Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv9696
Modified Files:
emboss.info emboss.patch
Log Message:
upstream patches
Index: emboss.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.patch,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- emboss.patch 20 Apr 2009 01:48:05 -0000 1.14
+++ emboss.patch 15 Aug 2009 20:08:45 -0000 1.15
@@ -1,758 +1,1102 @@
-diff -Naur EMBOSS-6.0.1/ajax/ajacd.c EMBOSS-6.0.1-patched/ajax/ajacd.c
---- EMBOSS-6.0.1/ajax/ajacd.c 2008-07-14 10:47:38.000000000 -0400
-+++ EMBOSS-6.0.1-patched/ajax/ajacd.c 2009-04-07 06:44:12.000000000 -0400
-@@ -8256,8 +8256,16 @@
- acdReplyInit(thys, ajStrGetPtr(gdev), &acdReplyDef);
- else
- #ifndef WIN32
-+#ifndef X_DISPLAY_MISSING /* X11 is available */
- acdReplyInit(thys, "x11", &acdReplyDef);
- #else
-+#ifdef PLD_png /* if png/gd/zlib libraries available for png driver
*/
[...1739 lines suppressed...]
+-fi
- /* Get maximum path score and save position */
-- pathmax = -(float) INT_MAX;
-+ pathmax = -(double) INT_MAX;
- for(row=0;row<proflen;++row)
- for(column=0;column<seqlen;++column)
- if(path[row*seqlen+column] > pathmax)
-diff -Naur EMBOSS-6.0.1/nucleus/embprop.c
EMBOSS-6.0.1-patched/nucleus/embprop.c
---- EMBOSS-6.0.1/nucleus/embprop.c 2008-07-14 18:13:33.000000000 -0400
-+++ EMBOSS-6.0.1-patched/nucleus/embprop.c 2008-08-27 03:32:32.000000000
-0400
-@@ -880,6 +880,7 @@
- if(allpartials)
- {
-+ lim = defcnt;
- for(i=0;i<lim;++i)
- for(j=i+1;j<lim;++j)
- {
+ #
Index: emboss.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -d -r1.29 -r1.30
--- emboss.info 15 Jul 2009 23:30:48 -0000 1.29
+++ emboss.info 15 Aug 2009 20:08:44 -0000 1.30
@@ -1,6 +1,6 @@
Package: emboss
Version: 6.1.0
-Revision: 1
+Revision: 2
#Distribution: 10.4
Depends: %N-ajax6-shlibs (>= %v-%r), %N-nucleus6-shlibs (>= %v-%r),
%N-plplot6-shlibs (>= %v-%r), x11, x11-shlibs, libpng3-shlibs, libjpeg-shlibs,
gd2-shlibs, system-java14, expat1-shlibs, fontconfig2-shlibs
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev,
freetype219, expat1, fontconfig2-dev, fink (>= 0.24.12)
@@ -10,12 +10,22 @@
Primary: ftp://emboss.open-bio.org/pub/EMBOSS/
<<
Source-MD5: 6c5163c571bc0be94d64420ce0d71824
+Source2: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/client.jar
+Source2-MD5: 01b8ae4b36ee465206f8911e13677a87
+
#SetCPPFLAGS: -Dstat64=stat
-#PatchFile: %n.patch
-#PatchFile-MD5: a0c6f408a906b0694452bd473bafb367
+PatchFile: %n.patch
+PatchFile-MD5: f185ca807918ee23755840d3bef46e49
ConfigureParams:
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
--disable-dependency-tracking --libdir=%p/lib/EMBOSS
+
+CompileScript: <<
+ mv ../client.jar %b/jemboss/lib/
+ ./configure %c
+ make
+<<
+
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/include/EMBOSS
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