Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv3152

Modified Files:
        emboss.info emboss.patch 
Log Message:
new upstream, crossing my fingers :)

Index: emboss.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.patch,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- emboss.patch        6 Dec 2009 09:31:32 -0000       1.16
+++ emboss.patch        25 Jan 2010 13:33:20 -0000      1.17
@@ -1,1132 +1,67 @@
-diff -Naur EMBOSS-6.1.0/ajax/Makefile.in EMBOSS-6.1.0-patched/ajax/Makefile.in
---- EMBOSS-6.1.0/ajax/Makefile.in      2009-07-14 19:15:58.000000000 -0400
-+++ EMBOSS-6.1.0-patched/ajax/Makefile.in      2009-12-06 03:14:06.000000000 
-0500
-@@ -103,7 +103,7 @@
-       $(libajax_la_LDFLAGS) $(LDFLAGS) -o $@
- @iscygwin_fa...@am_libajax_la_rpath = -rpath $(libdir)
- @iscygwin_t...@am_libajax_la_rpath = -rpath $(libdir)
+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
[...1155 lines suppressed...]
++++ EMBOSS-6.2.0-patched/nucleus/Makefile.in   2010-01-24 07:46:36.000000000 
-0500
 @@ -72,7 +72,7 @@
    sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
  am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
  LTLIBRARIES = $(lib_LTLIBRARIES)
 -libnucleus_la_LIBADD =
-+libnucleus_la_LIBADD = ../ajax/libajax.la
++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la 
../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
  am__objects_1 = embaln.lo embcom.lo embcons.lo embdata.lo embdbi.lo \
        embdmx.lo embdomain.lo embest.lo embexit.lo embgroup.lo \
        embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo \
-diff -Naur EMBOSS-6.1.0/plplot/Makefile.in 
EMBOSS-6.1.0-patched/plplot/Makefile.in
---- EMBOSS-6.1.0/plplot/Makefile.in    2009-07-14 19:16:02.000000000 -0400
-+++ EMBOSS-6.1.0-patched/plplot/Makefile.in    2009-12-06 03:07:39.000000000 
-0500
+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
 @@ -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 1.33
retrieving revision 1.34
diff -u -d -r1.33 -r1.34
--- emboss.info 6 Dec 2009 09:31:32 -0000       1.33
+++ emboss.info 25 Jan 2010 13:33:20 -0000      1.34
@@ -1,6 +1,6 @@
 Package: emboss
-Version: 6.1.0
-Revision: 4
+Version: 6.2.0
+Revision: 1
 #Distribution: 10.4, 10.5
 Depends: <<
  %N-ajax6-shlibs (>= %v-%r), 
@@ -12,7 +12,6 @@
  libjpeg-shlibs, 
  gd2-shlibs, 
  system-java (>= 1.5.0), 
- expat1-shlibs, 
  fontconfig2-shlibs (>= 2.4.1-1),
  freetype219-shlibs (>= 2.3.8-2),
  libiconv
@@ -25,7 +24,6 @@
  x11-dev, 
  system-java-dev (>= 1.5.0), 
  freetype219, 
- expat1, 
  fontconfig2-dev (>= 2.4.1-1),
  freetype219 (>= 2.3.8-2),
  fink (>= 0.24.12)
@@ -34,14 +32,12 @@
 CustomMirror: <<
   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
+Source-MD5: 2e2937dd0493814ca0f64981f4c79319
 
 #SetCPPFLAGS: -Dstat64=stat
 
 PatchFile: %n.patch
-PatchFile-MD5: 8d3430963375ed7c192112faa369332e
+PatchFile-MD5: 883f84abeba1ecc40bbc4960fe49241c
 
 ConfigureParams: <<
  --with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home \
@@ -50,32 +46,46 @@
  --libdir=%p/lib/EMBOSS
 <<
 
-CompileScript: <<
- mv ../client.jar %b/jemboss/lib/
- ./configure %c
- make
-<<
-
 Installscript: <<
   make install DESTDIR=%d
   mkdir -p %i/include/EMBOSS
   mv %i/include/*.* %i/include/EMBOSS/
-  ln -s EMBOSS/lib{ajax,ajaxg,nucleus,eplplot}.dylib %i/lib
+  ln -s 
EMBOSS/lib{ajax,ajaxg,ajaxdb,nucleus,eplplot,acd,eexpat,ensemble,epcre,ezlib}.dylib
 %i/lib
   mv %i/lib/EMBOSS/*.*a %i/lib
 <<
 
 SplitOff10: <<
   Package: %N-ajax6-shlibs
-  Depends: %N-plplot3-shlibs (>= %v-%r), libpng3-shlibs, libjpeg-shlibs, 
gd2-shlibs, libiconv, x11-shlibs, fontconfig2-shlibs (>= 2.4.1-1), 
freetype219-shlibs (>= 2.3.8-2)
-
+  Depends: <<
+    %N-plplot3-shlibs (>= %v-%r), 
+    libpng3-shlibs, 
+    libjpeg-shlibs, 
+    gd2-shlibs, 
+    libiconv, 
+    x11-shlibs, 
+    fontconfig2-shlibs (>= 2.4.1-1), 
+    freetype219-shlibs (>= 2.3.8-2)
+  <<  
   DocFiles: ChangeLog COPYING README
   Files: <<
     lib/EMBOSS/libajax.6*.dylib
+    lib/EMBOSS/libajaxdb.6*.dylib
     lib/EMBOSS/libajaxg.6*.dylib
+    lib/EMBOSS/libacd.6*.dylib
+    lib/EMBOSS/libensembl.6*.dylib
+    lib/EMBOSS/libeexpat.1*.dylib
+    lib/EMBOSS/libepcre.7*.dylib
+    lib/EMBOSS/libezlib.1*.dylib
   <<
   Shlibs: <<
-    %p/lib/EMBOSS/libajax.6.dylib 7.0.0 %n (>= 6.1.0-4)
-    %p/lib/EMBOSS/libajaxg.6.dylib 7.0.0 %n (>= 6.1.0-4)
+    %p/lib/EMBOSS/libajax.6.dylib 7.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libajaxdb.6.dylib 7.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libajaxg.6.dylib 7.0.0 %n (>= 6.2.0-4)
+    %p/lib/EMBOSS/libacd.6.dylib 7.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libensembl.6.dylib 7.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libeexpat.1.dylib 3.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libepcre.7.dylib 8.0.0 %n (>= 6.2.0-1)
+    %p/lib/EMBOSS/libezlib.1.dylib 3.0.0 %n (>= 6.2.0-1)
   <<
 <<
 SplitOff11: <<
@@ -86,13 +96,31 @@
   DocFiles: ChangeLog COPYING README
   Files: <<
     lib/libajax*
+    lib/libacd*
+    lib/libensembl*
+    lib/libeexpat*
+    lib/libepcre*
+    lib/libezlib*
     lib/EMBOSS/libajax*
+    lib/EMBOSS/libacd*
+    lib/EMBOSS/libensembl*
+    lib/EMBOSS/libeexpat*
+    lib/EMBOSS/libepcre*
+    lib/EMBOSS/libezlib*
     include/EMBOSS/aj*.h
-    include/EMBOSS/pcre*
+    include/EMBOSS/crc32.h
+    include/EMBOSS/deflate.h
+    include/EMBOSS/ens*.h
+    include/EMBOSS/exp*.h
+    include/EMBOSS/inf*.h
+    include/EMBOSS/pcre*.h
+    include/EMBOSS/pcre_printint.src
+    include/EMBOSS/trees.h
+    include/EMBOSS/ucp.h
+    include/EMBOSS/z*.h
   <<
   BuildDependsOnly: True
 <<
-
 SplitOff20: <<
   Package: %N-nucleus6-shlibs
   Depends: %N-ajax6-shlibs (>= %v-%r)
@@ -102,7 +130,7 @@
     lib/EMBOSS/libnucleus.6*.dylib
   <<
   Shlibs: <<
-    %p/lib/EMBOSS/libnucleus.6.dylib 7.0.0 %n (>= 6.1.0-4)
+    %p/lib/EMBOSS/libnucleus.6.dylib 7.0.0 %n (>= 6.2.0-1)
   <<
 <<
 SplitOff21: <<
@@ -118,7 +146,6 @@
   <<
   BuildDependsOnly: True
 <<
-
 SplitOff30: <<
   Package: %N-plplot3-shlibs
   Depends: libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, libiconv, x11-shlibs, 
fontconfig2-shlibs (>= 2.4.1-1), freetype219-shlibs (>= 2.3.8-2)
@@ -130,7 +157,7 @@
     lib/EMBOSS/libeplplot.3*.dylib
   <<
   Shlibs: <<
-    %p/lib/EMBOSS/libeplplot.3.dylib 6.0.0 %n (>= 6.1.0-4)
+    %p/lib/EMBOSS/libeplplot.3.dylib 6.0.0 %n (>= 6.2.0-1)
   <<
 <<
 SplitOff31: <<
@@ -153,7 +180,7 @@
 <<
 
 DocFiles: <<
-  AUTHORS ChangeLog COMPAT COPYING FAQ INSTALL KNOWN_BUGS LICENSE NEWS ONEWS 
PROBLEMS README THANKS
+  AUTHORS ChangeLog COMPAT COPYING FAQ INSTALL KNOWN_BUGS LICENSE NEWS 
PROBLEMS README THANKS
 <<
 Description: Molecular Biology Open Software Suite
 DescDetail: <<


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