Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv11316
Modified Files:
emboss.info emboss.patch
Log Message:
upstream fix and removed obsolete pcre patch
Index: emboss.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- emboss.patch 6 Apr 2007 21:17:42 -0000 1.6
+++ emboss.patch 21 Sep 2007 03:01:11 -0000 1.7
@@ -1,24 +1,21 @@
-diff -Naur EMBOSS-4.1.0/ajax/ajjava.c EMBOSS-4.1.0-patched/ajax/ajjava.c
---- EMBOSS-4.1.0/ajax/ajjava.c 2006-06-20 05:12:35.000000000 -0400
-+++ EMBOSS-4.1.0-patched/ajax/ajjava.c 2007-04-06 12:09:04.000000000 -0400
-@@ -89,7 +89,7 @@
- #define _XOPEN_SOURCE
- #endif
-
--#if !defined(__ppc__) && !defined(__FreeBSD__)
-+#if !defined(__APPLE__) && !defined(__FreeBSD__)
- #include <crypt.h>
- #endif
-
-diff -Naur EMBOSS-4.1.0/emboss/jembossctl.c
EMBOSS-4.1.0-patched/emboss/jembossctl.c
---- EMBOSS-4.1.0/emboss/jembossctl.c 2007-01-16 07:11:18.000000000 -0500
-+++ EMBOSS-4.1.0-patched/emboss/jembossctl.c 2007-04-06 12:09:29.000000000
-0400
-@@ -115,7 +115,7 @@
- #define _XOPEN_SOURCE
- #endif
+--- EMBOSS-5.0.0/emboss/psiphi.c 2007-07-06 08:15:29.000000000 -0400
++++ EMBOSS-5.0.0-patch/emboss/psiphi.c 2007-07-27 05:28:27.000000000 -0400
+@@ -160,7 +160,7 @@
+ finishres = ajAcdGetInt("finishresiduenumber");
--#if !defined(__ppc__) && !defined(__FreeBSD__)
-+#if !defined(__APPLE__) && !defined(__FreeBSD__)
- #include <crypt.h>
- #endif
+ /* reserve memory for and read in structure */
+- /* JISON */ pdb = ajPdbReadoldNew(pdbfile);
++ /* JISON */ pdb = ajPdbReadNew(pdbfile,0);
+
+ /* check and set number of chain to be analysed */
+ highest = pdb->Nchn;
+@@ -440,6 +440,9 @@
+ ajint lowestres = 0;
+ AjPAtom inlist = NULL;
++
++ if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
++ ajFatal("Chain %d has no atoms",myindex+1);
+
+ /* read first atom in list into memory, but keep it on list */
+ ajListPeek(pdb->Chains[myindex]->Atoms,
Index: emboss.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- emboss.info 17 Sep 2007 01:28:10 -0000 1.15
+++ emboss.info 21 Sep 2007 03:01:11 -0000 1.16
@@ -1,6 +1,6 @@
Package: emboss
Version: 5.0.0
-Revision: 2
+Revision: 3
Depends: %N-ajax5-shlibs (>= %v-%r), %N-nucleus5-shlibs (>= %v-%r),
%N-plplot5-shlibs (>= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs,
system-java14
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
#Replaces: emboss (<< 5.0.0)
@@ -10,13 +10,7 @@
<<
Source-MD5: be4c895220ad34afd65d450ba7d8e34b
SetCPPFLAGS: -Dstat64=stat
-#Patch: %n.patch
-PatchScript: <<
- perl -pi -e 's,([<"])(pcre)(.*.h[>"]),\1EMBOSS/\2\3,' ajax/*
- perl -pi -e 's,(pcre\S*\.h),EMBOSS/\1,g' ajax/Makefile.in
- mkdir ajax/EMBOSS
- mv ajax/pcre*.h ajax/EMBOSS
-<<
+Patch: %n.patch
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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