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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-commits