	2015-03-04 19:35:15 UTC (rev 18909)
+++ trunk/packages/spades/trunk/debian/patches/series	2015-03-04 22:25:13 UTC (rev 18910)
@@ -9,3 +9,4 @@
 # use-debian-packaged-samtools.patch
 # bamtools-cmake.patch
 # use-debian-packaged-bamtools.patch   ## <<-- does not work - see patch description
+# use-debian-packaged-yaml-cpp.patch   ## <<-- does not work - see patch description

Modified: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bamtools.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bamtools.patch	2015-03-04 19:35:15 UTC (rev 18909)
+++ trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bamtools.patch	2015-03-04 22:25:13 UTC (rev 18910)
@@ -1,9 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
-Description: SPAdes originally contained code copies of
- python-yaml and python-joblib.  These code copies are removed
- and this patch is just fixing the cmake input file
- .
+Description: Try to replace code copy of bamtools
  FIXME: This does not work.  If you run
     /usr/bin/spades.py --test
  this ends up in

Added: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-yaml-cpp.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use-debian-packaged-yaml-cpp.patch	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/use-debian-packaged-yaml-cpp.patch	2015-03-04 22:25:13 UTC (rev 18910)
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
+Description: Try to replace code copy of yaml-cpp
+ FIXME: This does not work.  If you run
+    /usr/bin/spades.py --test
+ this ends up in
+ .
+ ===== Assembling started.
+ == Running assembler: K21
+ Exception caught /home/andreas/debian-maintain/repack/spades/orig/SPAdes-3.5.0/spades_test/K21/configs/config.info(3): cannot open include file simplification.info
+ == Error ==  system call for: "['/usr/bin/spades', '/home/andreas/debian-maintain/repack/spades/orig/SPAdes-3.5.0/spades_test/K21/configs/config.info']" finished abnormally, err code: 4
+
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -2,7 +2,6 @@
+ 
+ add_subdirectory(jemalloc)
+ add_subdirectory(nlopt)
+-add_subdirectory(yaml-cpp)
+ add_subdirectory(ConsensusCore)
+ add_subdirectory(bamtools)
+ add_subdirectory(samtools)