Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv15261
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 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- emboss.patch 25 Jan 2010 13:33:20 -0000 1.17
+++ emboss.patch 8 Mar 2010 16:40:52 -0000 1.18
@@ -1,7 +1,6 @@
-Binary files EMBOSS-6.2.0/ajax/.DS_Store and
EMBOSS-6.2.0-patched/ajax/.DS_Store differ
diff -Nurd EMBOSS-6.2.0/ajax/acd/Makefile.in
EMBOSS-6.2.0-patched/ajax/acd/Makefile.in
--- EMBOSS-6.2.0/ajax/acd/Makefile.in 2010-01-15 05:54:39.000000000 -0500
-+++ EMBOSS-6.2.0-patched/ajax/acd/Makefile.in 2010-01-24 08:32:58.000000000
-0500
++++ EMBOSS-6.2.0-patched/ajax/acd/Makefile.in 2010-03-08 08:52:52.000000000
-0500
@@ -72,7 +72,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
@@ -13,7 +12,7 @@
libacd_la_OBJECTS = $(am_libacd_la_OBJECTS)
diff -Nurd EMBOSS-6.2.0/ajax/ajaxdb/Makefile.in
EMBOSS-6.2.0-patched/ajax/ajaxdb/Makefile.in
[...6437 lines suppressed...]
+ continue;
+
+@@ -4737,6 +4782,10 @@
+
+ break;
+ case 6:
++ if(thys->m && mismatch >= thys->m)
++ ajFatal("embPatCompileII: Mismatches (%d) must be less than the "
++ "real pattern length (%d)",mismatch,thys->m);
++
+ if (!thys->skipm)
+ {
+ AJCNEW(thys->skipm,thys->m);
diff -Nurd EMBOSS-6.2.0/plplot/Makefile.in
EMBOSS-6.2.0-patched/plplot/Makefile.in
--- EMBOSS-6.2.0/plplot/Makefile.in 2010-01-15 05:54:43.000000000 -0500
-+++ EMBOSS-6.2.0-patched/plplot/Makefile.in 2010-01-23 17:44:52.000000000
-0500
++++ EMBOSS-6.2.0-patched/plplot/Makefile.in 2010-03-08 08:55:10.000000000
-0500
@@ -71,7 +71,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgincludedir)"
Index: emboss.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.35
retrieving revision 1.36
diff -u -d -r1.35 -r1.36
--- emboss.info 25 Jan 2010 19:21:37 -0000 1.35
+++ emboss.info 8 Mar 2010 16:40:52 -0000 1.36
@@ -1,6 +1,6 @@
Package: emboss
Version: 6.2.0
-Revision: 1
+Revision: 2
#Distribution: 10.4, 10.5
Depends: <<
%N-ajax6-shlibs (>= %v-%r),
@@ -34,10 +34,19 @@
<<
Source-MD5: 2e2937dd0493814ca0f64981f4c79319
+Source2: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/jemboss.jar
+Source2-MD5: 739d0910e28b20c7defef3283b392c8b
+
+Source3: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/density.2.density.gif
+Source3-MD5: e8a55a1427719238d983c078937db4f6
+
+Source4: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/density.3.density.gif
+Source4-MD5: e47d9c3ad7496289d21665edeb7cecdc
+
#SetCPPFLAGS: -Dstat64=stat
PatchFile: %n.patch
-PatchFile-MD5: 883f84abeba1ecc40bbc4960fe49241c
+PatchFile-MD5: 0fcc3349a801bec9a141e5603211e06a
ConfigureParams: <<
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home \
@@ -46,6 +55,14 @@
--libdir=%p/lib/EMBOSS
<<
+CompileScript: <<
+ mv ../jemboss.jar %b/jemboss/lib/
+ mv ../density.2.density.gif %b/doc/programs/html/
+ mv ../density.3.density.gif %b/doc/programs/html/
+ ./configure %c
+ make
+<<
+
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/include/EMBOSS
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
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proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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