rpms/clipper/F-10 clipper.spec, NONE, 1.1 fftw_fixes.patch, NONE, 1.1 import.log, NONE, 1.1 stdlib_fixes.patch, NONE, 1.1 string_fixes.patch, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2

[Timothy Fenn]

Author: timfenn

Update of /cvs/pkgs/rpms/clipper/F-10
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv29837/F-10

Modified Files:
	.cvsignore sources 
Added Files:
	clipper.spec fftw_fixes.patch import.log stdlib_fixes.patch 
	string_fixes.patch 
Log Message:
* Mon Nov 17 2008 Tim Fenn <fenn at stanford.edu> - 2.0-20
- initial CVS commit




--- NEW FILE clipper.spec ---
Name: clipper
Summary: Clipper C++ crystallographic library
URL: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
Version: 2.0
Release: 20%{?dist}
License: LGPLv2+
Source0: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz
Source1: clipper-patches-2.0.tar.gz
Patch0: fftw_fixes.patch
Patch1: string_fixes.patch
Patch2: stdlib_fixes.patch
Group: System Environment/Libraries
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: autoconf
BuildRequires: automake
BuildRequires: libtool
BuildRequires: fftw2-devel
BuildRequires: gpp4-devel
BuildRequires: mmdb-devel

%description
There are currently two major pressures on crystallographic computing:

Increased automation to increase throughput in line with genomics applications.

Increased data complexity, as data from more sources is combined and
carried through the whole calculation to solve more difficult
problems.

The Clipper project is an initiative to address these pressures.

%package devel
Summary: Libraries and header files for clipper development
Group: Development/Libraries
Requires: %{name} = %{version}-%{release}
Requires: pkgconfig
Requires: fftw2-devel
Requires: gpp4-devel
Requires: mmdb-devel

%description devel

the clipper-devel package contains the header files and libraries
necessary for developing programs using the clipper C++
crystallographic library.

%prep
%setup -q -c -a 1
%patch0 -p0
%patch1 -p0
%patch2 -p0
./autogen.sh

sed -i 's/\r//' dox/coordtypes.dox
sed -i 's/\r//' dox/develop.dox
chmod 644 dox/wheretolook.dox

%build
%configure --disable-static
make %{?_smp_mflags}

%install
rm -rf %{buildroot}
make install DESTDIR=$RPM_BUILD_ROOT INSTALL='install -p' CPPROG="cp -p"

# remove unpackaged files from the buildroot
rm -f $RPM_BUILD_ROOT%{_libdir}/*.la

%clean
rm -rf %{buildroot}

%post -p /sbin/ldconfig

%postun -p /sbin/ldconfig

%files
%defattr(-,root,root,-)
%doc NEWS README AUTHORS COPYING
%{_bindir}/caniso
%{_bindir}/cecalc
%{_bindir}/cfft
%{_bindir}/chltofom
%{_bindir}/cinvfft
%{_bindir}/convert2mtz
%{_bindir}/cpatterson
%{_bindir}/cphasecombine
%{_bindir}/cphasematch
%{_bindir}/csfcalc
%{_bindir}/csigmaa
%{_bindir}/cmakereference
%{_libdir}/libclipper.so.*

%files devel
%defattr(-,root,root,-)
%doc dox
%{_libdir}/libclipper.so
%{_includedir}/clipper
%{_libdir}/pkgconfig/clipper.pc

%changelog
* Sat Nov 15 2008 Tim Fenn <fenn at stanford.edu> - 2.0-20
- patch to examples/Makefile.am

* Fri Nov 14 2008 Tim Fenn <fenn at stanford.edu> - 2.0-19
- dynamically link executables
- fix double file listings in -devel

* Thu Nov 13 2008 Tim Fenn <fenn at stanford.edu> - 2.0-18
- edit license tag
- add mmdb/gpp4/fftw to requires for -devel
- timestamp preservation in make install
- edit defattr
- remove install and changelog from docs
- include clipper dir in -devel ownership
- fix CRLF/permissions issues

* Wed Nov 12 2008 Tim Fenn <fenn at stanford.edu> - 2.0-17
- add more string patches
- add stdlib patches

* Tue Nov 11 2008 Tim Fenn <fenn at stanford.edu> - 2.0-16
- fix make and make install
- set up patch directives
- consolidate version/release tags
- fix buildrequires

* Wed Sep 10 2008 Tim Fenn <fenn at stanford.edu> - 2.0-15
- include binaries in main package, remove from devel
- add test calls to libs

* Wed Aug 20 2008 Tim Fenn <fenn at stanford.edu> - 2.0-14
- spec cleanup
- string patches

* Tue May 27 2008 Tim Fenn <fenn at stanford.edu> - 2.0-13
- remove static libs

* Mon May 26 2008 Tim Fenn <fenn at stanford.edu> - 2.0-12
- spec cleanup

* Mon Feb 25 2008 Tim Fenn <fenn at stanford.edu> - 2.0-11
- update to use Morten's LGPL licensed libraries

* Fri Oct 19 2007 Tim Fenn <fenn at stanford.edu> - 2.0-10
- resync to Cowtan's latest updates

* Fri Jul  6 2007 Tim Fenn <fenn at stanford.edu> - 2.0-9
- update to use CCI CCP4C library

* Fri Apr 20 2007 Tim Fenn <fenn at stanford.edu> - 2.0-8
- resync with Cowtan's latest updates, add examples

* Tue Nov 28 2006 Tim Fenn <fenn at stanford.edu> - 2.0-7
- sync with Cowtan's latest updates

* Sun Nov  5 2006 Tim Fenn <fenn at stanford.edu> - 2.0-6
- fix configure.ac to include math lib

* Sun Apr 30 2006 Tim Fenn <fenn at stanford.edu> - 2.0-5
- split package into clipper and clipper-ccp4

* Tue Apr 11 2006 Tim Fenn <fenn at stanford.edu>
- initial build

fftw_fixes.patch:

--- NEW FILE fftw_fixes.patch ---
--- clipper/core/fftmap.cpp	2006-01-19 04:34:39.000000000 -0800
+++ clipper/core-fix/fftmap.cpp	2006-04-22 16:06:55.000000000 -0700
@@ -44,8 +44,8 @@
 
 #include "hkl_datatypes.h"
 
-#include <fftw.h>
-#include <rfftw.h>
+#include <sfftw.h>
+#include <srfftw.h>
 
 
 namespace clipper {
--- clipper/core/fftmap_sparse.cpp	2006-01-19 04:34:39.000000000 -0800
+++ clipper/core-fix/fftmap_sparse.cpp	2006-04-22 16:07:02.000000000 -0700
@@ -44,8 +44,8 @@
 
 #include "hkl_datatypes.h"
 
-#include <fftw.h>
-#include <rfftw.h>
+#include <sfftw.h>
+#include <srfftw.h>
 
 
 namespace clipper {


--- NEW FILE import.log ---
clipper-2_0-20_f8:F-10:clipper-2.0-20.f8.src.rpm:1226967505

stdlib_fixes.patch:

--- NEW FILE stdlib_fixes.patch ---
--- examples/caniso.cpp_orig	2008-11-12 12:59:11.000000000 -0800
+++ examples/caniso.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( "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"
 
+extern "C" {
+#include <stdlib.h>
+}
+
 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 @@
 #include <clipper/clipper-ccp4.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 @@
 #include <clipper/clipper-ccp4.h>
 
 
+extern "C" {
+#include <stdlib.h>
+}
+
 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>
+}
+
 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 )
 {
   if ( argc == 1 ) {

string_fixes.patch:

--- NEW FILE string_fixes.patch ---
--- clipper/mmdb/clipper_mmdb.cpp_orig	2008-11-12 11:01:28.000000000 -0800
+++ clipper/mmdb/clipper_mmdb.cpp	2008-11-12 12:12:32.000000000 -0800
@@ -43,6 +43,9 @@
 
 #include <algorithm>
 
+extern "C" {
+#include <string.h>
+}
 
 namespace clipper {
 
--- clipper/ccp4/ccp4_mtz_io.cpp_orig	2008-11-12 11:02:16.000000000 -0800
+++ clipper/ccp4/ccp4_mtz_io.cpp	2008-11-12 12:12:15.000000000 -0800
@@ -45,6 +45,9 @@
 
 #include <ccp4/cmtzlib.h>
 
+extern "C" {
+#include <string.h>
+}
 
 namespace clipper {
 
--- clipper/cif/cif_data_io.cpp_orig	2008-11-12 12:11:17.000000000 -0800
+++ clipper/cif/cif_data_io.cpp	2008-11-12 12:11:49.000000000 -0800
@@ -46,6 +46,7 @@
 extern "C" {
 #include <stdlib.h>
 #include <stdio.h>
+#include <string.h>
 }
 #include <vector>
 #include <fstream>
--- clipper/minimol/minimol.cpp_orig	2008-11-12 12:22:06.000000000 -0800
+++ clipper/minimol/minimol.cpp	2008-11-12 12:23:05.000000000 -0800
@@ -41,6 +41,9 @@
 
 #include "minimol.h"
 
+extern "C" {
+#include <string.h>
+}
 
 namespace clipper {
 
--- examples/compress42.c_orig	2008-11-14 10:54:03.000000000 -0800
+++ examples/compress42.c	2008-11-14 11:09:52.000000000 -0800
@@ -140,6 +140,8 @@
 #include	<sys/types.h>
 #include	<sys/stat.h>
 #include	<errno.h>
+#include        <stdlib.h>
+#include        <string.h>
 
 #ifdef DIRENT
 #	include	<dirent.h>


Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/clipper/F-10/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- .cvsignore	16 Nov 2008 20:32:21 -0000	1.1
+++ .cvsignore	18 Nov 2008 00:18:43 -0000	1.2
@@ -0,0 +1,2 @@
+clipper-patches-2.0.tar.gz
+clipper20ac.latest.tar.gz


Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/clipper/F-10/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- sources	16 Nov 2008 20:32:21 -0000	1.1
+++ sources	18 Nov 2008 00:18:43 -0000	1.2
@@ -0,0 +1,2 @@
+8988607f341c90736f3ba2b5bef1e99e  clipper-patches-2.0.tar.gz
+cf5746cd7e040180c1e4cb429c7b2ac1  clipper20ac.latest.tar.gz