svn commit: r312918 - in head/biology/ugene: . files

[Alexey Dokuchaev]

Author: danfe
Date: Mon Feb 25 13:00:15 2013
New Revision: 312918
URL: http://svnweb.freebsd.org/changeset/ports/312918

Log:
  Unbreak on 7.X and i386 systems.
  
  Reported by:	QAT

Added:
  head/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp   (contents, props changed)
Modified:
  head/biology/ugene/Makefile
  head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
  head/biology/ugene/pkg-plist

Modified: head/biology/ugene/Makefile
==============================================================================
--- head/biology/ugene/Makefile	Mon Feb 25 12:52:33 2013	(r312917)
+++ head/biology/ugene/Makefile	Mon Feb 25 13:00:15 2013	(r312918)
@@ -31,6 +31,9 @@ MANCOMPRESSED=	yes
 .if ${ARCH} == "amd64"
 # need to manually tell the build we are on x64
 CARCH=		CONFIG+=x64
+PLIST_SUB=	NOX64="@comment "
+.else
+PLIST_SUB=	NOX64=""
 .endif
 
 # yes, bash is required, stuff will not execute with sh

Modified: head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
==============================================================================
--- head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp	Mon Feb 25 12:52:33 2013	(r312917)
+++ head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp	Mon Feb 25 13:00:15 2013	(r312918)
@@ -1,4 +1,4 @@
---- ./src/corelibs/U2Private/src/CrashHandler.cpp.old	2012-10-30 15:36:22.000000000 +0100
+--- ./src/corelibs/U2Private/src/CrashHandler.cpp.orig	2012-10-30 15:36:22.000000000 +0100
 +++ ./src/corelibs/U2Private/src/CrashHandler.cpp	2012-10-30 15:47:47.000000000 +0100
 @@ -253,7 +253,7 @@
      }

Added: head/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp	Mon Feb 25 13:00:15 2013	(r312918)
@@ -0,0 +1,30 @@
+--- ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp.orig	2012-12-26 17:43:44.000000000 +0800
++++ ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp	2013-02-25 17:25:06.000000000 +0800
+@@ -9,13 +9,6 @@
+ 	return (PROB) pow(2.0, (double) Score/INTSCALE);
+ 	}
+ 
+-static const double log2e = log2(exp(1.0));
+-
+-double lnTolog2(double ln)
+-	{
+-	return ln*log2e;
+-	}
+-
+ double log2(double x)
+ 	{
+ 	if (0 == x)
+@@ -27,6 +20,13 @@
+ 	return log(x)*dInvLn2;
+ 	}
+ 
++static const double log2e = log2(exp(1.0));
++
++double lnTolog2(double ln)
++	{
++	return ln*log2e;
++	}
++
+ SCORE ProbToScore(PROB Prob)
+ 	{
+ 	if (0.0 == Prob)

Modified: head/biology/ugene/pkg-plist
==============================================================================
--- head/biology/ugene/pkg-plist	Mon Feb 25 12:52:33 2013	(r312917)
+++ head/biology/ugene/pkg-plist	Mon Feb 25 13:00:15 2013	(r312918)
@@ -88,6 +88,7 @@ lib/ugene/plugins/librepeat_finder.so
 lib/ugene/plugins/libsitecon.so
 lib/ugene/plugins/libsmith_waterman.so
 lib/ugene/plugins/libtest_runner.so
+%%NOX64%%lib/ugene/plugins/libumuscle.so
 lib/ugene/plugins/libweight_matrix.so
 lib/ugene/plugins/libworkflow_designer.so
 lib/ugene/plugins/opencl_support.license
@@ -118,6 +119,8 @@ lib/ugene/plugins/smith_waterman.license
 lib/ugene/plugins/smith_waterman.plugin
 lib/ugene/plugins/test_runner.license
 lib/ugene/plugins/test_runner.plugin
+%%NOX64%%lib/ugene/plugins/umuscle.license
+%%NOX64%%lib/ugene/plugins/umuscle.plugin
 lib/ugene/plugins/weight_matrix.license
 lib/ugene/plugins/weight_matrix.plugin
 lib/ugene/plugins/workflow_designer.license