rpms/clipper/devel clipper.spec,1.2,1.3 stdlib_fixes.patch,1.1,1.2

[Timothy Fenn]

Author: timfenn

Update of /cvs/pkgs/rpms/clipper/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv31383

Modified Files:
	clipper.spec stdlib_fixes.patch 
Log Message:
* Sat Nov 22 2008 Tim Fenn <fenn at stanford.edu> - 2.1-2
- update patches




Index: clipper.spec
===================================================================
RCS file: /cvs/pkgs/rpms/clipper/devel/clipper.spec,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- clipper.spec	22 Nov 2008 22:47:15 -0000	1.2
+++ clipper.spec	22 Nov 2008 23:02:27 -0000	1.3
@@ -2,7 +2,7 @@
 Summary: Clipper C++ crystallographic library
 URL: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
 Version: 2.1
-Release: 1%{?dist}
+Release: 2%{?dist}
 License: LGPLv2+
 Source0: http://www.ysbl.york.ac.uk/~cowtan/%{name}/%{name}-%{version}-081118-ac.tar.gz
 Source1: clipper-patches-2.1.tar.gz
@@ -101,6 +101,9 @@
 %{_libdir}/pkgconfig/clipper.pc
 
 %changelog
+* Sat Nov 22 2008 Tim Fenn <fenn at stanford.edu> - 2.1-2
+- update patches
+
 * Fri Nov 21 2008 Tim Fenn <fenn at stanford.edu> - 2.1-1
 - update to 2.1
 

stdlib_fixes.patch:

Index: stdlib_fixes.patch
===================================================================
RCS file: /cvs/pkgs/rpms/clipper/devel/stdlib_fixes.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- stdlib_fixes.patch	18 Nov 2008 00:16:07 -0000	1.1
+++ stdlib_fixes.patch	22 Nov 2008 23:02:27 -0000	1.2
@@ -1,125 +1,8 @@
---- examples/caniso.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/caniso.cpp	2008-11-12 12:59:11.000000000 -0800
+--- examples/cmodeltoseq.cpp_orig	2008-11-22 01:14:56.000000000 -0800
++++ examples/cmodeltoseq.cpp	2008-11-22 01:15:18.000000000 -0800
 @@ -6,6 +6,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "caniso", "0.1", "$Date: 2007/03/01" );
---- examples/ccad.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/ccad.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -76,6 +76,10 @@
- 
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main()
- {
-   Message::set_message_level(1);
---- examples/cecalc.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cecalc.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -5,6 +5,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cecalc", "0.1", "$Date: 2004/07/01" );
---- examples/cfft.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cfft.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -10,6 +10,10 @@
- double pfunc( double t, int nt );
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cfft", "0.1", "$Date: 2004/05/01" );
---- examples/chltofom.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/chltofom.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -5,6 +5,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "chltofom", "0.1", "$Date: 2004/05/01" );
---- examples/cinvfft.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cinvfft.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -5,6 +5,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cinvfft", "0.1", "$Date: 2004/06/01" );
---- examples/cmakereference.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cmakereference.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -22,6 +22,10 @@
- extern void decompress(int,int);  // decompress lib
- }
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cmakereference", "0.2", "$Date: 2005/04/15" );
---- examples/cmaplocal.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cmaplocal.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -6,6 +6,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cmaplocal", "0.1", "$Date: 2004/05/01" );
---- examples/cns2mtz.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cns2mtz.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -8,6 +8,10 @@
- 
- #include "cns2mtz.h"
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cns2mtz", "0.2", "$Date: 2004/14/01" );
---- examples/convert2mtz.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/convert2mtz.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -8,6 +8,10 @@
- 
- #include "convert2mtz.h"
+ #include <clipper/clipper-minimol.h>
+ #include <fstream>
  
 +extern "C" {
 +#include <stdlib.h>
@@ -127,82 +10,32 @@
 +
  int main( int argc, char** argv )
  {
-   CCP4Program prog( "convert2mtz", "0.4", "$Date: 2007/03/30" );
---- examples/cpatterson.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cpatterson.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -6,6 +6,10 @@
+   CCP4Program prog( "cmodeltoseq", "0.1", "$Date: 2008/06/09" );
+--- examples/csymmatch.cpp_orig	2008-11-22 01:15:54.000000000 -0800
++++ examples/csymmatch.cpp	2008-11-22 01:16:21.000000000 -0800
+@@ -6,6 +6,9 @@
  #include <clipper/clipper-ccp4.h>
- 
+ #include <clipper/clipper-minimol.h>
  
 +extern "C" {
 +#include <stdlib.h>
 +}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cpatterson", "0.1", "$Date: 2004/07/01" );
---- examples/cphasecombine.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cphasecombine.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -5,6 +5,10 @@
- #include <clipper/clipper-ccp4.h>
- 
  
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cphasecombine", "0.1", "$Date: 2004/06/01" );
---- examples/cphasematch.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/cphasematch.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -6,6 +6,10 @@
+ class MapFilterFn_g5 : public clipper::MapFilterFn_base {
+ public: clipper::ftype operator() ( const clipper::ftype& radius ) const { return exp(-radius*radius/50.0); }
+--- examples/cncsfrommodel.cpp_orig	2008-11-22 01:15:59.000000000 -0800
++++ examples/cncsfrommodel.cpp	2008-11-22 01:39:11.000000000 -0800
+@@ -5,6 +5,13 @@
+ #include <clipper/clipper-minimol.h>
  #include <clipper/clipper-ccp4.h>
  
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
++#include <algorithm>
++#include <vector>
 +
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "cphasematch", "0.1", "$Date: 2004/06/01" );
---- examples/csfcalc.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/csfcalc.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -7,6 +7,10 @@
- #include <clipper/clipper-mmdb.h>
- 
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "csfcalc", "0.1", "$Date: 2004/06/01" );
---- examples/csigmaa.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/csigmaa.cpp	2008-11-12 12:59:11.000000000 -0800
-@@ -6,6 +6,10 @@
- #include <clipper/clipper-ccp4.h>
- 
- 
 +extern "C" {
 +#include <stdlib.h>
++#include <string.h>
 +}
-+
- int main( int argc, char** argv )
- {
-   CCP4Program prog( "csigmaa", "0.1", "$Date: 2004/06/01" );
---- examples/maketestdata.cpp_orig	2008-11-12 12:59:11.000000000 -0800
-+++ examples/maketestdata.cpp	2008-11-12 12:59:12.000000000 -0800
-@@ -10,6 +10,10 @@
  
- #include <fstream>
- 
-+extern "C" {
-+#include <stdlib.h>
-+}
-+
- int main( int argc, char** argv )
+ clipper::String chain_sequence( const clipper::MPolymer& mp )
  {
-   if ( argc == 1 ) {