Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv20016
Modified Files:
emboss.info
Added Files:
emboss.patch
Log Message:
upstream fixes
--- NEW FILE: emboss.patch ---
diff -Naur EMBOSS-6.0.1/ajax/ajseqwrite.c EMBOSS-6.0.1-patched/ajax/ajseqwrite.c
--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2008-07-14 10:58:07.000000000 -0400
+++ EMBOSS-6.0.1-patched/ajax/ajseqwrite.c 2008-12-15 05:40:32.000000000
-0500
@@ -3743,7 +3743,7 @@
ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
if(ajStrGetLen(outseq->Tax))
- ajFmtPrintF(outseq->File, "OS %S\n", outseq->Tax);
+ ajFmtPrintF(outseq->File, "OS %S.\n", outseq->Tax);
if(ajListGetLength(outseq->Taxlist) > 1)
{
diff -Naur EMBOSS-6.0.1/emboss/jaspscan.c EMBOSS-6.0.1-patched/emboss/jaspscan.c
--- EMBOSS-6.0.1/emboss/jaspscan.c 2008-06-26 04:39:09.000000000 -0400
+++ EMBOSS-6.0.1-patched/emboss/jaspscan.c 2008-08-27 03:32:24.000000000
-0400
@@ -293,7 +293,7 @@
jaspscan_scan(substr,begin,mfname, cp, thresh, both, hits);
- ajStrDel(&mfname);
+ ajListPushAppend(flist, (void **)mfname);
}
jaspscan_ReportHits(TabRpt,mattab,hits);
@@ -303,6 +303,10 @@
}
+ while(ajListPop(flist,(void **)&mfname))
+ ajStrDel(&mfname);
+
+
ajStrDel(&dir);
ajStrDel(&menu);
ajStrDel(&excl);
diff -Naur EMBOSS-6.0.1/emboss/vectorstrip.c
EMBOSS-6.0.1-patched/emboss/vectorstrip.c
--- EMBOSS-6.0.1/emboss/vectorstrip.c 2008-06-26 04:39:09.000000000 -0400
+++ EMBOSS-6.0.1-patched/emboss/vectorstrip.c 2008-12-15 05:23:57.000000000
-0500
@@ -174,7 +174,7 @@
vectorlist = ajListNew();
/* data from command line or file? */
- if(vec == AJTRUE)
+ if(vec && vectorfile)
vectorstrip_read_vector_data(vectorfile, vectorlist);
else
{
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 1.26
retrieving revision 1.27
diff -u -d -r1.26 -r1.27
--- emboss.info 20 Aug 2008 12:39:51 -0000 1.26
+++ emboss.info 19 Jan 2009 17:56:49 -0000 1.27
@@ -1,9 +1,9 @@
Package: emboss
Version: 6.0.1
-Revision: 2
+Revision: 3
#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
+BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev,
freetype219, expat1, fontconfig2-dev, fink (>= 0.24.12)
#Replaces: emboss (<< 5.0.0)
Source: mirror:custom:EMBOSS-%v.tar.gz
CustomMirror: <<
@@ -11,7 +11,10 @@
<<
Source-MD5: 2182b148dace6bea403deed8facae40d
#SetCPPFLAGS: -Dstat64=stat
-#Patch: %n.patch
+
+PatchFile: %n.patch
+PatchFile-MD5: 39d73351527ab8c827d905d01f858e03
+
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
Installscript: <<
make install DESTDIR=%d
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