[cvs] dists/10.4/stable/main/finkinfo/sci pointless.info, NONE, 1.1 pointless.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv17979

Added Files:
pointless.info pointless.patch 
Log Message:
ccp4-associated program pointless, updated version, promoted to stable

--- NEW FILE: pointless.patch ---
diff -ruN pointless-orig/Makefile pointless/Makefile
--- pointless-orig/Makefile 2007-11-23 05:49:31.0 -0800
+++ pointless/Makefile  2007-12-11 17:54:06.0 -0800
@@ -20,16 +20,20 @@
 #XCPPFLAGS= -ftemplate-depth-120 -fcoalesce-templates -Wno-long-double
 
 # CCTBX locations
-CCTBX=${CLIB}/cctbx
+CCTBX=/@prefix@/share/xtal/cctbx
 CCTBX_sources=${CCTBX}/cctbx_sources
 ## Blank for version 1
 CCTBX_VERSION=
 ## Set for version 2
-##CCTBX_VERSION=\#define CCTBX_VERSION_2
+##
+CCTBX_VERSION=\#define CCTBX_VERSION_2
 
 # Clipper location
-CLPR=${CLIB}/clipper
+# CLPR=${CLIB}/clipper
+CLPR=/@prefix@/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/clipper
 
+CLIB=/@prefix@/share/xtal/ccp4-onlylibs-dev-6.0.2/lib
+CCP4=/@prefix@/share/xtal/ccp4-onlylibs-dev-6.0.2
 # Includes
 # CCP4
 ICCP4=-I${CLIBS}
@@ -41,6 +45,7 @@
 # cctbx
 ITBX=\
 -I${CCTBX_sources}/boost \
+-I/@prefix@/share/xtal/cctbx/cctbx_build/include \
 -I${CCP4}/include \
 -I${CCTBX_sources}/cctbx/include \
 -I${CCTBX_sources}/scitbx/include
@@ -49,13 +54,13 @@
 
 # Libraries
 # CCP4
-LCCP4=-L${CLIB} -lccp4f -lccp4c -lm
+LCCP4=-L${CLIB} -lccp4f -lccp4c -lm -L/@prefix@/lib -ldrfftw -lfftw
 
 # Clipper
 LCLPR=-L${CLIB} -lclipper-ccp4 -lclipper-core 
 
 # cctbx
-LTBX= -L${CLIB} -lcctbx 
+LTBX= -L/@prefix@/share/xtal/cctbx/cctbx_build/lib -lcctbx 
 
 LDLIBS=${LTBX} ${LCLPR} ${LCCP4}
 

--- NEW FILE: pointless.info ---
Package: pointless
Version: 1.2.10
Revision: 1
Source: ftp://ftp.ccp4.ac.uk/ccp4/current/prerelease/%n-%v-src.tar.gz
Source-MD5: d2115796ea0aeaa42b2fe8f4ae16bcfd
Source2: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n.html
Source2-MD5: 9e26dd2b8892e400f82f7b14c4e5c285
Source3: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n-ccp4i-0.0.8.tar.gz
Source3-MD5: e4d9a43059ad3981ea7eda165c5ba5aa
NoSourceDirectory: yes
Depends: ccp4 (= 6.0.2), fftw-shlibs
BuildDepends: fftw, ccp4-onlylibs-dev (= 6.0.2-8) , cctbx-10.4 | cctbx-10.5
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchScript: 
 sed 's|@prefix@|%p|g' %a/%n.patch | patch -p1
 mv pointless pointless-ccp4i
#cp Makefile.linux Makefile
#perl -pi -e 's|CCTBX\=\${CLIB}/cctbx|CCTBX\=ccp4-6.0.2/lib/cctbx|g' Makefile
#perl -pi -e 's|lm|lm -L%p/lib -ldrfftw -lfftw|' Makefile

CompileScript:  
#!/bin/bash -efv
source %p/bin/init.sh
make

InstallScript: 
#!/bin/bash -efv
source %p/bin/init.sh
mkdir -p %i/share/xtal/ccp4-6.0.2/bin
mkdir -p %i/share/xtal/ccp4-6.0.2/html
cp %n  %i/share/xtal/ccp4-6.0.2/bin/.
cp %n.html  %i/share/xtal/ccp4-6.0.2/html/.
cd pointless-ccp4i
pwd
mkdir -p %i/share/xtal/pointless
cp modules.def %i/share/xtal/pointless
cp ccp4i_packages.def %i/share/xtal/pointless
mkdir -p %i/share/xtal/ccp4-6.0.2/ccp4i/templates
cp templates/pointless.com %i/share/xtal/ccp4-6.0.2/ccp4i/templates/. 
mkdir -p %i/share/xtal/ccp4-6.0.2/ccp4i/scripts
cp scripts/pointless_centre.script scripts/pointless_index.script 
scripts/pointless_laue.script %i/share/xtal/ccp4-6.0.2/ccp4i/scripts/. 
#mkdir -p %i/share/xtal/ccp4-6.0.2/ccp4i/help
# cppointless-ccp4i/help/* %i/share/xtal/ccp4-6.0.2/ccp4i/help/. 
mkdir -p %i/share/xtal/ccp4-6.0.2/ccp4i/tasks
cp tasks/pointless.def  tasks/pointless_index.def tasks/pointless_laue.tcl 
tasks/pointless_centre.def tasks/pointless_index.tcl tasks/pointless_utils.tcl 
tasks/pointless_centre.tcl tasks/pointless_laue.def  
%i/share/xtal/ccp4-6.0.2/ccp4i/tasks/. 

Description: CCP4 point and space group and index tests
DescDetail: 
Pointless has several possible functions:
1. Determination of Laue group and space group (LAUEGROUP mode).
2. Testing of alternative indexing schemes
3. Checking the centre of the diffraction pattern
4. Reindexing

Detailed description available on package homepage link and by issuing
the command ccp4help pointless

To use the CCP4i interface with pointless, first execute the commands
mkdir -p ~/.CCP4/unix
touch ~/.CCP4/unix/modules.def
cat %p/share/xtal/pointless/modules.def  ~/.CCP4/unix/modules.def

License: Restrictive 
Homepage: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/pointless.html
Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/stable/main/finkinfo/sci mosflm-small.info, NONE, 1.1 mosflm.info, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18810

Added Files:
mosflm-small.info mosflm.info 
Log Message:
ccp4-associated program mosflm, updated version, promoted to stable

--- NEW FILE: mosflm-small.info ---
Package: mosflm-small
Version: 7.0.1
Revision: 2
Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
SourceDirectory: mosflm701
Source-MD5: 9cca259141a3dabaacbe29a90af96e49 
Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000)
BuildDepends: gcc42 (= 4.2.1-1000) , ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
PatchScript: 
# This is merely a hack to get the ppc version to compile with gfortran
# It does so on intel by default
perl -pi -e 's|powerpc|intel-pc|g'   build
perl -pi -e 's|macintosh|intel-pc|g' build

CompileScript:  
#!/bin/zsh -efv
export MOSROOT=$PWD:h
./to_small.csh
./build
cd bin
mv ipmosflm ipmosflm-small

InstallScript: 
#!/bin/zsh -efv
 mkdir -p %i/bin
 cd bin
 cp ipmosflm-* %i/bin

Description: X-ray data processing, small display version
DescDetail: 
Mosflm is a program for integrating single crystal diffraction data 
from area detectors. It is assumed that the experiment was conducted
using the Arndt-Wonacott oscillation method, and also that 
monochromatic radiation was used.
Mosflm can process data from a wide variety of modern area 
detectors, e.g. from Mar Research, Rigaku/MSC, ADSC, DIP etc.

This small display version is suitable for laptops and 
lower-resolution monitors.  The large version is included in CCP4 by
default and the latest version is in the mosflm fink
package.  

Invoke with ipmosflm-small

Authors:  
Harry Powell and 
Andrew G.W. Leslie
MRC Laboratory of Molecular Biology
Hills Road,
Cambridge CB2 2QH
UK
E-mail: harry AT mrc-lmb DOT cam DOT ac DOT uk
http://www.mrc-lmb.cam.ac.uk/harry/frames/

License: GPL
Maintainer: W. G. Scott [EMAIL PROTECTED] 

--- NEW FILE: mosflm.info ---
Package: mosflm
Version: 7.0.1
Revision: 2
Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
SourceDirectory: mosflm701
Source-MD5: 9cca259141a3dabaacbe29a90af96e49 
Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000) 
BuildDepends: gcc42 (= 4.2.1-1000), ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
PatchScript: 
# This is merely a hack to get the ppc version to compile with gfortran
# It does so on intel by default
perl -pi -e 's|powerpc|intel-pc|g'   build
perl -pi -e 's|macintosh|intel-pc|g' build

CompileScript:  
#!/bin/zsh -efv
export MOSROOT=$PWD:h
export FOPTIM=-O0
./build
cd bin
mv ipmosflm ipmosflm-701

InstallScript: 
#!/bin/zsh -efv
 mkdir -p %i/bin
 cd bin
 cp ipmosflm-* %i/bin/.
 cp ipmosflm-* %i/bin/ipmosflm
 cp ipmosflm-* %i/bin/mosflm

Description: X-ray data processing, large display
DescDetail: 
Mosflm is a program for integrating single crystal diffraction data 
from area detectors. It is assumed that the experiment was conducted
using the Arndt-Wonacott oscillation method, and also that 
monochromatic radiation was used.
Mosflm can process data from a wide variety of modern area 
detectors, e.g. from Mar Research, Rigaku/MSC, ADSC, DIP etc.

Invoke with ipmosflm or ipmosflm-701 or mosflm

Authors:  
Harry Powell and 
Andrew G.W. Leslie
MRC Laboratory of Molecular Biology
Hills Road,
Cambridge CB2 2QH
UK
E-mail: harry AT mrc-lmb DOT cam DOT ac DOT uk

Homepage: 
http://www.mrc-lmb.cam.ac.uk/harry/frames/

License: GPL
Maintainer: W. G. Scott [EMAIL PROTECTED] 


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[cvs] dists/10.4/unstable/main/finkinfo/sci refmac.info, 1.12, 1.13 refmac.patch, 1.6, 1.7

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv13512

Modified Files:
refmac.info refmac.patch 
Log Message:
version update with bug fixes and other improvements from upstream

Index: refmac.patch
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- refmac.patch26 Jul 2007 15:10:46 -  1.6
+++ refmac.patch30 Dec 2007 06:54:47 -  1.7
@@ -1,21 +1,22 @@
-diff -ruN refmac-5.4-orig/atom_com.fh refmac-5.4/atom_com.fh
 refmac-5.4-orig/atom_com.fh2007-07-02 09:26:55.0 -0700
-+++ refmac-5.4/atom_com.fh 2007-07-12 20:31:41.0 -0700
-@@ -74,7 +74,7 @@
- C
- C --
-   INTEGER MAXATOM
--  PARAMETER (MAXATOM = 12)
-+  PARAMETER (MAXATOM = 80)
-   INTEGER MAXATSD
-   PARAMETER (MAXATSD   = 1)
-   INTEGER MAXNSO
-diff -ruN refmac-5.4-orig/makefile_gfortran refmac-5.4/makefile_gfortran
 refmac-5.4-orig/makefile_gfortran  2007-04-25 12:39:20.0 -0700
-+++ refmac-5.4/makefile_gfortran   2007-07-12 20:43:36.0 -0700
-@@ -1,4 +1,4 @@
--VERSION = gfortran
-+VERSION = -5.4 
- FC  = gfortran
- FOPTIM  = -O3
- COPTIM  = -O
+diff -ruN refmac-orig/makefile_fink refmac/makefile_fink
+--- refmac-orig/makefile_fink  1969-12-31 16:00:00.0 -0800
 refmac/makefile_fink   2007-12-29 21:57:57.0 -0800
+@@ -0,0 +1,18 @@
++VERSION = -5.4
++FC  = gfortran
++FOPTIM  = -O3
++COPTIM  = -O
++XFFLAGS = -fno-second-underscore
++
++XCFLAGS = -DGFORTRAN -DPROTOTYPE
++FFLAGS = $(FOPTIM) $(XFFLAGS)  -static-libgcc
++ 
++CFLAGS = $(COPTIM) $(XCFLAGS)
++
++
++LLIBCIF = 
++LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a  $(BLAS_DIR)/libLAPACK.dylib  
$(BLAS_DIR)/libBLAS.dylib  $(FORTLIB)/libgfortran.a
++LLIBOTHERS = -lstdc++ $(FORTLIB)/libgfortran.a   
$(FORTLIB2)/libgfortranbegin.a  $(FORTLIB2)/libgcc.a  
++
++
++include make_refmac.inc

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -d -r1.12 -r1.13
--- refmac.info 26 Jul 2007 15:10:46 -  1.12
+++ refmac.info 30 Dec 2007 06:54:47 -  1.13
@@ -1,21 +1,34 @@
 Package: refmac
 Version: 5.4
-Revision: 1
+# version 5.4.0066  : 12/07/07##
+Revision: 2
 Source: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_source.tar.gz
-Source-MD5: e06dd93e3d4a65d8876e73a998b8118b
+Source-MD5: ca5d41fcf45ceeb6d91b7a7c3af1c5fb
 SourceRename: %n-%v.tar.gz
-Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.3_dictionary.tar.gz
-Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
+Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
+Source2-MD5: 9f6d945927751531505298b0b8789687
 NoSourceDirectory: yes
-Depends: ccp4 (= 6.0.2-1) | ccp4-g77, gcc42-shlibs
-BuildDepends: ccp4-dev (= 6.0.2-1) | ccp4-g77-dev, gcc42, ccp4 (= 6.0.2-1) | 
ccp4-g77
+Depends: ccp4 (= 6.0.2-7), gcc42-shlibs
+BuildDepends: ccp4-dev (= 6.0.2-7), gcc42, ccp4 (= 6.0.2-7) 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 Patch: refmac.patch
 CompileScript:  
 #!/bin/bash -efv
-source %p/bin/init.sh
-make -f makefile_gfortran
+export CLIB=%p/lib/ccp4-6.0.2
+export 
BLAS_DIR=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A
+export FORTLIB=%p/lib/gcc4.2/lib
+export FORTLIB2=${FORTLIB}/gcc/$(gfortran -dumpmachine)/$(gfortran 
-dumpversion | head -n 1 | awk '{print $NF}')
+ # Reality checks
+if [[ ! -d $CLIB || ! -d $FORTLIB2 ]];then
+echo Failed to find required library directory.
+echo Check ccp4 and gcc42 installations.
+   return 10
+else
+ echo  ; echo Found ${FORTLIB2} ;   echo 
+fi
+#
+make -f makefile_fink
 
 InstallScript: 
 #!/bin/bash -efv


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.53,1.54

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16453

Modified Files:
coot.info 
Log Message:
coot revision with fix to nucleotide builder menu

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.53
retrieving revision 1.54
diff -u -d -r1.53 -r1.54
--- coot.info   25 Dec 2007 02:21:28 -  1.53
+++ coot.info   30 Dec 2007 19:42:57 -  1.54
@@ -1,14 +1,14 @@
 Package:coot
-Version: 0.4-pre-2-revision-612
+Version: 0.4.0-pre-2-revision-622
 Revision: 1
 GCC: 4.0 
 #Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz
-Source-MD5: 75a9a5d0138c8b0ce97234cf5cd058d2
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
+Source-MD5: acf1f0776075d165527e3e1ea872ac8b
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-2
-Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz
-Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
+Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
+Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 #
@@ -60,7 +60,7 @@
  librsvg2-gtk,
  libtool14  ,
  pango1-xft2-dev,
- pygtk2-py25-dev ,
+ pygtk2-gtk-py25-dev ,
  python25,
  swig
 
@@ -98,8 +98,8 @@
  libtool14-shlibs ,
  librsvg2-gtk ,
  pango1-xft2-shlibs   ,
- pygtk2-py25  ,
- python25 ,   
+ pygtk2-gtk-py25  ,
+ python25 
 
 #
 ###
@@ -149,13 +149,14 @@
 # py_path=%p/bin/python2.5 \
 #
 #remake the  src/coot_wrap_python.cc and src/coot_wrap_guile.cc files
-/bin/rm -f **/coot_wrap_*.cc  
-cd src 
-make coot_wrap_guile.cc 
-make coot_wrap_python.cc 
-cp coot_wrap_guile_pre.cc coot_wrap_guile.cc 
-cd ..
-make
+   /bin/rm -f **/coot_wrap_**.cc  
+   cd src 
+   touch c-interface-database.hh
+   make coot_wrap_guile.cc 
+   make coot_wrap_python.cc 
+   cp coot_wrap_guile_pre.cc coot_wrap_guile.cc 
+   cd ..
+   make
 
 ###
 InstallScript: 


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.19, 1.20

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv6398

Modified Files:
zsh-templates.info 
Log Message:
version upgrade

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- zsh-templates.info  22 Nov 2007 20:24:25 -  1.19
+++ zsh-templates.info  31 Dec 2007 06:10:12 -  1.20
@@ -1,8 +1,9 @@
 Package: zsh-templates
-Version: 1.2.5
+Version: 1.2.11
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: fcaf764e301bf7ebbb7393aa79c41090  
+Source-MD5: 6443b8ffa51e9905a02a684a9ea4c54a
+SourceDirectory: zsh-templates-osx  
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.54,1.55

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv5510

Modified Files:
coot.info 
Log Message:
finally a non-pre-release version 0.4

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.54
retrieving revision 1.55
diff -u -d -r1.54 -r1.55
--- coot.info   30 Dec 2007 19:42:57 -  1.54
+++ coot.info   3 Jan 2008 01:05:51 -   1.55
@@ -1,12 +1,12 @@
 Package:coot
-Version: 0.4.0-pre-2-revision-622
+Version: 0.4.0.0
 Revision: 1
 GCC: 4.0 
-#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
-Source-MD5: acf1f0776075d165527e3e1ea872ac8b
+Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-0.4.tar.gz
+#Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
+Source-MD5: bcf10546ea703a745a85b4dfa3f919b6
 #SourceDirectory: %n-%v
-SourceDirectory: %n-0.4-pre-2
+SourceDirectory: %n-0.4
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.55,1.56

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv14157

Modified Files:
coot.info 
Log Message:
the stable release introduced an instability so back to pre622 until 4.1

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -d -r1.55 -r1.56
--- coot.info   3 Jan 2008 01:05:51 -   1.55
+++ coot.info   3 Jan 2008 01:26:44 -   1.56
@@ -1,12 +1,12 @@
 Package:coot
-Version: 0.4.0.0
+Version: 0.4.0.622
 Revision: 1
 GCC: 4.0 
-Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-0.4.tar.gz
-#Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
-Source-MD5: bcf10546ea703a745a85b4dfa3f919b6
+#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-0.4.tar.gz
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
+Source-MD5: acf1f0776075d165527e3e1ea872ac8b
 #SourceDirectory: %n-%v
-SourceDirectory: %n-0.4
+SourceDirectory: %n-0.4-pre-2
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.56,1.57

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv27591

Modified Files:
coot.info 
Log Message:
the fix is in

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.56
retrieving revision 1.57
diff -u -d -r1.56 -r1.57
--- coot.info   3 Jan 2008 01:26:44 -   1.56
+++ coot.info   3 Jan 2008 08:51:03 -   1.57
@@ -1,12 +1,10 @@
 Package:coot
-Version: 0.4.0.622
+Version: 0.4.1
 Revision: 1
 GCC: 4.0 
-#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-0.4.tar.gz
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-2-revision-622.tar.gz
-Source-MD5: acf1f0776075d165527e3e1ea872ac8b
-#SourceDirectory: %n-%v
-SourceDirectory: %n-0.4-pre-2
+Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
+Source-MD5: f04fbae59acd61aa0e1c3bbdc7ce5e18
+SourceDirectory: %n-%v
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -218,35 +216,35 @@
 lib/libcootaneer*.dylib
 
Shlibs: 
-   %p/lib/libccp4mg-surface.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libccp4mg-utils.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-analysis.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-AngleInfo.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-atomutils.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-cabuild.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-compat.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-coord-extras.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-coord-utils.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-coords.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-db-main.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-geometry.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-high-res.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-ideal.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-isosurface.0.0.0.dylib   1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-ligand.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-map-heavy.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-map-utils.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-mini-mol.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-mmtz-extras.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-sequence-view.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-shelx.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-skeleton.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-surface.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-tw.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-utils.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-wrap-guile.0.0.0.dylib   1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-wrap-python.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcootaneer.0.0.0.dylib 
1.0.0 %n (= 0.3-1)
+   %p/lib/libccp4mg-surface.0.0.0.dylib1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libccp4mg-utils.0.0.0.dylib  
1.0.0 %n (= 0.4.1-1)
+   %p/lib/libcoot-analysis.0.0.0.dylib 1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libcoot-AngleInfo.0.0.0.dylib1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libcoot-atomutils.0.0.0.dylib1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libcoot-cabuild.0.0.0.dylib  
1.0.0 %n (= 0.4.1-1)
+   %p/lib/libcoot-compat.0.0.0.dylib   
1.0.0 %n (= 0.4.1-1)
+   %p/lib/libcoot-coord-extras.0.0.0.dylib 1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libcoot-coord-utils.0.0.0.dylib  1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libcoot-coords.0.0.0.dylib

[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.20, 1.21

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv3120

Modified Files:
zsh-templates.info 
Log Message:
command-line tools for creating and removing users and groups are updated for 
10.5

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -d -r1.20 -r1.21
--- zsh-templates.info  31 Dec 2007 06:10:12 -  1.20
+++ zsh-templates.info  8 Jan 2008 05:08:04 -   1.21
@@ -1,9 +1,10 @@
 Package: zsh-templates
-Version: 1.2.11
+Version: 1.3.0
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: 6443b8ffa51e9905a02a684a9ea4c54a
-SourceDirectory: zsh-templates-osx  
+Source-MD5: 002863476f18ed61de8137d07b9811c4
+#SourceDirectory: zsh-templates-osx  
+SourceDirectory: %n-%v
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv30073

Modified Files:
coot.info 
Log Message:
a stable release of coot for fink stable

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- coot.info   29 Dec 2007 19:57:20 -  1.10
+++ coot.info   12 Jan 2008 02:20:54 -  1.11
@@ -1,14 +1,12 @@
 Package:coot
-Version: 0.4.0-pre-1
+Version: 0.4.1
 Revision: 1
 GCC: 4.0 
-#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-1.tar.gz
-Source-MD5: 0efaa27595a7b1d15fe53ad2ddd612f5
-#SourceDirectory: %n-%v
-SourceDirectory: %n-0.4-pre-1
-Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz
-Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
+Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
+Source-MD5: f04fbae59acd61aa0e1c3bbdc7ce5e18
+SourceDirectory: %n-%v
+Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
+Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 #
@@ -60,6 +58,7 @@
  librsvg2-gtk,
  libtool14  ,
  pango1-xft2-dev,
+ pygtk2-gtk-py25-dev ,
  python25,
  swig
 
@@ -97,6 +96,7 @@
  libtool14-shlibs ,
  librsvg2-gtk ,
  pango1-xft2-shlibs   ,
+ pygtk2-gtk-py25  ,
  python25 
 
 #
@@ -216,35 +216,35 @@
 lib/libcootaneer*.dylib
 
Shlibs: 
-   %p/lib/libccp4mg-surface.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libccp4mg-utils.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-analysis.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-AngleInfo.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-atomutils.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-cabuild.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-compat.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-coord-extras.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-coord-utils.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-coords.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-db-main.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-geometry.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-high-res.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-ideal.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-isosurface.0.0.0.dylib   1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-ligand.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-map-heavy.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-map-utils.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-mini-mol.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-mmtz-extras.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-sequence-view.0.0.0.dylib1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-shelx.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-skeleton.0.0.0.dylib 1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-surface.0.0.0.dylib  
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-tw.0.0.0.dylib   
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-utils.0.0.0.dylib
1.0.0 %n (= 0.3-1)
-   %p/lib/libcoot-wrap-guile.0.0.0.dylib   1.0.0 
%n (= 0.3-1)
-   %p/lib/libcoot-wrap-python.0.0.0.dylib  1.0.0 
%n (= 0.3-1)
-   %p/lib/libcootaneer.0.0.0.dylib 
1.0.0 %n (= 0.3-1)
+   %p/lib/libccp4mg-surface.0.0.0.dylib1.0.0 
%n (= 0.4.1-1)
+   %p/lib/libccp4mg-utils.0.0.0.dylib  
1.0.0 %n (= 0.4.1-1)
+   %p/lib/libcoot-analysis.0.0.0.dylib 1.0.0 
%n (= 

[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.21, 1.22

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv31580

Modified Files:
zsh-templates.info 
Log Message:
update to enable command-line user and group creation/deletion on 10.5

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -d -r1.21 -r1.22
--- zsh-templates.info  8 Jan 2008 05:08:04 -   1.21
+++ zsh-templates.info  25 Jan 2008 16:47:42 -  1.22
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.3.0
+Version: 1.3.1
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: 002863476f18ed61de8137d07b9811c4
+Source-MD5: 37e67daf5fc7bebb08b726bd5591f65e
 #SourceDirectory: zsh-templates-osx  
 SourceDirectory: %n-%v
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh.info, 1.12, 1.13 zsh-multibyte.info, 1.6, 1.7

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv24198

Modified Files:
zsh.info zsh-multibyte.info 
Log Message:
zsh version update

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -d -r1.12 -r1.13
--- zsh.info2 Nov 2007 14:45:59 -   1.12
+++ zsh.info1 Feb 2008 15:22:16 -   1.13
@@ -1,6 +1,6 @@
 Package: zsh 
-Version: 4.3.4
-Revision: 3
+Version: 4.3.5
+Revision: 1
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/%n-%v.tar.bz2
-Source-MD5: 8410a30e4f5c6160790bc3afc096424f
+Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
+Source2-MD5: 2edea09b823ffa7528dbd447485630c9
 ConfigureParams:
 --mandir=%p/share/man --infodir=%p/share/info --enable-etcdir=%p/etc/%n   \
 --enable-maildir-support --enable-pcre --enable-zsh-secure-free   \

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- zsh-multibyte.info  2 Nov 2007 14:45:59 -   1.6
+++ zsh-multibyte.info  1 Feb 2008 15:22:16 -   1.7
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
-Version: 4.3.4
-Revision: 3
+Version: 4.3.5
+Revision: 1
 Conflicts: zsh
 Replaces: zsh
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source-MD5: 8410a30e4f5c6160790bc3afc096424f
-Source2: mirror:custom:/zsh-%v-doc.tar.bz2
-Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
+Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
+Source2: mirror:custom:zsh-%v-doc.tar.bz2
+Source2-MD5: 2edea09b823ffa7528dbd447485630c9
 ConfigureParams: 
 --mandir=%p/share/man --infodir=%p/share/info \
 --enable-etcdir=%p/etc/zsh --enable-maildir-support \


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-helpfiles.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv29444

Modified Files:
zsh-helpfiles.info 
Log Message:
zsh helpfiles for new zsh version

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- zsh-helpfiles.info  19 Apr 2007 14:18:23 -  1.7
+++ zsh-helpfiles.info  9 Feb 2008 18:07:57 -   1.8
@@ -1,5 +1,5 @@
 Package: zsh-helpfiles
-Version: 4.3.4
+Version: 4.3.5
 Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
@@ -25,8 +25,8 @@
   nam-US: http://mirrors.theonlinerecordstore.com/zsh/
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source2: 
http://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh/Library/init/zsh/local-functions/run-help
-Source-MD5: 8410a30e4f5c6160790bc3afc096424f 
+Source2: 
http://code.google.com/p/zsh-templates-osx/source/browse/trunk/Library/init/zsh/local-functions/general/run-help
+Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:
 #!/bin/zsh -efv


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.22, 1.23

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28909

Modified Files:
zsh-templates.info 
Log Message:
fixed open completion for new zsh version

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -d -r1.22 -r1.23
--- zsh-templates.info  25 Jan 2008 16:47:42 -  1.22
+++ zsh-templates.info  9 Feb 2008 18:06:13 -   1.23
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.3.1
+Version: 1.3.2
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: 37e67daf5fc7bebb08b726bd5591f65e
+Source-MD5: d6378af4c83faad246bbae8a378c7f52
 #SourceDirectory: zsh-templates-osx  
 SourceDirectory: %n-%v
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.23, 1.24

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv1336

Modified Files:
zsh-templates.info 
Log Message:
properly fixed open completion for new zsh version

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -d -r1.23 -r1.24
--- zsh-templates.info  9 Feb 2008 18:06:13 -   1.23
+++ zsh-templates.info  11 Feb 2008 17:01:46 -  1.24
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.3.2
+Version: 1.3.3
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: d6378af4c83faad246bbae8a378c7f52
+Source-MD5: deee71a861dacfbda96f65b5c7ca7c75
 #SourceDirectory: zsh-templates-osx  
 SourceDirectory: %n-%v
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)


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[cvs] dists/10.4/unstable/main/finkinfo/sci mosflm-small.info, 1.17, 1.18 mosflm.info, 1.16, 1.17

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv19123

Modified Files:
mosflm-small.info mosflm.info 
Log Message:
mosflm version update

Index: mosflm-small.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm-small.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- mosflm-small.info   13 Dec 2007 06:01:17 -  1.17
+++ mosflm-small.info   3 Mar 2008 15:23:50 -   1.18
@@ -1,9 +1,9 @@
 Package: mosflm-small
-Version: 7.0.1
-Revision: 2
-Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
-SourceDirectory: mosflm701
-Source-MD5: 9cca259141a3dabaacbe29a90af96e49 
+Version: 7.0.3
+Revision: 1
+Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
+SourceDirectory: mosflm703
+Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
 Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000)
 BuildDepends: gcc42 (= 4.2.1-1000) , ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
 PatchScript: 

Index: mosflm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- mosflm.info 13 Dec 2007 06:01:17 -  1.16
+++ mosflm.info 3 Mar 2008 15:23:50 -   1.17
@@ -1,9 +1,9 @@
 Package: mosflm
-Version: 7.0.1
-Revision: 2
-Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
-SourceDirectory: mosflm701
-Source-MD5: 9cca259141a3dabaacbe29a90af96e49 
+Version: 7.0.3
+Revision: 1
+Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
+SourceDirectory: mosflm703
+Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
 Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000) 
 BuildDepends: gcc42 (= 4.2.1-1000), ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
 PatchScript: 
@@ -18,7 +18,7 @@
 export FOPTIM=-O0
 ./build
 cd bin
-mv ipmosflm ipmosflm-701
+mv ipmosflm ipmosflm-703
 
 InstallScript: 
 #!/bin/zsh -efv
@@ -37,7 +37,7 @@
 Mosflm can process data from a wide variety of modern area 
 detectors, e.g. from Mar Research, Rigaku/MSC, ADSC, DIP etc.
 
-Invoke with ipmosflm or ipmosflm-701 or mosflm
+Invoke with ipmosflm or ipmosflm-703 or mosflm
 
 Authors:  
 Harry Powell and 


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[cvs] dists/10.4/stable/main/finkinfo/sci coot-10.5.info,1.1,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18407

Removed Files:
coot-10.5.info 
Log Message:
coot-10.5 is obsolete

--- coot-10.5.info DELETED ---


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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.11,1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18826

Modified Files:
coot.info 
Log Message:
patch to fix broken refmac interface

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- coot.info   12 Jan 2008 02:20:54 -  1.11
+++ coot.info   8 Mar 2008 17:38:47 -   1.12
@@ -1,6 +1,6 @@
 Package:coot
 Version: 0.4.1
-Revision: 1
+Revision: 2
 GCC: 4.0 
 Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
 Source-MD5: f04fbae59acd61aa0e1c3bbdc7ce5e18
@@ -9,6 +9,8 @@
 Source2-MD5: 9f6d945927751531505298b0b8789687
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
+Source4: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/0.4.1-src-c-interface-build.cc.patch
+Source4-MD5: 64c44981a394f8920fb56103d05e2be8
 #
 ###
 Description: Crystallographic molecular graphics
@@ -121,6 +123,9 @@
 echo (set-display-lists-for-maps 0)  | scheme/group-settings.scm
 # Fix configure to work with gpp4 library instead of ccp4c
 # perl -pi -e 's|ccp4c|gpp4|g' configure
+# Refmac patch
+/usr/bin/patchsrc/c-interface-build.cc  
../0.4.1-src-c-interface-build.cc.patch
+return $?
 
 ###
 ConfigureParams:   


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.57,1.58

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv9014

Modified Files:
coot.info 
Log Message:
coot version update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.57
retrieving revision 1.58
diff -u -d -r1.57 -r1.58
--- coot.info   3 Jan 2008 08:51:03 -   1.57
+++ coot.info   8 Mar 2008 19:51:43 -   1.58
@@ -1,9 +1,10 @@
 Package:coot
-Version: 0.4.1
-Revision: 1
+Version: 0.5-pre-1
+Revision: 852
 GCC: 4.0 
-Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: f04fbae59acd61aa0e1c3bbdc7ce5e18
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v-revision-%r.tar.gz
+# Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
+Source-MD5: 4ad2eaa736158aefe013d4966939aee2
 SourceDirectory: %n-%v
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
@@ -121,6 +122,8 @@
 echo (set-display-lists-for-maps 0)  | scheme/group-settings.scm
 # Fix configure to work with gpp4 library instead of ccp4c
 # perl -pi -e 's|ccp4c|gpp4|g' configure
+perl -pi -e s|guile -c|guile-1.8  -c|g configure
+perl -pi -e 's|\(goosh\)|\(goosh goosh\)|g' configure
 
 ###
 ConfigureParams:   
@@ -134,7 +137,7 @@
 ###
 CompileScript: 
 #!/bin/zsh -efx
-export PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
+export 
PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH:%p/share/guile/1.8/goosh
 export SED=/usr/bin/sed
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 export 
PYTHONPATH=%p/share/coot/python:%p/lib/python2.5:%p/lib/python2.5/site-packages:%p/lib/python2.5/site-packages/gtk-2.0:%p/lib/python2.5/site-packages/gtk-2.0


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[cvs] dists/10.4/unstable/main/finkinfo/sci mosflm.info,1.18,1.19

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18527

Modified Files:
mosflm.info 
Log Message:
changed for gcc43 gfortran

Index: mosflm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- mosflm.info 9 Mar 2008 22:16:09 -   1.18
+++ mosflm.info 9 Mar 2008 22:19:05 -   1.19
@@ -1,6 +1,6 @@
 Package: mosflm
 Version: 7.0.3
-Revision: 1
+Revision: 2
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
 SourceDirectory: mosflm703
 Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info, 1.28, 1.29 ccp4.patch, 1.12, 1.13

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv17396

Modified Files:
ccp4.info ccp4.patch 
Log Message:
changed for gcc43 gfortran

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -d -r1.28 -r1.29
--- ccp4.info   30 Dec 2007 04:13:12 -  1.28
+++ ccp4.info   9 Mar 2008 22:16:58 -   1.29
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.2
-Revision: 7
+Revision: 8
 GCC: 4
 Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
 Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
@@ -23,10 +23,10 @@
 Source8-MD5: 26a124b160c4215d6b20749f20932920
 Source9: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/crystal.C-r1.5-r1.6.diff
 Source9-MD5: 5c62b4a7399aded0f0c896c4315cfff6
-Source10: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/export-r1_12.tcl
-Source10-MD5: 984f7305ba151d961bef2ac25b1b9925
-Source11: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/export-r1_6.def
-Source11-MD5: 3babc1ee652fed6d2bb976bde41450a8
+Source10: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patched_files/export-r1_13.tcl
+Source10-MD5: 92c05d767ab7d29b62ab2d6d6fa7da10
+Source11: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patched_files/export-r1_7.def
+Source11-MD5: 8b10e6226833c6783bfc983e7215084b 
 Source12: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various-r1_132.f
 Source12-MD5: 7ed02a1cd000a912ecef8a61a59d8560
 Source13: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various-r1_40.html
@@ -35,6 +35,14 @@
 Source14-MD5: 6471fce214ad8e3a1345fce4ce3ccf5b
 Source15: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/rstats.f-r1.39-r1.40.diff
 Source15-MD5: 05578c1bfd0eeb3a554170ae02b85ea9
+Source16: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/beast_MPI.f-r1.1-r1.2.diff
+Source16-MD5: f0765c071d86a9cb62450e0eec14558d
+Source17: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/rharvest.fh-r1.13-r1.14.diff
+Source17-MD5: 54f39fb8e8249b98f8e6be7399adc303
+Source18: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/detwin.tcl
+Source18-MD5: f945d86150e37b6cff942c3fc16438b4
+Source19: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patched_files/refmac5.tcl
+Source19-MD5: 6b2b87f5fec217b0353824a5bc94e730
 #
 DescPort: 
CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
@@ -75,15 +83,15 @@
x11, 
tcltk,
blt,
-   gcc42-shlibs,
-   fftw-shlibs, %N-shlibs (= %v-%r)
+   gcc43-shlibs,
+   fftw-shlibs (=2.1.5-1014), %N-shlibs (= %v-%r)
 
 BuildDepends: 
-   gcc42, 
+   gcc43, 
f2c, 
fort77, 
tcltk-dev, 
-   fftw
+   fftw (=2.1.5-1014)
 
 Replaces: 
mosflm (= 6.2.3-2), 
@@ -146,11 +154,14 @@
/usr/bin/patchsrc/bp3_/crystal.C   
../crystal.C-r1.5-r1.6.diff
/usr/bin/patchsrc/fft.f
../fft.f-r1.98-r1.100.diff
/usr/bin/patchsrc/rstats.f 
../rstats.f-r1.39-r1.40.diff
-   cp../export-r1_12.tcl   ccp4i/tasks/export.tcl
-   cp../export-r1_6.defccp4i/tasks/export.def
+   #/usr/bin/patchsrc/beast_/beast_MPI/beast_MPI.f  
../beast_MPI.f-r1.1-r1.2.diff
+   /usr/bin/patchsrc/refmac5_/rharvest.fh  
../rharvest.fh-r1.13-r1.14.diff
+   cp../export-r1_13.tcl   ccp4i/tasks/export.tcl
+   cp../export-r1_7.defccp4i/tasks/export.def
cp../mtz2various-r1_132.f   src/mtz2various.f
cp../mtz2various-r1_40.html html/mtz2various.html
-   #
+   cp../detwin.tcl ccp4i/tasks/detwin.tcl
+   cp../refmac5.tclccp4i/tasks/refmac5.tcl
 
 

 CompileScript: 
@@ -194,9 +205,9 @@
 # Disable building of pdb_extract and phaser in 10.5.  CCP4 6.1 will fix 
this.
 
 if [[ $(sw_vers -productVersion)  10.5 ]]; then
- FC=%p/lib/gcc4.2/bin/gfortran F_LIBS=-L%p/lib/gcc4.2/lib 
./configure --with-shared-libs --with-fftw=%p --with-x Darwin
+ FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --with-shared-libs --with-fftw=%p --with-x Darwin
 else
- FC=%p/lib/gcc4.2/bin/gfortran F_LIBS=-L%p/lib/gcc4.2/lib 
./configure --disable-pdb_extract --disable-cctbx --disable-phaser  
--with-shared-libs --with-fftw=%p --with-x Darwin
+ FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --disable-pdb_extract --disable-cctbx --disable-phaser  
--with-shared-libs --with-fftw=%p --with-x Darwin
 fi
 
#  fix some post-configure bugs by getting rid of -lg2c
@@ -205,7 +216,7 @@
 
 
  if [[ $(uname -p) != powerpc ]];then 
- perl -pi.bak -e 's|%p/lib/gcc4.2/bin/||g' lib/clipper/**/Makefile*
+ perl -pi.bak 

[cvs] dists/10.4/unstable/main/finkinfo/sci tinker.info, 1.5, 1.6 refmac.info, 1.13, 1.14 ccp4-onlylibs-dev.info, 1.17, 1.18 mosflm-small.info, 1.18, 1.19 mosflm.info, 1.17, 1.18

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv17345

Modified Files:
tinker.info refmac.info ccp4-onlylibs-dev.info 
mosflm-small.info mosflm.info 
Log Message:
changed for gcc43 gfortran

Index: mosflm-small.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm-small.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- mosflm-small.info   3 Mar 2008 15:23:50 -   1.18
+++ mosflm-small.info   9 Mar 2008 22:16:08 -   1.19
@@ -1,11 +1,11 @@
 Package: mosflm-small
 Version: 7.0.3
-Revision: 1
+Revision: 2
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
 SourceDirectory: mosflm703
 Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
-Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000)
-BuildDepends: gcc42 (= 4.2.1-1000) , ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
+Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs
+BuildDepends: gcc43, ccp4-dev (= 6.0.2-7), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 # This is merely a hack to get the ppc version to compile with gfortran
 # It does so on intel by default

Index: mosflm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- mosflm.info 3 Mar 2008 15:23:50 -   1.17
+++ mosflm.info 9 Mar 2008 22:16:09 -   1.18
@@ -4,8 +4,8 @@
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
 SourceDirectory: mosflm703
 Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
-Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc42-shlibs (= 4.2.1-1000) 
-BuildDepends: gcc42 (= 4.2.1-1000), ccp4-dev (= 6.0.2-7), x11, libjpeg, 
libgettext3-shlibs
+Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs 
+BuildDepends: gcc43, ccp4-dev (= 6.0.2-7), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 # This is merely a hack to get the ppc version to compile with gfortran
 # It does so on intel by default

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- ccp4-onlylibs-dev.info  22 Dec 2007 01:20:39 -  1.17
+++ ccp4-onlylibs-dev.info  9 Mar 2008 22:16:08 -   1.18
@@ -1,7 +1,7 @@
 Package: ccp4-onlylibs-dev
 # Use version numbering to sync with the current CCP4 release:
 Version: 6.0.2
-Revision: 9
+Revision: 10
 GCC: 4.0
 Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz
 #Source: ftp://ftp.ccp4.ac.uk/prerelease/ccp4-onlylibs-dev.tar.gz
@@ -13,8 +13,8 @@
 Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
 Source2-MD5: ea307964e3786bef0868ea560471
 #
-Depends:  gcc42-shlibs
-BuildDepends: gcc42
+Depends:  gcc43-shlibs
+BuildDepends: gcc43
 # BuildDepends: fort77
 BuildDependsOnly: false
 NoSetCPPFLAGS: true

Index: tinker.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/tinker.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- tinker.info 29 Jan 2007 01:11:52 -  1.5
+++ tinker.info 9 Mar 2008 22:16:08 -   1.6
@@ -1,12 +1,12 @@
 Package: tinker
 Version: 4.2.1
-Revision: 4
+Revision: 5
 Source: ftp://dasher.wustl.edu/pub/%n.tar.gz
 SourceRename: %n-%v.tar.gz 
 SourceDirectory: %n
 Source-MD5: 5618d8a373896f00e452b137200223fd  
-BuildDepends: gcc42
-Depends: gcc42-shlibs
+BuildDepends: gcc43
+Depends: gcc43-shlibs
 PatchScript: 
 cp apple/gnu/*.make source/.
 cp apple/gnu/*.f source/.

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -d -r1.13 -r1.14
--- refmac.info 30 Dec 2007 06:54:47 -  1.13
+++ refmac.info 9 Mar 2008 22:16:08 -   1.14
@@ -1,15 +1,15 @@
 Package: refmac
 Version: 5.4
 # version 5.4.0066  : 12/07/07##
-Revision: 2
+Revision: 3
 Source: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_source.tar.gz
 Source-MD5: ca5d41fcf45ceeb6d91b7a7c3af1c5fb
 SourceRename: %n-%v.tar.gz
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
 NoSourceDirectory: yes
-Depends: ccp4 (= 6.0.2-7), gcc42-shlibs
-BuildDepends: ccp4-dev (= 6.0.2-7), gcc42, ccp4 (= 6.0.2-7) 
+Depends: ccp4 (= 6.0.2-7), gcc43-shlibs
+BuildDepends: 

[cvs] dists/10.4/unstable/main/finkinfo/sci mosflm.info, 1.19, 1.20 mosflm-small.info, 1.19, 1.20 refmac.info, 1.14, 1.15

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv24218

Modified Files:
mosflm.info mosflm-small.info refmac.info 
Log Message:
requires rev 8 of ccp4 to compile

Index: mosflm-small.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm-small.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- mosflm-small.info   9 Mar 2008 22:16:08 -   1.19
+++ mosflm-small.info   9 Mar 2008 23:52:15 -   1.20
@@ -4,8 +4,8 @@
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
 SourceDirectory: mosflm703
 Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
-Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs
-BuildDepends: gcc43, ccp4-dev (= 6.0.2-7), x11, libjpeg, libgettext3-shlibs
+Depends: x11, ccp4 (= 6.0.2-8), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs
+BuildDepends: gcc43, ccp4-dev (= 6.0.2-8), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 # This is merely a hack to get the ppc version to compile with gfortran
 # It does so on intel by default

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- refmac.info 9 Mar 2008 22:16:08 -   1.14
+++ refmac.info 9 Mar 2008 23:52:15 -   1.15
@@ -8,8 +8,8 @@
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
 NoSourceDirectory: yes
-Depends: ccp4 (= 6.0.2-7), gcc43-shlibs
-BuildDepends: ccp4-dev (= 6.0.2-7), gcc43, ccp4 (= 6.0.2-7) 
+Depends: ccp4 (= 6.0.2-8), gcc43-shlibs
+BuildDepends: ccp4-dev (= 6.0.2-8), gcc43, ccp4 (= 6.0.2-8) 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 Patch: refmac.patch

Index: mosflm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- mosflm.info 9 Mar 2008 22:19:05 -   1.19
+++ mosflm.info 9 Mar 2008 23:52:15 -   1.20
@@ -4,8 +4,8 @@
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/build-it-yourself/mosflm703.tgz
 SourceDirectory: mosflm703
 Source-MD5: 4ca2505fa3c75e2ba2de6e5de9d9baae 
-Depends: x11, ccp4 (= 6.0.2-7), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs 
-BuildDepends: gcc43, ccp4-dev (= 6.0.2-7), x11, libjpeg, libgettext3-shlibs
+Depends: x11, ccp4 (= 6.0.2-8), libjpeg-shlibs, libgettext3-shlibs, 
gcc43-shlibs 
+BuildDepends: gcc43, ccp4-dev (= 6.0.2-8), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 # This is merely a hack to get the ppc version to compile with gfortran
 # It does so on intel by default


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[cvs] dists/10.4/stable/main/finkinfo/sci tinker.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv20806

Added Files:
tinker.info 
Log Message:
user requested move to stable works fine

--- NEW FILE: tinker.info ---
Package: tinker
Version: 4.2.1
Revision: 5
Source: ftp://dasher.wustl.edu/pub/%n.tar.gz
SourceRename: %n-%v.tar.gz 
SourceDirectory: %n
Source-MD5: 5618d8a373896f00e452b137200223fd  
BuildDepends: gcc42
Depends: gcc42-shlibs
PatchScript: 
cp apple/gnu/*.make source/.
cp apple/gnu/*.f source/.
chmod +x source/*.make
# Use gfortran instead of g77 to compile this.
perl -pi.bak -e 's|g77|gfortran|g' source/*.make

CompileScript:  
 cd source; ./compile.make
 cd source; ./library.make
 cd source; ranlib libtinker.a
 cd source; ./link.make
 mkdir -p bin
 cd source; ./rename.make
 cd source; rm -f *.o

InstallScript: 
 mkdir -p %i/share/%n
 cp -R * %i/share/%n/.
 mkdir -p %i/share/doc/%n
 cp -R  %i/share/%n/doc/* %i/share/doc/%n/.
 mkdir -p %i/etc/profile.d
 echo set path = ( %p/share/%n/bin \$path )   %i/etc/profile.d/%n.csh
 echo PATH=%p/share/%n/bin:\$PATH  %i/etc/profile.d/%n.sh
 echo export PATH  %i/etc/profile.d/%n.sh
 chmod 755 %i/etc/profile.d/%n.*

Description: Molecular modeling software package 
DescDetail: 
The TINKER molecular modeling software is a complete and general package 
for molecular mechanics and dynamics, with some special features for 
biopolymers.

License:  Restrictive
Homepage: http://dasher.wustl.edu/tinker/
Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.29,1.30

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv31502

Modified Files:
ccp4.info 
Log Message:
ccp4 to use its own fftw

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -d -r1.29 -r1.30
--- ccp4.info   9 Mar 2008 22:16:58 -   1.29
+++ ccp4.info   12 Mar 2008 20:13:53 -  1.30
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.2
-Revision: 8
+Revision: 9
 GCC: 4
 Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
 Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
@@ -84,14 +84,13 @@
tcltk,
blt,
gcc43-shlibs,
-   fftw-shlibs (=2.1.5-1014), %N-shlibs (= %v-%r)
+   %N-shlibs (= %v-%r)
 
 BuildDepends: 
gcc43, 
f2c, 
fort77, 
-   tcltk-dev, 
-   fftw (=2.1.5-1014)
+   tcltk-dev
 
 Replaces: 
mosflm (= 6.2.3-2), 
@@ -205,9 +204,11 @@
 # Disable building of pdb_extract and phaser in 10.5.  CCP4 6.1 will fix 
this.
 
 if [[ $(sw_vers -productVersion)  10.5 ]]; then
- FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --with-shared-libs --with-fftw=%p --with-x Darwin
+ FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --with-shared-libs  --with-x Darwin
+   # --with-fftw=%p
 else
- FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --disable-pdb_extract --disable-cctbx --disable-phaser  
--with-shared-libs --with-fftw=%p --with-x Darwin
+ FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib 
./configure --disable-pdb_extract --disable-cctbx --disable-phaser  
--with-shared-libs  --with-x Darwin
+   # --with-fftw=%p
 fi
 
#  fix some post-configure bugs by getting rid of -lg2c


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.58,1.59

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv26930

Modified Files:
coot.info 
Log Message:
coot version update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -d -r1.58 -r1.59
--- coot.info   8 Mar 2008 19:51:43 -   1.58
+++ coot.info   18 Mar 2008 16:27:16 -  1.59
@@ -1,10 +1,10 @@
 Package:coot
 Version: 0.5-pre-1
-Revision: 852
+Revision: 860
 GCC: 4.0 
 Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v-revision-%r.tar.gz
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 4ad2eaa736158aefe013d4966939aee2
+Source-MD5: fca502f49bffb8e08d8b118de01e964e
 SourceDirectory: %n-%v
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.59,1.60

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv25778

Modified Files:
coot.info 
Log Message:
fix for window resize instability

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.59
retrieving revision 1.60
diff -u -d -r1.59 -r1.60
--- coot.info   18 Mar 2008 16:27:16 -  1.59
+++ coot.info   23 Mar 2008 23:59:35 -  1.60
@@ -1,10 +1,10 @@
 Package:coot
 Version: 0.5-pre-1
-Revision: 860
+Revision: 874
 GCC: 4.0 
 Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v-revision-%r.tar.gz
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: fca502f49bffb8e08d8b118de01e964e
+Source-MD5: 7b9f7fa229ca7ece142d104d3706bc70
 SourceDirectory: %n-%v
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687
@@ -142,7 +142,7 @@
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 export 
PYTHONPATH=%p/share/coot/python:%p/lib/python2.5:%p/lib/python2.5/site-packages:%p/lib/python2.5/site-packages/gtk-2.0:%p/lib/python2.5/site-packages/gtk-2.0
 FLIBS=-L%p/lib \
-CPPFLAGS=-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include 
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib 
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/ssm -I%p/include \
+CPPFLAGS=-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include 
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib 
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/ssm -I%p/include 
-I$PWD/ccp4mg-utils -I$PWD/src \
 LDFLAGS=-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib -L/usr/lib 
-lSystemStubs -flat_namespace -L%p/lib/python2.5/config 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
 CXX=/usr/bin/g++ \
 CC=/usr/bin/gcc \


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.60,1.61

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv30451

Modified Files:
coot.info 
Log Message:
coot version update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.60
retrieving revision 1.61
diff -u -d -r1.60 -r1.61
--- coot.info   23 Mar 2008 23:59:35 -  1.60
+++ coot.info   1 Apr 2008 01:43:53 -   1.61
@@ -1,10 +1,10 @@
 Package:coot
 Version: 0.5-pre-1
-Revision: 874
+Revision: 906
 GCC: 4.0 
 Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v-revision-%r.tar.gz
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 7b9f7fa229ca7ece142d104d3706bc70
+Source-MD5: cf19c5272d505407ecbf5529a8bed7c0
 SourceDirectory: %n-%v
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 9f6d945927751531505298b0b8789687


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh.info,1.13,1.14

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28984

Modified Files:
zsh.info 
Log Message:
zsh version update

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -d -r1.13 -r1.14
--- zsh.info1 Feb 2008 15:22:16 -   1.13
+++ zsh.info2 Apr 2008 13:16:02 -   1.14
@@ -1,5 +1,5 @@
 Package: zsh 
-Version: 4.3.5
+Version: 4.3.6
 Revision: 1
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/%n-%v.tar.bz2
-Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
+Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 2edea09b823ffa7528dbd447485630c9
+Source2-MD5: cab29228a90f58b1431a66ab24a0a0c2
 ConfigureParams:
 --mandir=%p/share/man --infodir=%p/share/info --enable-etcdir=%p/etc/%n   \
 --enable-maildir-support --enable-pcre --enable-zsh-secure-free   \


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-multibyte.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv759

Modified Files:
zsh-multibyte.info 
Log Message:
new zsh version

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- zsh-multibyte.info  1 Feb 2008 15:22:16 -   1.7
+++ zsh-multibyte.info  2 Apr 2008 13:25:29 -   1.8
@@ -1,5 +1,5 @@
 Package: zsh-multibyte
-Version: 4.3.5
+Version: 4.3.6
 Revision: 1
 Conflicts: zsh
 Replaces: zsh
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
+Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
 Source2: mirror:custom:zsh-%v-doc.tar.bz2
-Source2-MD5: 2edea09b823ffa7528dbd447485630c9
+Source2-MD5: cab29228a90f58b1431a66ab24a0a0c2
 ConfigureParams: 
 --mandir=%p/share/man --infodir=%p/share/info \
 --enable-etcdir=%p/etc/zsh --enable-maildir-support \


-
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-helpfiles.info, 1.8, 1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv2404

Modified Files:
zsh-helpfiles.info 
Log Message:
new version of zsh

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- zsh-helpfiles.info  9 Feb 2008 18:07:57 -   1.8
+++ zsh-helpfiles.info  2 Apr 2008 13:29:06 -   1.9
@@ -1,5 +1,5 @@
 Package: zsh-helpfiles
-Version: 4.3.5
+Version: 4.3.6
 Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
@@ -26,7 +26,7 @@
 
 Source: mirror:custom:/zsh-%v.tar.bz2
 Source2: 
http://code.google.com/p/zsh-templates-osx/source/browse/trunk/Library/init/zsh/local-functions/general/run-help
-Source-MD5: db0d4b71da8e5877fa1e29d4cea38b8c
+Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:
 #!/bin/zsh -efv


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dists/10.4-transitional/unstable/main/finkinfo/sci apbs.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32314

Added Files:
apbs.info 
Log Message:
apbs adaptive Poisson-Boltzman solver for macromolecular electrostatic 
calculations

--- NEW FILE: apbs.info ---
Package: apbs
Version: 0.3.2
Revision: 7
Source: mirror:sourceforge:%n/%n-%v.tar.gz
Source-MD5: b2a417c1d9c102157f45cf00fd0ae196 
SourceDirectory: %n-%v
Depends: maloc, readline-shlibs, gnuplot
BuildDepends: g77, maloc
Conflicts: apbs-mpi
Replaces: apbs-mpi
ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib FETK_PREFIX=%p
setCFLAGS: -I%p/include/maloc
setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r)
Description: Adaptive Poisson-Boltzmann Solver
CompileScript: 
#!/bin/zsh -f
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
./configure %c --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib
# perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
 perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
 perl -pi -e 's|python2|python|g' **/* 2/dev/null
make

InstallScript: 
#!/bin/zsh -f
make install DESTDIR=%d
rm -Rf **/CVS  # fink validate complains if this junk is left behind.
mkdir -p %i/share/%n
mv tools/manip/psize.py tools/manip/psize.py-dist
sed s/usr\/bin\/python2/usr\/bin\/python/g tools/manip/psize.py-dist  
tools/manip/psize.py
mv examples %i/share/%n
mv tools %i/share/%n
mkdir -p %i/bin
ln -s %p/bin/powerpc-apple-darwin$(uname -r)/apbs %i/bin/apbs

PostInstScript: 
# per request of software's author
open http://agave.wustl.edu/apbs/download/

Homepage: http://apbs.sourceforge.net/
RunTimeVars: 
  APBS_PSIZE:%p/share/%n/tools/manip

DescDetail: 
APBS is a software package for the numerical solution of the 
Poisson-Boltzmann equation, a popular continuum model for describing 
electrostatic interactions between molecular solutes over a wide range 
of length scales. Fink's pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code.  Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/

License: GPL  
Maintainer: W. G. Scott [EMAIL PROTECTED]



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dists/10.4-transitional/unstable/main/finkinfo/sci maloc.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32409

Added Files:
maloc.info 
Log Message:
maloc hardware abstraction code required for apbs

--- NEW FILE: maloc.info ---
Package: maloc
Version: 0.1-2
Revision: 4
Conflicts: maloc-mpi
Replaces: maloc-mpi
Source: http://scicomp.ucsd.edu/~mholst/codes/maloc/%n-%v.tar.gz
Source-MD5: 4eb2a2788ab52118775227014db834cc 
SourceDirectory: %n
Depends: readline-shlibs
BuildDepends: readline-shlibs
CompileScript: 
#!/bin/zsh -f
export FETK_INCLUDE=%p/include
export FETK_LIBRARY=%p/lib
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
./configure %c --disable-blas --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework 
-Wl,vecLib
make

Maintainer: W. G. Scott [EMAIL PROTECTED]
License: GPL
Description: Hardware abstraction library (1 cpu version)
DescDetail: 
MALOC (Minimal Abstraction Layer for Object-oriented C) is a small, portable,
abstract C environment library for object-oriented C programming. MALOC is
used as the foundation layer for a number of scientific applications,
including MC, SG, and APBS. MALOC can be used as a small stand-alone
abstraction environment for writing portable C programs that need access to
resources that are typically architecture-dependent, such as INET sockets,
timing routines, and so on. MALOC provides abstract datatypes, memory
management routines, timing routines, machine epsilon, access to UNIX and
INET sockets, MPI, and so on. All things that can vary from one architecture
to another are abstracted out of an application code and placed in MALOC. To
port the application code to a new architecture, only the small MALOC library
needs to be ported (usually just ./configure ; make). MALOC takes the pain
of varying UNIX (and Win32) platforms with differing library and header
layous completely out of the software development picture.
.
By default, MALOC builds libblas.a.  This default is disabled because OS X
provides its own BLAS in the Accelerate.framework.
.
maloc-mpi should be used for multi-processor machines.  maloc can be used with
any number of processors.

Homepage: http://scicomp.ucsd.edu/~mholst/codes/maloc/



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dists/10.4-transitional/unstable/main/finkinfo/sci apbs-mpi.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10968

Added Files:
apbs-mpi.info 
Log Message:
apbs adaptive Poisson-Boltzman solver for macromolecular electrostatic 
calculations

--- NEW FILE: apbs-mpi.info ---
Package: apbs-mpi
Version: 0.3.2
Revision: 8
Conflicts: apbs
Replaces: apbs
Source: http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-%v.tar.gz
Source-MD5: b2a417c1d9c102157f45cf00fd0ae196 
SourceDirectory: apbs-%v
Depends: maloc-mpi, lammpi, readline-shlibs, gnuplot
BuildDepends: g77, lammpi-dev, maloc-mpi
ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib 
FETK_MPI_INCLUDE=%p/include FETK_MPI_LIBRARY=%p/lib FETK_PREFIX=%p
setCFLAGS: -I%p/include/maloc
setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r) -llam
Description: Adaptive Poisson-Boltzmann Solver
CompileScript: 
#!/bin/zsh -f
export FETK_INCLUDE=%p/include  
export FETK_LIBRARY=%p/lib 
export FETK_MPI_INCLUDE=%p/include 
export FETK_MPI_LIBRARY=%p/lib 
export FETK_PREFIX=%p
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
./configure %c --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib 
--with-mpi
# perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
 perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
 perl -pi -e 's|python2|python|g' **/* 2/dev/null
make

InstallScript: 
#!/bin/zsh -f
make install DESTDIR=%d
rm -Rf **/CVS  # fink validate complains if this junk is left behind.
mkdir -p %i/share/apbs
mv tools/manip/psize.py tools/manip/psize.py-dist
sed s/usr\/bin\/python2/usr\/bin\/python/g tools/manip/psize.py-dist  
tools/manip/psize.py
mv examples %i/share/apbs
mv tools %i/share/apbs
mkdir -p %i/bin
ln -s %p/bin/powerpc-apple-darwin$(uname -r)/apbs %i/bin/apbs

PostInstScript: 
open http://agave.wustl.edu/apbs/download/

Homepage: http://apbs.sourceforge.net/
RunTimeVars: 
  APBS_PSIZE:%p/share/apbs/tools/manip

DescDetail: 
APBS is a software package for the numerical solution of the 
Poisson-Boltzmann equation, a popular continuum model for describing 
electrostatic interactions between molecular solutes over a wide range 
of length scales. Fink's pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code.  Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/

License: GPL  
Maintainer: W. G. Scott [EMAIL PROTECTED]



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dists/10.4-transitional/unstable/main/finkinfo/sci maloc-mpi.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11084

Added Files:
maloc-mpi.info 
Log Message:
maloc hardware abstraction code required for apbs

--- NEW FILE: maloc-mpi.info ---
Package: maloc-mpi
Version: 0.1-2
Revision: 5
Conflicts: maloc
Replaces: maloc
Source: http://scicomp.ucsd.edu/~mholst/codes/maloc/maloc-%v.tar.gz
Source-MD5: 4eb2a2788ab52118775227014db834cc 
SourceDirectory: maloc
Depends: lammpi, readline-shlibs
BuildDepends: lammpi-dev, readline-shlibs
CompileScript: 
#!/bin/zsh -f
export FETK_INCLUDE=%p/include
export FETK_LIBRARY=%p/lib
export FETK_MPI_INCLUDE=%p/include
export FETK_MPI_LIBRARY=%p/lib
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
./configure %c  --enable-mpi --disable-blas  --with-blas=-L${BLAS_DIR} -lblas 
-Wl,-framework -Wl,vecLib --with-mpi
make

Maintainer: W. G. Scott [EMAIL PROTECTED]
License: GPL
Description: Hardware abstraction library (mpi version)
DescDetail: 
MALOC (Minimal Abstraction Layer for Object-oriented C) is a small, portable,
abstract C environment library for object-oriented C programming. MALOC is
used as the foundation layer for a number of scientific applications,
including MC, SG, and APBS. MALOC can be used as a small stand-alone
abstraction environment for writing portable C programs that need access to
resources that are typically architecture-dependent, such as INET sockets,
timing routines, and so on. MALOC provides abstract datatypes, memory
management routines, timing routines, machine epsilon, access to UNIX and
INET sockets, MPI, and so on. All things that can vary from one architecture
to another are abstracted out of an application code and placed in MALOC. To
port the application code to a new architecture, only the small MALOC library
needs to be ported (usually just ./configure ; make). MALOC takes the pain
of varying UNIX (and Win32) platforms with differing library and header
layous completely out of the software development picture.
.
By default, MALOC builds libblas.a.  This default is disabled because OS X
provides its own BLAS in the Accelerate.framework.
.
maloc-mpi should be used for multi-processor machines.  maloc can be used with
any number of processors.

Homepage: http://scicomp.ucsd.edu/~mholst/codes/maloc/



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dists/10.4-transitional/unstable/main/finkinfo/shells zsh.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28899

Modified Files:
zsh.info 
Log Message:
Adding lines to DescDetail requested by K. Horton. No need for revision change.

Index: zsh.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- zsh.info13 Sep 2005 04:40:06 -  1.3
+++ zsh.info19 Nov 2005 18:23:20 -  1.4
@@ -48,6 +48,11 @@
 DocFiles: Doc/zsh.dvi Doc/*.html StartupFiles/* ChangeLog* INSTALL LICENCE 
META-FAQ README 
 Description: The Z Shell
 DescDetail: 
+To make the Fink zsh your default user shell, do the following:
+  1. Add the line /sw/bin/zsh to the file /etc/shells
+  2. Execute the following command: chsh -s /sw/bin/zsh
+  3. Open a new terminal session.
+.
 Zsh is a shell designed for interactive use, although it is also 
 a powerful scripting language. Many of the useful features of bash, 
 ksh, and tcsh were incorporated into zsh; many original 



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dists/10.4-transitional/unstable/main/finkinfo/sci gromacs-mpi.patch,NONE,1.1 gromacs-mpi.info,1.1,1.2 gromacs.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19971

Modified Files:
gromacs-mpi.info gromacs.info 
Added Files:
gromacs-mpi.patch 
Log Message:
Version update to gromacs molecular dynamics packages

Index: gromacs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gromacs.info27 Apr 2005 03:26:22 -  1.1
+++ gromacs.info20 Nov 2005 19:42:30 -  1.2
@@ -1,14 +1,14 @@
 Package: gromacs
-Version: 3.2.1
-Revision: 5
-Depends: %N-shlibs (= %v-%r), fftw | fftw-mpi, x11, openmotif3-shlibs
-BuildDepends: fftw | fftw-mpi, x11-dev
-BuildDependsOnly: true
+Version: 3.3
+Revision: 1
+Depends: %N-shlibs (= %v-%r), fftw3-shlibs, x11, openmotif3-shlibs
+BuildDepends: fftw3, x11-dev
+BuildDependsOnly: false
 Source: mirror:custom:%n-%v.tar.gz
 CustomMirror: 
-Primary: ftp://ftp.gromacs.org/pub/gromacs/source/
+Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: d298386495f6ee39b3155ce951984485 
+Source-MD5: 99ea6f25a89f1511f51c350a66a2fdc4
 ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share 
 DocFiles: AUTHORS COPYING README
 PatchScript: 
@@ -22,25 +22,25 @@
 
 SplitOff: 
 Package: %N-shlibs
-Depends: fftw-shlibs | fftw-mpi-shlibs, x11, openmotif3-shlibs
+Depends: fftw3-shlibs, x11, openmotif3-shlibs
 Files: 
-   lib/libgmx.3.0.0.dylib
-lib/libgmx.3.dylib
-lib/libgmxana.3.0.0.dylib
-lib/libgmxana.3.dylib
-lib/libmd.3.0.0.dylib
-lib/libmd.3.dylib
+   lib/libgmx.4.0.0.dylib
+lib/libgmx.4.dylib
+lib/libgmxana.4.0.0.dylib
+lib/libgmxana.4.dylib
+lib/libmd.4.0.0.dylib
+lib/libmd.4.dylib
 
 Shlibs: 
-%p/lib/libgmx.3.dylib 4.0.0 %n (= 3.2.1-3)
-%p/lib/libgmxana.3.dylib 4.0.0 %n (= 3.2.1-3)
-%p/lib/libmd.3.dylib 4.0.0 %n (= 3.2.1-3)
+%p/lib/libgmx.4.dylib 5.0.0 %n (= 3.3-1)
+%p/lib/libgmxana.4.dylib 5.0.0 %n (= 3.3-1)
+%p/lib/libmd.4.dylib 5.0.0 %n (= 3.3-1)
 
 DocFiles: AUTHORS COPYING README
 
 SplitOff2: 
 Package: %N-dev
-Depends: %N-shlibs (= %v-%r), fftw | fftw-mpi, x11, openmotif3-shlibs
+Depends: %N-shlibs (= %v-%r), fftw3-shlibs, x11, openmotif3-shlibs
 Files: 
lib/*.a
lib/*.la

--- NEW FILE: gromacs-mpi.patch ---
--- gromacs-3.3/src/gmxlib/Makefile.in  2005-10-11 06:36:48.0 -0400
+++ gromacs-3.3/src/gmxlib/Makefile.in.fixed2005-11-17 23:14:35.0 
-0500
@@ -178,7 +178,7 @@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
+LIBS = @LIBS@ -Wl,-single_module
 LIBSUFFIX = @LIBSUFFIX@
 LIBTOOL = @LIBTOOL@
 LN_S = @LN_S@

Index: gromacs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs-mpi.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gromacs-mpi.info27 Apr 2005 03:26:22 -  1.1
+++ gromacs-mpi.info20 Nov 2005 19:42:30 -  1.2
@@ -1,14 +1,15 @@
 Package: gromacs-mpi
-Version: 3.2.1
-Revision: 5
-Depends: gromacs (= %v-%r), %N-shlibs (= %v-%r), fftw-mpi, x11, 
openmotif3-shlibs, lammpi (= 7.0.6-11)
-BuildDepends: fftw-mpi, x11-dev, lammpi-dev (= 7.0.6-11)
-BuildDependsOnly: true
+Version: 3.3
+Revision: 1
+Depends: gromacs (= %v-%r), %N-shlibs (= %v-%r), fftw3-shlibs, x11, 
openmotif3-shlibs, lammpi (= 7.0.6-11)
+BuildDepends: fftw3, x11-dev, lammpi-dev (= 7.0.6-11)
+BuildDependsOnly: false
 Source: mirror:custom:gromacs-%v.tar.gz
+Patch: %n.patch
 CustomMirror: 
- Primary: ftp://ftp.gromacs.org/pub/gromacs/source/
+ Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: d298386495f6ee39b3155ce951984485 
+Source-MD5: 99ea6f25a89f1511f51c350a66a2fdc4
 ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share  --enable-mpi --program-suffix=_mpi
 DocFiles: AUTHORS COPYING README
 CompileScript: 
@@ -20,22 +21,22 @@
 
 SplitOff: 
 Package: %N-shlibs
-Depends: lammpi (= 7.0.6-11), fftw-mpi
+Depends: lammpi (= 7.0.6-11), fftw3-shlibs
 Files: 
-   lib/libgmx_mpi.3.0.0.dylib
-   lib/libgmx_mpi.3.dylib
-   lib/libmd_mpi.3.0.0.dylib
-   lib/libmd_mpi.3.dylib
+   lib/libgmx_mpi.4.0.0.dylib
+   lib/libgmx_mpi.4.dylib
+   lib/libmd_mpi.4.0.0.dylib
+   lib/libmd_mpi.4.dylib
 
 Shlibs: 
-   %p/lib/libgmx_mpi.3.0.0.dylib 4.0.0 %n (= 3.2.1-3)
-   %p/lib/libmd_mpi.3.0.0.dylib 4.0.0 %n (= 3.2.1-3)
+   %p/lib/libgmx_mpi.4.0.0.dylib 5.0.0 %n (= 3.3-1)
+   %p/lib/libmd_mpi.4.0.0.dylib 5.0.0 %n (= 3.3-1)
 
 DocFiles: AUTHORS COPYING README
  
 SplitOff2: 
 Package: %N-dev
-Depends: lammpi-dev (= 7.0.6-11), fftw-mpi
+Depends: lammpi-dev (= 7.0.6-11), fftw3-shlibs
 Files: 
 

dists/10.4-transitional/unstable/main/finkinfo/sci apbs-mpi.info,1.1,1.2 apbs.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27980

Modified Files:
apbs-mpi.info apbs.info 
Log Message:
revision of apbs to improve postinstall script

Index: apbs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs-mpi.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- apbs-mpi.info   16 Nov 2005 22:12:48 -  1.1
+++ apbs-mpi.info   21 Nov 2005 03:31:58 -  1.2
@@ -1,6 +1,6 @@
 Package: apbs-mpi
 Version: 0.3.2
-Revision: 8
+Revision: 9
 Conflicts: apbs
 Replaces: apbs
 Source: http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-%v.tar.gz
@@ -39,7 +39,16 @@
 ln -s %p/bin/powerpc-apple-darwin$(uname -r)/apbs %i/bin/apbs
 
 PostInstScript: 
-open http://agave.wustl.edu/apbs/download/
+# per request of software's author
+echo 
+echo 
+
+echo Please issue \open http://agave.wustl.edu/apbs/download/\,;
+echo to register your use of this software to help the author 
+echo maintain funding for apbs.  apbs is released under the GPL and this is
+echo not required, but would be very helpful.
+echo 
+
+echo 
+sleep 5
 
 Homepage: http://apbs.sourceforge.net/
 RunTimeVars: 

Index: apbs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- apbs.info   15 Nov 2005 07:04:29 -  1.1
+++ apbs.info   21 Nov 2005 03:31:58 -  1.2
@@ -1,6 +1,6 @@
 Package: apbs
 Version: 0.3.2
-Revision: 7
+Revision: 8
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: b2a417c1d9c102157f45cf00fd0ae196 
 SourceDirectory: %n-%v
@@ -35,6 +35,15 @@
 
 PostInstScript: 
 # per request of software's author
+echo 
+echo 
+
+echo Please issue \open http://agave.wustl.edu/apbs/download/\,;
+echo to register your use of this software to help the author
+echo maintain funding for apbs.  apbs is released under the GPL and this is
+echo not required, but would be very helpful.
+echo 
+
+echo 
+sleep 5
 open http://agave.wustl.edu/apbs/download/
 
 Homepage: http://apbs.sourceforge.net/



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dists/10.4-transitional/unstable/main/finkinfo/sci pymol-py.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1869

Modified Files:
pymol-py.info 
Log Message:
pymol package corrected to add missing blt dependencies required for loading of 
pmw gui

Index: pymol-py.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- pymol-py.info   6 Oct 2005 05:48:56 -   1.3
+++ pymol-py.info   22 Nov 2005 00:20:13 -  1.4
@@ -10,8 +10,8 @@
 
 Source-MD5: 096cc1d06fa36eb1c8ad30560d06b81e
 SourceDirectory: pymol-%v
-Depends: python%type_pkg[python], libpng3-shlibs, numeric-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.2-1), freeglut-shlibs|glut-shlibs (= 
3.7-3)
-BuildDepends: libpng3, freeglut|glut (= 3.7-3), db43-ssl|db43, readline (= 
4.3-5), gdbm3, expat, tcltk-dev
+Depends: python%type_pkg[python], libpng3-shlibs, numeric-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.2-1), freeglut-shlibs|glut-shlibs (= 
3.7-3), blt-shlibs
+BuildDepends: libpng3, freeglut|glut (= 3.7-3), db43-ssl|db43, readline (= 
4.3-5), gdbm3, expat, tcltk-dev, blt
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24
 Replaces: pymol, pymol-py22, pymol-py23, pymol-py24
 PatchScript: sed 's|@FINKPREFIX@|%p|g' %a/pymol-py.patch | sed 
's|python2.X|python%type_raw[python]|g' | sed 
's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1



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dists/10.4-transitional/unstable/main/finkinfo/shells zsh-templates.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4864

Modified Files:
zsh-templates.info 
Log Message:
zsh-templates bug fix

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- zsh-templates.info  13 Sep 2005 04:41:48 -  1.9
+++ zsh-templates.info  24 Nov 2005 19:28:08 -  1.10
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 0.9.5
-Revision: 1
+Version: 0.9.6
+Revision: 2
 Source:  http://chemistry.ucsc.edu/~wgscott/mystuff/%n-%v.tgz
-Source-MD5: b79aa97a8c2a47f68b9ad5f22c5bf372  
+Source-MD5: ebb74cbd72495831537093121f20bf2b  
 Depends: macosx, zsh (= 4.2.1-13)
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]
@@ -11,6 +11,10 @@
 #!/bin/zsh -f
 perl -pi.bak -e 's|ALT_SWPREFIX|%p|g' etc/zshenv
 rm -f etc/*.bak
+perl -pi.bak -e 's|eval|noglob eval|g' Library/init/zsh/environment
+rm -f Library/init/zsh/environment.bak
+perl -pi.bak -e 's|tail -250|tail -n 250|g' Library/init/zsh/functions.local
+rm -r Library/init/zsh/functions.local.bak
 
 CompileScript:
 



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dists/10.4-transitional/unstable/main/finkinfo/shells zsh-templates.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9658

Modified Files:
zsh-templates.info 
Log Message:
zsh-templates md5sum fix mismatch

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- zsh-templates.info  24 Nov 2005 19:28:08 -  1.10
+++ zsh-templates.info  25 Nov 2005 04:34:22 -  1.11
@@ -1,8 +1,8 @@
 Package: zsh-templates
 Version: 0.9.6
-Revision: 2
+Revision: 3
 Source:  http://chemistry.ucsc.edu/~wgscott/mystuff/%n-%v.tgz
-Source-MD5: ebb74cbd72495831537093121f20bf2b  
+Source-MD5: 1ae8a24e2beb53f87791c48fce88743a  
 Depends: macosx, zsh (= 4.2.1-13)
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]



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dists/10.4-transitional/unstable/main/finkinfo/sci ccp4lib.info,1.3,NONE ccp4lib.patch,1.3,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3612

Removed Files:
ccp4lib.info ccp4lib.patch 
Log Message:
remove ccp4lib -- obsolete for upgrade I am about to add

--- ccp4lib.info DELETED ---

--- ccp4lib.patch DELETED ---



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dists/10.4-transitional/unstable/main/finkinfo/sci ccp4.info,1.5,1.6 ccp4.patch,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20544

Modified Files:
ccp4.info ccp4.patch 
Log Message:
ccp4 version upgrade 10.4-tran sci

Index: ccp4.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- ccp4.info   8 Jun 2005 23:59:16 -   1.5
+++ ccp4.info   2 Dec 2005 05:02:44 -   1.6
@@ -1,34 +1,20 @@
 Package: ccp4
-Version: 5.0.2
-Revision: 203
-#
-#  Revision 200 is specific to 10-4 transitional and includes these 
-#  post-release patches obtained from CCP4 web site 7 June, 2005.
-#
-#  CCP4_utils-25Aug2004.tcl.diff  cmtzlib_f-10Aug2004.c.diff  
lsqkab-9Aug2004.f.diff
-#  abs.f-18Aug2004.f  dmmulti-12Aug2004.f.diff
refmac5-13Aug2004.tcl.diff
-#  ccp4_parser-25Aug2004.c.diff   dmmulti_dmlib-12Aug2004.f.diff  
unsupported-Makefile.in-11Aug2004.diff
-#  pdb_utils-17Sep2004.tclmaprot-20Sep2004.f  
mapmask-20Sep2004.f
-#  ccp4i/templates/mapmask.comccp4i mail interface fixed to work with OSX 
Mail.app
-#  autosnd-15Nov2004.fcmtzlib_f-24Dec2004.c.diff  
cmtzlib_f-14Jan2005.c
-#  ncsref-26Jan2005.script.diff   truncate-02Mar2005.com.diff 
truncate-02Mar2005.def.diff  
-#  truncate-02Mar2005.tcl.diff`   mtzutils-11May2005.f.diff   
mok-harvest-src.patch 
-#  mok-harvest-includes.patch refmac5-19May2005.com.diff  
sftools-25May2005.f.diff 
-#  local-20Apr2005.tcl.diff  
-# 
-#
-Source: ftp://ftp.%n.ac.uk/%n/current/packed/%n-%v.tar.gz
-Source-MD5: 7888f73c0e92bc684f9da8bd75413e64   
+Version: 5.99.5
+Revision: 1
+Source: ftp://ftp.%n.ac.uk/%n/%v/packed/%n-core.tar.gz
+Source2: ftp://ftp.%n.ac.uk/%n/%v/packed/phaser-cctbx.tar.gz
+Source-MD5: 1dc37afc2597bceaabd971ba20d86ac3  
+Source2-MD5: ac745815cdff2c4c719e9171f029b3ba
 SourceDirectory: %n-%v
-Source2: http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
-Source2-MD5: 21568dd2475505929573a3fd452c538f
-#
-Depends: x11, tcltk, blt, ccp4lib (= %v-200 ), ccp4lib-shlibs (= %v-200 )
-BuildDepends: g77 (= 3.4.0-2), f2c, fort77, tcltk-dev, ccp4lib (= %v-200 ), 
ccp4lib-shlibs (= %v-200 )
-Replaces: mosflm (= 6.2.3-2), mosflm-small (= 6.2.3-2), refmac (= 5.1999-3)
+Source3: http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
+Source3-MD5: 21568dd2475505929573a3fd452c538f
+Depends: x11, tcltk, blt, ccp4-shlibs (= %v-%r)
+BuildDepends: g77 (= 3.4.0-2), f2c, fort77, tcltk-dev
+Replaces: mosflm (= 6.2.3-2), mosflm-small (= 6.2.3-2), refmac (= 
5.1999-3), ccp4lib, ccp4lib-shlibs
+Conflicts: ccp4lib, ccp4lib-shlibs
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
-#CXXFLAGS: -fabi-version=2
+#
 Patch: %n.patch
 PatchScript: 
 #!/bin/zsh -f
@@ -37,61 +23,49 @@
 # setup script for tcsh, zsh and bash users
 export TEMPXTAL=$PWD:h
 #
-perl -pi.bak -e 's|/swprefix|%p|g' include/%n.setup*# location of 
tcktk, blt
-perl -pi.bak -e 's|SW_PREFIX|%p|g' **/configure  
-perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/%n.setup*# build prefix 
(changed in install) 
-perl -pi.bak -e 's|\$CCP4/lib|%p/lib/%n-%v|g' include/%n.setup* 
-cp include/%n.setup-dist include/%n.setup
-rm -f include/%n.setup-bash
+perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup*   # build prefix 
(changed in install)
+perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*# location of 
tcktk, blt
+perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*   # same
 #
-# Quick-fix for some compilation header omissions
- cp %p/include/f2c.hlib/ccif/g2c.h   
- cp %p/include/f2c.hlib/src/g2c.h
- cp %p/include/f2c.hlib/g2c.h
- cp %p/include/f2c.hx-windows/Mosflm/cbf/src/g2c.h
- cp %p/include/f2c.hx-windows/Mosflm/src/g2c.h
- cp %p/include/f2c.hx-windows/RasMol/src/g2c.h
- cp %p/include/f2c.hx-windows/ipdisp/src/g2c.h
- cp %p/include/f2c.hx-windows/xdl_view/src/g2c.h
+perl -pi.bak -e 's|SW_PREFIX|%p|g' **/configure# location of 
tcktk, blt  
+cp include/%n.setup-dist include/%n.setup
+rm -f include/%n.setup-bash **/configure.bak include/ccp4.setup*.bak
 #
 # Set up XCCPJiffy wrapper scripts in $CCP4/etc
+# These are small wrapper scripts for xplot84driver and xloggraph generated by 
the patch
 chmod a+x etc/x*
-#
-perl -pi.bak -e 's|L\${CCP4_LIB}|L%p/lib/%n-%v|g' **/configure
-perl -pi.bak -e 's|\-lstdc|\-L/usr/lib/gcc/darwin/3.3 \-lstdc|g' **/configure*
 
 CompileScript: 
 #!/bin/zsh -f
- umask 0022
+umask 0022
 export TEMPXTAL=$PWD:h
-. include/%n.setup-sh
-export CLIB=%p/lib/ccp4lib
-export DYLD_LIBRARY_PATH=%p/lib/ccp4lib
-# ./configure --with-x Darwin
- ./configure --with-x --disable-pdb_extract Darwin
-# Use the library contents compiled with ccp4lib, but protect the original 
contents by copying
- mv lib lib-dist
- cp -r  

dists/10.4-transitional/unstable/main/finkinfo/sci mosflm-small.info,1.3,1.4 mosflm.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23253

Modified Files:
mosflm-small.info mosflm.info 
Log Message:
10.4-tran sci , mosflm packages bumped to rebuild against latest ccp4

Index: mosflm-small.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/mosflm-small.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- mosflm-small.info   30 Aug 2005 20:18:34 -  1.3
+++ mosflm-small.info   2 Dec 2005 05:20:58 -   1.4
@@ -1,29 +1,19 @@
 Package: mosflm-small
 Version: 6.2.5
-Revision: 1
-#Type: nosource  
+Revision: 5
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver625/build-it-yourself/mosflm625.tgz
-#
 SourceDirectory: mosflm625
-# NoSourceDirectory: true
 Source-MD5: 08c0730fa588d71bed219a7763322672 
-Depends: x11, ccp4, ccp4lib, libjpeg-shlibs, ccp4lib-shlibs, libgettext3-shlibs
-#Replaces: mosflm
-BuildDepends: g77, ccp4, x11, libjpeg, ccp4lib-shlibs, ccp4lib, 
libgettext3-shlibs
+Depends: x11, ccp4 (= 5.99.5-1), libjpeg-shlibs, libgettext3-shlibs
+BuildDepends: g77, ccp4 (= 5.99.5-1), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 #!/bin/zsh -f
-print $PWD
 perl -pi.bak -e 's|-lcc_dynamic||g' setup
-#cp -R $CCP4/x-windows/Mosflm .
 
 CompileScript:  
 #!/bin/zsh -f
-#cd Mosflm
-print $PWD
-#make clean
 mv bin/ipmosflm bin/ipmosflm-big
 ./to_small.csh
-#make
 ./build
 cd bin
 mv ipmosflm ipmosflm-small

Index: mosflm.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- mosflm.info 30 Aug 2005 20:17:26 -  1.2
+++ mosflm.info 2 Dec 2005 05:20:58 -   1.3
@@ -1,29 +1,18 @@
 Package: mosflm
 Version: 6.2.5
-Revision: 1
-#Type: nosource  
+Revision: 5
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver625/build-it-yourself/mosflm625.tgz
-#
 SourceDirectory: mosflm625
-# NoSourceDirectory: true
 Source-MD5: 08c0730fa588d71bed219a7763322672 
-Depends: x11, ccp4, ccp4lib, libjpeg-shlibs, ccp4lib-shlibs, libgettext3-shlibs
-#Replaces: mosflm
-BuildDepends: g77, ccp4, x11, libjpeg, ccp4lib-shlibs, ccp4lib, 
libgettext3-shlibs
+Depends: x11, ccp4 (= 5.99.5-1), libjpeg-shlibs, libgettext3-shlibs
+BuildDepends: g77, ccp4 (= 5.99.5-1), x11, libjpeg, libgettext3-shlibs
 PatchScript: 
 #!/bin/zsh -f
 print $PWD
 perl -pi.bak -e 's|-lcc_dynamic||g' setup
-#cp -R $CCP4/x-windows/Mosflm .
 
 CompileScript:  
 #!/bin/zsh -f
-#cd Mosflm
-print $PWD
-#make clean
-#mv bin/ipmosflm bin/ipmosflm-big
-#./to_small.csh
-#make
 ./build
 cd bin
 mv ipmosflm ipmosflm-625



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dists/10.4-transitional/unstable/main/finkinfo/sci cctbx.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29677

Added Files:
cctbx.info 
Log Message:
Computational Crystallography Toolbox for 10.4-trans sci

--- NEW FILE: cctbx.info ---
Package:cctbx
Version: 51021
Revision: 1
BuildDependsOnly: false
NoSourceDirectory: true
NoSetLDFLAGS: true
Source: 
http://cci.lbl.gov/cctbx_build/results/2005_10_21_1046/cctbx_python_242_bundle.tar.gz
Source-MD5: 3b7c5fe0a23415b848504305dbe08ff9
Description: Computational Crystallography Toolbox
DescDetail: 
The Computational Crystallography Toolbox (cctbx) is being developed as the
open source component of the PHENIX system. The goal of the PHENIX project is
to advance automation of macromolecular structure determination. PHENIX
depends on the cctbx, but not vice versa. This hierarchical approach enforces
a clean design as a reusable library. The cctbx is therefore also useful for
small-molecule crystallography and even general scientific applications.

The cctbx code base is available without restrictions and free of charge to
all interested developers, both academic and commercial. The entire community
is invited to actively participate in the development of the code base. A
sophisticated technical infrastructure that enables community based software
development is provided by SourceForge. This service is also free of charge
and open to the entire world.

The cctbx is designed with an open and flexible architecture to promote
extendability and easy incorporation into other software environments. The
package is organized as a set of ISO C++ classes with Python bindings. This
organization combines the computational efficiency of a strongly typed
compiled language with the convenience and flexibility of a dynamically typed
scripting language in a strikingly uniform and very maintainable way.

Use of the Python interfaces is highly recommended, but optional. The cctbx
can also be used purely as a C++ class library. The SourceForge cctbx project
currently contains these modules:

libtbx: The build system common to all other modules. This is a very thin
wrapper around the SCons software construction tool.

boost_adaptbx: A very small adaptor toolbox with platform-independent
instructions for building the Boost.Python library.

scitbx: Libraries for general scientific computing (i.e.  libraries that are
not specific to crystallographic applications): a family of high-level C++
array types, a fast Fourier transform library, and a C++ port of the popular
LBFGS conjugate gradient minimizer, all including Python bindings. These
libraries are separated from the crystallographic code base to make them
easily accessible for non-crystallographic application developers.

cctbx: Libraries for general crystallographic applications, useful for both
small-molecule and macro-molecular crystallography. The libraries in the cctbx
module cover everything from algorithms for the handling of unit cells to
high-level building blocks for refinement algorithms. Note the distinction
between the cctbx project and the cctbx module. In retrospect we should have
chosen a different name for the project, but the current naming reflects how
the modules have evolved and it would be too disruptive to start a grand
renaming.

iotbx: The youngest member in the family: evolving libraries for reading and
writing established file formats.

CompileScript: 
#!/bin/zsh -f
mkdir cctbx_build
cd cctbx_build
# requires a Framwork python build
/System/Library/Frameworks/Python.framework/Versions/Current/bin/python \
../cctbx_sources/libtbx/configure.py  mmtbx 
# The last command initializes the cctbx_build directory and creates 
# a file setpaths.csh (among others). This file must be used to initialize
# a new shell or process with the cctbx settings:

source setpaths.sh

# Find the number of cpus:
num_cpu=$( system_profiler -detailLevel -2 | grep Number Of CPUs | awk 
'{print $4}' )
# On a machine with multiple CPUs enter:

libtbx.scons -j $num_cpu .

InstallScript: 
#!/bin/zsh -f
perl -pi.bak -e 's|prepend|append|g' cctbx_build/setpaths.*sh
mkdir -p %i/share/xtal/%n
cp -R *  %i/share/xtal/%n/. 
#
# Set up startup scripts
mkdir -p %i/etc/profile.d
echo source %p/share/xtal/%n/%n_build/setpaths.sh | %i/etc/profile.d/%n.sh
echo source %p/share/xtal/%n/%n_build/setpaths.csh | %i/etc/profile.d/%n.csh
chmod a+x %i/etc/profile.d/%n.*

PostInstScript: 
# This changes the paths for the shell and python scripts to those of the
# final install point rather than the build or debian root directory.
cd %p/share/xtal/%n/cctbx_build
/System/Library/Frameworks/Python.framework/Versions/Current/bin/python \
../cctbx_sources/libtbx/configure.py mmtbx
#

License: OSI-Approved
Maintainer: W. G. Scott [EMAIL PROTECTED] 
Homepage: http://cctbx.sourceforge.net/



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dists/10.4-transitional/unstable/main/finkinfo/sci mmtk.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4053

Modified Files:
mmtk.info 
Log Message:
update to working mmtk for 10.4 with permission from maintaniner

Index: mmtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/mmtk.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- mmtk.info   27 Apr 2005 03:26:22 -  1.1
+++ mmtk.info   5 Dec 2005 15:49:02 -   1.2
@@ -1,9 +1,9 @@
 Package: mmtk
-Version: 2.3.2
+Version: 2.4.4
 Revision: 1
 Source: http://starship.python.net/crew/hinsen/MMTK/MMTK-%v.tar.gz
-Source-MD5: 9068fe4f6de22298cc29a5ff560b4764
-Depends: scientificpython-py23
+Source-MD5: c8792f57f2fc5e877d980272a8171626
+Depends: scientificpython-py24, netcdf
 Description: Molecular Modelling Toolkit
 DescDetail: 
 The Molecular Modelling Toolkit (MMTK) is an Open Source program
@@ -20,10 +20,10 @@
 perl -pi.bak -e 's/include malloc.h//g' **/*.h
 
 CompileScript: 
-%p/bin/python2.3 setup.py build
+%p/bin/python2.4 setup.py build
 
 InstallScript: 
-%p/bin/python2.3 setup.py install --root %d
+%p/bin/python2.4 setup.py install --root %d
 mkdir -p %i/share/doc/%n/HTML
 mkdir -p %i/share/doc/%n/PDF
 mkdir -p %i/share/doc/%n/XML



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dists/10.4-transitional/unstable/main/finkinfo/shells zsh.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14226

Modified Files:
zsh.info 
Log Message:
zsh version update that fixes poll bug without hack

Index: zsh.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- zsh.info19 Nov 2005 18:23:20 -  1.4
+++ zsh.info5 Dec 2005 21:16:14 -   1.5
@@ -1,6 +1,6 @@
 Package: zsh 
-Version: 4.2.5
-Revision: 22
+Version: 4.2.6
+Revision: 1
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs
 BuildDepends: libiconv-dev, pcre, pcre-bin, libncurses5
 CustomMirror: 
@@ -25,19 +25,17 @@
   nam-US: http://mirrors.theonlinerecordstore.com/zsh/
 
 Source: mirror:custom:/%n-%v.tar.bz2
-Source-MD5: e2060f743dcdf3b383e80e862a6548fe 
+Source-MD5: 2cefebf742c190cbc611baded825db64 
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 6dc896b52a3bc20a514148d621e13282 
+Source2-MD5: 3ca3b7c199db6eb942f2a296e3fad270 
 ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info 
--enable-etcdir=%p/etc/%n --enable-maildir-support --enable-pcre 
--enable-zsh-secure-free --enable-fndir=%p/share/%n --enable-function-subdirs 
--with-curses-terminfo --with-tcsetpgrp
 CompileScript:
 perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
  ./configure %c
 perl -pi.bak -e s;-ldl -ltinfo -lm  -lc;-L%p/lib -lpcre -L%p/lib -lncurses 
-L%p/lib -liconv -ltinfo -ldl -lm -lc; Makefile
 perl -pi.bak -e s;-bundle -flat_namespace -undefined suppress;-bundle 
-twolevel_namespace -undefined dynamic_lookup; Makefile
-#perl -pi.bak -e s;#define HAVE_POLL 1;#define HAVE_POLL 0; config.h
-#perl -pi.bak -e s;#define HAVE_POLL_H 1;#define HAVE_POLL_H 0; config.h
-cp config.h config.h.bak 
-grep -v HAVE_POLL config.h.bak  config.h 
+#cp config.h config.h.bak 
+#grep -v HAVE_POLL config.h.bak  config.h 
 make
 
 InstallScript:



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dists/10.4-transitional/unstable/main/finkinfo/shells zsh-helpfiles.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15589

Modified Files:
zsh-helpfiles.info 
Log Message:
zsh-helpfules to sync with new zsh version

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- zsh-helpfiles.info  13 Sep 2005 05:05:44 -  1.1
+++ zsh-helpfiles.info  5 Dec 2005 21:21:04 -   1.2
@@ -1,8 +1,8 @@
 Package: zsh-helpfiles
-Version: 4.2.5
+Version: 4.2.6
 Revision: 1
-Depends: zsh (= 4.2.5)
-BuildDepends: zsh (= 4.2.5)
+Depends: zsh (= 4.2.6)
+BuildDepends: zsh (= 4.2.6)
 CustomMirror: 
   Master: ftp://ftp.zsh.org/pub/
   eur: ftp://ftp.lysator.liu.se/pub/unix/zsh/
@@ -25,7 +25,7 @@
   nam-US: http://mirrors.theonlinerecordstore.com/zsh/
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source-MD5: e2060f743dcdf3b383e80e862a6548fe 
+Source-MD5: 2cefebf742c190cbc611baded825db64 
 Source2: 
http://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh/Library/init/zsh/local-functions/run-help
 Source2-MD5: 371638ce4c255993ea9c528981b3d113
 CompileScript:



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dists/10.4-transitional/unstable/main/finkinfo/graphics raster3d.info,1.1,1.2 raster3d.patch,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/graphics
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13883

Modified Files:
raster3d.info raster3d.patch 
Log Message:
remove -lcc_dynamic from raster3d info and patch files for 10.4

Index: raster3d.patch
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/graphics/raster3d.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- raster3d.patch  27 Apr 2005 03:25:46 -  1.1
+++ raster3d.patch  8 Dec 2005 15:53:34 -   1.2
@@ -43,7 +43,7 @@
 -INCDIRS  =-I/usr/include -I/usr/local/include
 -LIBDIRS  =-L/usr/local/lib
 +INCDIRS  =-I/usr/include [EMAIL PROTECTED]@/include
-+LIBDIRS  =[EMAIL PROTECTED]@/lib -lcc_dynamic
++LIBDIRS  =[EMAIL PROTECTED]@/lib
  
  #
  # TIFF support (enabled by default)

Index: raster3d.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/graphics/raster3d.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- raster3d.info   27 Apr 2005 03:25:46 -  1.1
+++ raster3d.info   8 Dec 2005 15:53:34 -   1.2
@@ -1,6 +1,6 @@
 Package: raster3d
 Version: 2.7b
-Revision: 21
+Revision: 22
 Maintainer: None fink-devel@lists.sourceforge.net
 Source: http://www.bmsc.washington.edu/%n/Raster3D_%v.tar.gz
 Source-MD5: 7599cb74fc9a20b6b1cf04812fdc144f
@@ -8,7 +8,6 @@
 BuildDepends: g77 (= 3.1-20020420-2), libjpeg, libpng3, libtiff, x11-dev
 PatchScript: sed 's|@FINKPREFIX@|%p|g' %a/%n.patch | patch -p1
 CompileScript: make linux; make all
-SetLDFLAGS: -lcc_dynamic
 InstallScript: 
  mkdir -p %i/bin
  make install prefix=%i



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dists/10.4-transitional/unstable/main/finkinfo/sci procheck.info,NONE,1.1 procheck.patch,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13207

Added Files:
procheck.info procheck.patch 
Log Message:
procheck added 10.4 sci unst. checks protein structures

--- NEW FILE: procheck.patch ---
--- procheck/nb.c.org   2005-12-09 21:54:59.0 -0500
+++ procheck/nb.c   2005-12-09 22:16:12.0 -0500
@@ -1987,6 +1987,18 @@
 
 
/**/
 
+char *getsafe(char *buffer, int count)
+{
+   char *result = buffer, *np;
+   if ((buffer == NULL) || (count  1))
+  result = NULL;
+   else if (count == 1)
+  *result = '\0';
+   else if ((result = fgets(buffer, count, stdin)) != NULL)
+  if (np = strchr(buffer, '\n'))
+ *np = '\0';
+   return result;
+}
 
 main()
 {
@@ -2009,7 +2021,7 @@
 /* CHECK v.2.0
 printf(\nEnter table output filename (or '@' for multiple files):);
 
-gets(tmpstr);
+getsafe(tmpstr,sizeof(tmpstr));
 sscanf(tmpstr, %s, tablefn);
 if (tablefn[0] != '@')
 {
@@ -2027,7 +2039,7 @@
 printf(  @file name for a file holding names of Brookhaven );
 printf(format files.\n);
 printf(If you've had enough, a blank line lets you escape!\n\n);
-gets(tmpstr);
+getsafe(tmpstr,sizeof(tmpstr));
 if (tmpstr[0] == '\0' || tmpstr[0] == '\n')
 break;
 if (tmpstr[0] == '@')
@@ -2057,7 +2069,7 @@
 
 /* CHECK v.2.0 */
 printf(\nEnter the name of original coordinates file\n);
-gets(tmpstr);
+getsafe(tmpstr,sizeof(tmpstr));
 if (tmpstr[0] != '\0'  tmpstr[0] != '\n')
 {
 ierror = getnam(tmpstr,istart,iend);
diff -uNr procheck/Makefile procheck.new/Makefile
--- procheck/Makefile   Thu Jan 11 11:16:16 2001
+++ procheck.new/Makefile   Tue Aug 31 07:37:29 2004
@@ -3,11 +3,11 @@
 #
 # Andrew C.R. Martin, University of Reading
 #
-F77   = f77  # Your FORTRAN compiler
+F77   = g77  # Your FORTRAN compiler
 CC= cc   # Your C compiler
 CLIBS = -lm  # Your C maths library
-COPTS = -g   # Compile/link options for C
-FOPTS = -g   # Compile/link options for FORTRAN
+COPTS = -O3  # Compile/link options for C
+FOPTS = -O3  # Compile/link options for FORTRAN
 
 ##
 # Shouldn't need to alter anything below here
diff -uNr procheck/setup.scr procheck.new/setup.scr
--- procheck/setup.scr  Wed Jan 10 08:26:23 2001
+++ procheck.new/setup.scr  Tue Aug 31 07:39:31 2004
@@ -8,8 +8,8 @@
 
 # PROCHECK environments and aliases
 # -
-setprodir =  @@_procheck_program_directory_@@
-setenv prodir   '@@_procheck_program_directory_@@'
+setprodir =  @PREFIX@/share/procheck
+setenv prodir   '@PREFIX@/share/procheck'
 alias procheck  $prodir'/procheck.scr'
 alias procheck_comp $prodir'/procheck_comp.scr'
 alias procheck_nmr  $prodir'/procheck_nmr.scr'
diff -uNr procheck/setup.sh procheck.new/setup.sh
--- procheck/setup.sh   Wed Jan 10 08:27:00 2001
+++ procheck.new/setup.sh   Tue Aug 31 07:38:45 2004
@@ -8,7 +8,7 @@
 
 # PROCHECK environments and aliases
 # -
-prodir=@@_procheck_program_directory_@@
[EMAIL PROTECTED]@/share/procheck
 export prodir
-alias procheck= $prodir'/procheck.scr'
+alias procheck=$prodir'/procheck.scr'
 alias procheck_comp=$prodir'/procheck_comp.scr'

--- NEW FILE: procheck.info ---
Package: procheck
Version: 3.5.4
Revision: 1
Maintainer: Jack Howarth [EMAIL PROTECTED]
Source: ftp://ftp.biochem.ucl.ac.uk/pub/procheck/tar3_5/procheck.tar.Z
Source-MD5: ce04de5542d6136694b2021cb5c06a27
BuildDepends: g77
PatchScript: sed 's|@PREFIX@|%p|g'  %a/%n.patch | patch -p1
CompileScript: 
#!/bin/sh
make all

InstallScript: 
mkdir -p %i/share/procheck
mkdir -p %i/etc/profile.d
rm *.f *.c *.inc *.o Makefile
cp * %i/share/procheck
cp setup.scr %i/etc/profile.d/procheck.csh
cp setup.sh %i/etc/profile.d/procheck.sh
chmod 755 %i/share/procheck/setup.sh
chmod 755 %i/etc/profile.d/procheck.csh
chmod 755 %i/etc/profile.d/procheck.sh

PostInstScript: more %p/share/procheck/confid.doc
Description: Protein Structure Validation Suite
License: Restrictive
Homepage: http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html



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dists/10.4-transitional/unstable/main/finkinfo/sci procheck.info,1.1,1.2 procheck.patch,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25551

Modified Files:
procheck.info procheck.patch 
Log Message:
procheck fixed patch and info

Index: procheck.patch
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/procheck.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- procheck.patch  11 Dec 2005 05:45:48 -  1.1
+++ procheck.patch  13 Dec 2005 04:54:39 -  1.2
@@ -78,10 +78,9 @@
  alias procheck  $prodir'/procheck.scr'
  alias procheck_comp $prodir'/procheck_comp.scr'
  alias procheck_nmr  $prodir'/procheck_nmr.scr'
-diff -uNr procheck/setup.sh procheck.new/setup.sh
 procheck/setup.sh  Wed Jan 10 08:27:00 2001
-+++ procheck.new/setup.sh  Tue Aug 31 07:38:45 2004
-@@ -8,7 +8,7 @@
+--- procheck/setup.sh   2005-12-12 20:07:07.0 -0500
 procheck/setup.sh.new   2005-12-12 20:05:40.0 -0500
+@@ -8,9 +8,9 @@
  
  # PROCHECK environments and aliases
  # -
@@ -91,3 +90,6 @@
 -alias procheck= $prodir'/procheck.scr'
 +alias procheck=$prodir'/procheck.scr'
  alias procheck_comp=$prodir'/procheck_comp.scr'
+ alias procheck_nmr=$prodir'/procheck_nmr.scr'
+ alias proplot=$prodir'/proplot.scr'
+

Index: procheck.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/procheck.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- procheck.info   11 Dec 2005 05:45:48 -  1.1
+++ procheck.info   13 Dec 2005 04:54:39 -  1.2
@@ -1,13 +1,13 @@
 Package: procheck
 Version: 3.5.4
-Revision: 1
+Revision: 2
 Maintainer: Jack Howarth [EMAIL PROTECTED]
 Source: ftp://ftp.biochem.ucl.ac.uk/pub/procheck/tar3_5/procheck.tar.Z
 Source-MD5: ce04de5542d6136694b2021cb5c06a27
 BuildDepends: g77
 PatchScript: sed 's|@PREFIX@|%p|g'  %a/%n.patch | patch -p1
 CompileScript: 
-#!/bin/sh
+#!/bin/sh -ev
 make all
 
 InstallScript: 
@@ -21,7 +21,6 @@
 chmod 755 %i/etc/profile.d/procheck.csh
 chmod 755 %i/etc/profile.d/procheck.sh
 
-PostInstScript: more %p/share/procheck/confid.doc
 Description: Protein Structure Validation Suite
 License: Restrictive
 Homepage: http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html



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dists/10.4-transitional/unstable/main/finkinfo/sci procheck.patch,1.2,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29326

Removed Files:
procheck.patch 
Log Message:
remove procheck.  No good deed goes unpunished

--- procheck.patch DELETED ---



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dists/10.4-transitional/unstable/main/finkinfo/sci procheck.info,1.2,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29425

Removed Files:
procheck.info 
Log Message:
remove procheck.  No good deed goes unpunished

--- procheck.info DELETED ---



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dists/10.4-transitional/unstable/main/finkinfo/sci apbs.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12446

Modified Files:
apbs.info 
Log Message:
apbs version upgrade

Index: apbs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- apbs.info   21 Nov 2005 03:31:58 -  1.2
+++ apbs.info   21 Dec 2005 06:00:28 -  1.3
@@ -1,24 +1,26 @@
 Package: apbs
-Version: 0.3.2
-Revision: 8
+Version: 0.4.0
+Revision: 1
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
-Source-MD5: b2a417c1d9c102157f45cf00fd0ae196 
+Source-MD5: a9d5f8b24a40087998267c9df3eecceb 
 SourceDirectory: %n-%v
-Depends: maloc, readline-shlibs, gnuplot
-BuildDepends: g77, maloc
+Depends: maloc, readline-shlibs, gnuplot, python, pdb2pqr 
+BuildDepends: g77, maloc, python 
 Conflicts: apbs-mpi
 Replaces: apbs-mpi
 ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib FETK_PREFIX=%p
 setCFLAGS: -I%p/include/maloc
+#setCFLAGS: -I%p/include/maloc -I%p/include/python2.4
 setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r)
 Description: Adaptive Poisson-Boltzmann Solver
 CompileScript: 
 #!/bin/zsh -f
+function python { /usr/bin/python $@ }
 
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
 ./configure %c --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib
 # perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
  perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
- perl -pi -e 's|python2|python|g' **/* 2/dev/null
+ perl -pi -e 's|python2 |python |g' **/* 2/dev/null
 make
 
 InstallScript: 
@@ -44,7 +46,6 @@
 echo 
+
 echo 
 sleep 5
-open http://agave.wustl.edu/apbs/download/
 
 Homepage: http://apbs.sourceforge.net/
 RunTimeVars: 



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dists/10.4-transitional/unstable/main/finkinfo/sci pdb2pqr.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12644

Added Files:
pdb2pqr.info 
Log Message:
ancilliary dependency for apbs

--- NEW FILE: pdb2pqr.info ---
Package: pdb2pqr
Version: 1.0.2
Revision: 1
Source: mirror:sourceforge:%n/%n-%v.tar.gz
Source-MD5: 4294713d22ae34079fcd4f652f2c793a 
SourceDirectory: %n-%v
Depends: python 
BuildDepends: g77, python
Description: Converts pdb files to pqr
CompileScript: 
#!/bin/zsh -ef
./configure %c 
 perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
 perl -pi -e 's|python2 |python |g' **/* 2/dev/null
make
rm -f **/*.o

InstallScript: 
#!/bin/zsh -ef
mkdir -p %i/share/pdb2pqr
cp -R * %i/share/pdb2pqr
mkdir -p %i/bin
ln -s %p/share/pdb2pqr/pdb2pqr.py %i/bin/pdb2pqr
ln -s %p/share/pdb2pqr/propka/propka %i/bin/propka

Homepage: http://pdb2pqr.sourceforge.net/
DescDetail: 
PDB2PQR is a Python software package that automates many of the common tasks
of preparing structures for continuum electrostatics calculations, providing
a platform-independent utility for converting protein files in PDB format to
PQR format. These tasks include: Adding a limited number of missing heavy
atoms to biomolecular structures Determining side-chain pKas Placing missing
hydrogens Optimizing the protein for favorable hydrogen bonding Assigning
charge and radius parameters from a variety of force fields PDB2PQR was
ported to Python by Todd Dolinsky while working with Nathan Baker at
Washington University in St. Louis. The PDB2PQR code is based on C++ design
and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to
facilitate structure preparation for APBS.  PDB2PQR uses PropKa to determine
protein pKa values. PropKa is developed by the Jensen Research Group at the
University of Iowa. More information about PropKa can be found at
http://propka.chem.uiowa.edu.  

License: GPL  
Maintainer: W. G. Scott [EMAIL PROTECTED]



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dists/10.4-transitional/unstable/main/finkinfo/sci apbs-mpi.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9025

Modified Files:
apbs-mpi.info 
Log Message:
apbs version upgrade

Index: apbs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs-mpi.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- apbs-mpi.info   21 Nov 2005 03:31:58 -  1.2
+++ apbs-mpi.info   22 Dec 2005 15:50:03 -  1.3
@@ -1,33 +1,36 @@
 Package: apbs-mpi
-Version: 0.3.2
-Revision: 9
+Version: 0.4.0
+Revision: 1
 Conflicts: apbs
 Replaces: apbs
 Source: http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-%v.tar.gz
-Source-MD5: b2a417c1d9c102157f45cf00fd0ae196 
+Source-MD5: a9d5f8b24a40087998267c9df3eecceb
+Source2: http://agave.wustl.edu/apbs/download/apbs-0.4.0/configure
+Source2-MD5: cd114bc8e4fcfa052cc6c3e69210d31c
 SourceDirectory: apbs-%v
 Depends: maloc-mpi, lammpi, readline-shlibs, gnuplot
 BuildDepends: g77, lammpi-dev, maloc-mpi
 ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib 
FETK_MPI_INCLUDE=%p/include FETK_MPI_LIBRARY=%p/lib FETK_PREFIX=%p
 setCFLAGS: -I%p/include/maloc
-setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r) -llam
+setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r) 
 Description: Adaptive Poisson-Boltzmann Solver
 CompileScript: 
-#!/bin/zsh -f
+#!/bin/zsh -ef
+cp ../configure .
 export FETK_INCLUDE=%p/include  
 export FETK_LIBRARY=%p/lib 
 export FETK_MPI_INCLUDE=%p/include 
 export FETK_MPI_LIBRARY=%p/lib 
 export FETK_PREFIX=%p
 
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
-./configure %c --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib 
--with-mpi
+ ./configure %c --with-blas=-L%p/lib -llammpio -llamf77mpi -lmpi -llam 
-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib --with-mpi --with-mpilib=%p/lib 
 --with-mpiinc=%p/include
 # perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
  perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
- perl -pi -e 's|python2|python|g' **/* 2/dev/null
+ perl -pi -e 's|python2 |python |g' **/* 2/dev/null
 make
 
 InstallScript: 
-#!/bin/zsh -f
+#!/bin/zsh -ef
 make install DESTDIR=%d
 rm -Rf **/CVS  # fink validate complains if this junk is left behind.
 mkdir -p %i/share/apbs



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dists/10.4-transitional/unstable/main/finkinfo/sci pymol-py.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9285

Modified Files:
pymol-py.info 
Log Message:
pymol with updated apbs plugin

Index: pymol-py.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pymol-py.info   12 Dec 2005 23:39:49 -  1.5
+++ pymol-py.info   22 Dec 2005 15:51:29 -  1.6
@@ -1,14 +1,16 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 0.98
-Revision: 4
+Revision: 5
 Maintainer: Jack Howarth [EMAIL PROTECTED]
 Type: python (2.2 2.3 2.4)
 Source: mirror:custom:pymol/pymol-0_98-src.tgz
 CustomMirror: 
 Primary: http://easynews.dl.sourceforge.net/sourceforge
 
-Source-MD5: 096cc1d06fa36eb1c8ad30560d06b81e
+Source-MD5: 096cc1d06fa36eb1c8ad30560d06b81e 
+Source2: http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py
+Source2-MD5: f9f97d1b5237609664febfff85cc395f
 SourceDirectory: pymol-%v
 Depends: python%type_pkg[python], libpng3-shlibs, numeric-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.2-1), freeglut-shlibs, blt-shlibs
 BuildDepends: libpng3, freeglut, db43-ssl|db43, readline (= 4.3-5), gdbm3, 
expat, tcltk-dev, blt
@@ -17,6 +19,7 @@
 PatchScript: sed 's|@FINKPREFIX@|%p|g' %a/pymol-py.patch | sed 
's|python2.X|python%type_raw[python]|g' | sed 
's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1
 CompileScript: 
 (cd setup; cp Rules.osx-fink %b/Rules.make)
+cp ../apbs_tools.py modules/pmg_tk/startup/. 
 make
 
 InstallScript: 



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dists/10.4-transitional/unstable/main/finkinfo/sci pdb2pqr.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13224

Modified Files:
pdb2pqr.info 
Log Message:
ancilliary dependency for apbs, revised

Index: pdb2pqr.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- pdb2pqr.info21 Dec 2005 06:01:37 -  1.1
+++ pdb2pqr.info23 Dec 2005 08:07:17 -  1.2
@@ -1,17 +1,22 @@
 Package: pdb2pqr
 Version: 1.0.2
-Revision: 1
+Revision: 3
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 4294713d22ae34079fcd4f652f2c793a 
 SourceDirectory: %n-%v
-Depends: python 
-BuildDepends: g77, python
+BuildDepends: g77
 Description: Converts pdb files to pqr
+NoSetCPPFLAGS: true
+NoSetLDFLAGS: true
+SetLDFLAGS: -F/System/Library/Frameworks/Python.framework
+ConfigureParams: py_path=/usr/bin/python2.3
 CompileScript: 
 #!/bin/zsh -ef
-./configure %c 
- perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
- perl -pi -e 's|python2 |python |g' **/* 2/dev/null
+ PATH=/usr/bin:$PATH
+ perl -pi.bak -e 's|python2.2|python2.3|g' **/* 2/dev/null
+ perl -pi.bak -e 's|python2 |python2.3 |g' **/* 2/dev/null
+ perl -pi.bak -e s|/usr/bin/python2.3|/usr/bin/python|g **/*.py 2/dev/null
+py_path=/usr/bin/python2.3 
LDFLAGS=-F/System/Library/Frameworks/Python.framework  ./configure
 make
 rm -f **/*.o
 



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dists/10.4-transitional/unstable/main/finkinfo/sci apbs-mpi.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24925

Modified Files:
apbs-mpi.info 
Log Message:
apbs-mpi version upgrade, adding py_path=/usr/bin/python2.3

Index: apbs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs-mpi.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- apbs-mpi.info   23 Dec 2005 08:15:34 -  1.4
+++ apbs-mpi.info   24 Dec 2005 16:52:23 -  1.5
@@ -1,6 +1,6 @@
 Package: apbs-mpi
 Version: 0.4.0
-Revision: 2
+Revision: 3
 Conflicts: apbs
 Replaces: apbs
 Source: http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-%v.tar.gz
@@ -10,7 +10,7 @@
 SourceDirectory: apbs-%v
 Depends: maloc-mpi, lammpi, readline-shlibs, gnuplot
 BuildDepends: g77, lammpi-dev, maloc-mpi
-ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib 
FETK_MPI_INCLUDE=%p/include FETK_MPI_LIBRARY=%p/lib FETK_PREFIX=%p
+ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib 
FETK_MPI_INCLUDE=%p/include FETK_MPI_LIBRARY=%p/lib FETK_PREFIX=%p 
py_path=/usr/bin/python2.3
 setCFLAGS: -I%p/include/maloc
 setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r) 
 Description: Adaptive Poisson-Boltzmann Solver
@@ -24,7 +24,7 @@
 export FETK_MPI_LIBRARY=%p/lib 
 export FETK_PREFIX=%p
 
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
- ./configure %c --with-blas=-L%p/lib -llammpio -llamf77mpi -lmpi -llam 
-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib --with-mpi --with-mpilib=%p/lib 
 --with-mpiinc=%p/include
+py_path=/usr/bin/python2.3  ./configure %c --with-blas=-L%p/lib -llammpio 
-llamf77mpi -lmpi -llam -L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib 
--with-mpi --with-mpilib=%p/lib  --with-mpiinc=%p/include
 # perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
  perl -pi -e 's|python2.2|python|g' **/* 2/dev/null
  perl -pi -e 's|python2 |python |g' **/* 2/dev/null



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dists/10.4-transitional/unstable/main/finkinfo/sci apbs.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24996

Modified Files:
apbs.info 
Log Message:
apbs version upgrade, adding py_path=/usr/bin/python2.3

Index: apbs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- apbs.info   23 Dec 2005 08:13:21 -  1.4
+++ apbs.info   24 Dec 2005 16:53:14 -  1.5
@@ -1,6 +1,6 @@
 Package: apbs
 Version: 0.4.0
-Revision: 2
+Revision: 3
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: a9d5f8b24a40087998267c9df3eecceb 
 SourceDirectory: %n-%v
@@ -8,7 +8,7 @@
 BuildDepends: g77, maloc
 Conflicts: apbs-mpi
 Replaces: apbs-mpi
-ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib FETK_PREFIX=%p
+ConfigureParams: FETK_INCLUDE=%p/include  FETK_LIBRARY=%p/lib FETK_PREFIX=%p 
py_path=/usr/bin/python2.3
 setCFLAGS: -I%p/include/maloc
 setLDFLAGS: -L%p/lib/powerpc-apple-darwin$(uname -r)
 Description: Adaptive Poisson-Boltzmann Solver
@@ -16,7 +16,7 @@
 #!/bin/zsh -ef
 PATH=/usr/bin:$PATH
 
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
-./configure %c --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib
+py_path=/usr/bin/python2.3 ./configure %c --with-blas=-L${BLAS_DIR} -lblas 
-Wl,-framework -Wl,vecLib
 # perl -pi.bak -e 's|\-L%p/lib|\-lcc_dynamic \-L%p/lib|g' **/Makefile
  perl -pi.bak -e 's|python2.2|python|g' **/* 2/dev/null
  perl -pi.bak -e 's|python2 |python |g' **/* 2/dev/null



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dists/10.4-transitional/unstable/main/finkinfo/sci molmol.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31000

Modified Files:
molmol.info 
Log Message:
molmol 10.4-transitional sci unstable -- removed dead mirror, cleaned up 
install, freeglut dependeny

Index: molmol.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- molmol.info 14 Jun 2005 21:33:30 -  1.4
+++ molmol.info 25 Dec 2005 05:43:11 -  1.5
@@ -1,17 +1,17 @@
 Package: molmol
 Version: 2k.2.0
-Revision: 20
+Revision: 31
 CustomMirror: 
  eur-CH: ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/
- nam-US: ftp://freedom7.swmed.edu/pub/software/MOLMOL/
+# nam-US: ftp://freedom7.swmed.edu/pub/software/MOLMOL/
 
 Source: mirror:custom:unix-gzip/%n-%v-src.tar.gz
 Source-MD5: e1f4416d8041a67fa08cadb03ed91c7c
 SourceDirectory: ../%f
 Source2: mirror:custom:unix-gzip/%n-%v-doc.tar.gz
 Source2-MD5: 517545b60b0179ab691a679ed29903a7
-Depends: x11, glut-shlibs, openmotif3-shlibs, libtiff-shlibs, libjpeg-shlibs, 
libpng3-shlibs
-BuildDepends: glut, openmotif3-shlibs, openmotif3, libtiff, libjpeg, libpng3, 
x11-dev, gcc3.3
+Depends: x11, freeglut-shlibs, openmotif3-shlibs, libtiff-shlibs, 
libjpeg-shlibs, libpng3-shlibs
+BuildDepends: freeglut, openmotif3-shlibs, openmotif3, libtiff, libjpeg, 
libpng3, x11-dev, gcc3.3
 PatchScript: 
 chmod -R +w *
 sed 's|@PREFIX@|%p|g' %a/%n.patch | patch -p1
@@ -20,6 +20,8 @@
 make
 
 InstallScript: 
+#!/bin/zsh -ef
+ /bin/rm -f **/*.o **/*.c
  mkdir -p %i/share/molmol
  cp -R * %i/share/molmol/.
  mkdir -p %i/bin



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dists/10.4-transitional/unstable/main/finkinfo/sci infernal.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23969

Modified Files:
infernal.info 
Log Message:
infernal version upgrade

Index: infernal.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/infernal.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- infernal.info   27 Apr 2005 03:26:22 -  1.1
+++ infernal.info   25 Dec 2005 21:39:15 -  1.2
@@ -1,11 +1,13 @@
 Package: infernal
-Version: 0.55
-Revision: 10
+Version: 0.7 
+Revision: 1
 Source:  ftp://ftp.genetics.wustl.edu/pub/eddy/software/%n/%n.tar.gz
-Source-MD5: 84b71405f458185d388a467c7a865b8f
+Source-MD5: 092602a4ce64b0595f8e69a46955d9c4
+SourceRename: %n-%v.tar.gz
 SourceDirectory: %n-%v
+GCC: 3.3
 CompileScript:  
-./configure --prefix=%i
+CXX=g++-3.3 CC=gcc-3.3 ./configure --prefix=%i
 make
 
 InstallScript: 



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dists/10.4-transitional/unstable/main/finkinfo/sci chooch.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29271

Added Files:
chooch.info 
Log Message:
new package chooch for determination of Xray anom. scattering factors

--- NEW FILE: chooch.info ---
Package: chooch 
Version: 5.0.2
Revision: 1
Source: ftp://ftp.ccp4.ac.uk/chooch/current/packed/chooch.tar.gz
Source-MD5: fbb9ca11264f003eacc62358f3e8f5c6   
SourceDirectory: chooch
Depends: gsl (= 1.1 ), cgraph, pgplot
BuildDepends: gsl (= 1.1 ), cgraph, pgplot
SetLDFLAGS: -L%p/lib/pgplot
CompileScript: 
#!/bin/zsh -ef
cd %n-%v
./configure --prefix=%p  --with-gsl-prefix=%p --with-cgraph-prefix=%p 
--with-pgplot-prefix=%p --mandir=%p/share/man
make

InstallScript: 
#!/bin/zsh -ef
cd %n-%v
make install DESTDIR=%d

Maintainer: W. G. Scott [EMAIL PROTECTED]
License: GPL
Description: Anomalous f' and f from Xray flourescence
DescDetail: 
One of the most successful methods of structure determination over the last
15 years has been the MAD (multiple wavelength anomalous diffraction)
method. A key step in MAD experiments is the determination of the
absorption edge structure in order to allow the correct selection of
appropriate X-ray energies for data collection. The program CHOOCH
determines values of anomalous scattering factors from raw fluorescence
spectra and pinpoints the position of the f'' maximum and the f' minumum
values.

Homepage: http://www.gwyndafevans.co.uk/



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dists/10.4-transitional/unstable/main/finkinfo/sci cgraph.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29416

Added Files:
cgraph.info 
Log Message:
cgraph is a dependency for previously added package chooch

--- NEW FILE: cgraph.info ---
Package: cgraph
Version: 2.04 
Revision: 1
Source: ftp://ftp.ccp4.ac.uk/chooch/current/packed/chooch.tar.gz
Source-MD5: fbb9ca11264f003eacc62358f3e8f5c6   
SourceDirectory: chooch
BuildDependsOnly: false
CompileScript: 
#!/bin/zsh -ef
cd %n-%v
./configure --prefix=%p
make

InstallScript: 
#!/bin/zsh -ef
cd %n-%v
make install DESTDIR=%d

Maintainer: W. G. Scott [EMAIL PROTECTED]
License: Public Domain
Description: Postscript plotting library in C
DescDetail: 
This is a C source code library that contains a set of C functions that
generate PostScript for publication quality scientific plots. It is
possible to launch Preview.app automatically on generated PS/EPS files. The
Cgraph Library source code, examples, and documentation are in the public
domain.  Why do we want something like this, when Mac and Windows apps can
finally produce nice plots? Those GUI apps are OK for small number of
plots, but if you ever need to plot tens or hundreds of similarly formatted
graphs fast, GUIs become very tedius. Also, if you need to generate plots
automatically, e.g., those stock price charts updated every tens of minutes
available from some Web sites, a program that incorporates this library may
be used to generate EPS files from current data, which can be piped into
Ghostscript (or DPS) to update GIF images without manual intervention.

Homepage: http://neurovision.berkeley.edu/software/A_Cgraph.html



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dists/10.4-transitional/unstable/main/finkinfo/sci chooch.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30180

Modified Files:
chooch.info 
Log Message:
added dependency on g77

Index: chooch.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/chooch.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- chooch.info 26 Dec 2005 05:22:04 -  1.1
+++ chooch.info 26 Dec 2005 05:30:20 -  1.2
@@ -5,7 +5,7 @@
 Source-MD5: fbb9ca11264f003eacc62358f3e8f5c6   
 SourceDirectory: chooch
 Depends: gsl (= 1.1 ), cgraph, pgplot
-BuildDepends: gsl (= 1.1 ), cgraph, pgplot
+BuildDepends: gsl (= 1.1 ), cgraph, pgplot, g77
 SetLDFLAGS: -L%p/lib/pgplot
 CompileScript: 
 #!/bin/zsh -ef



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dists/10.4-transitional/unstable/main/finkinfo/sci ssmlib.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31473

Modified Files:
ssmlib.info 
Log Message:
ssmlib version upgrade

Index: ssmlib.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ssmlib.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- ssmlib.info 27 Apr 2005 03:26:24 -  1.1
+++ ssmlib.info 26 Dec 2005 05:42:15 -  1.2
@@ -1,17 +1,18 @@
 Package: ssmlib
-Version: 0.0-pre-1-ysbl
-Revision: 2
+Version: 0.1
+Revision: 3
 BuildDepends: mmdb
+BuildDependsOnly: false
 Depends: mmdb
 Replaces: libssm
-Source: http://www.ysbl.york.ac.uk/~emsley/software/extras/SSMlib-%v.tar.gz
-Source-MD5: 7e8ed12c0055104ab0e8ec3ae733f373
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/SSMlib-0.0-pre-1.tar.gz
+Source-MD5: 29e6ac40c6c9294689d93df1518e57ed
 NoSetLDFLAGS: true 
 ConfigureParams: --with-mmdb-prefix=%p
 DocFiles: README AUTHORS NEWS COPYING 
-Description: CCP4 Macromolecular ssm Library
+Description: CCP4 sequence matching library
 DescDetail: 
-MMDB is CCP4's Macromolecular smm Library written by Eugene
+SSM is CCP4's Macromolecular smm Library written by Eugene
 Krissinel at the EBI.
 
 # PatchScript:  perl -pi.bak -e 's/include malloc.h//g' **/*.c



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dists/10.4-transitional/unstable/main/finkinfo/sci coot.info,1.6,1.7

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10081

Modified Files:
coot.info 
Log Message:
coot minor version upgrade

Index: coot.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- coot.info   14 Dec 2005 09:20:24 -  1.6
+++ coot.info   26 Dec 2005 07:28:37 -  1.7
@@ -1,12 +1,13 @@
 Package:coot
-Version: 0.0.33
-Revision: 2
-BuildDepends: clipper (= cvs-14-nov-2003-10), glib, gtk+2, glut, gtkglarea, 
guile16, guile16-dev, gsl, libglade2,  gtk-canvas (= 0.1.1-20), libart2 (= 
2.3.16-2), libart2-shlibs (= 2.3.16-2), guile16-net-http, glut, gtk+2-dev, 
libgettext3-dev, imlib, libjpeg, libtiff, giflib, libpng3, gnome-libs-dev, 
fftw, libiconv-dev
-Depends: clipper(= cvs-14-nov-2003-10), guile16-shlibs, gtk-canvas (= 
0.1.1-20), gsl-shlibs, libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, 
guile16-goosh (= 1.3-2), ssmlib, guile16, guile16-net-http, glut-shlibs
+Version: 0.0.34
+Revision: 1
+BuildDepends: clipper (= cvs-14-nov-2003-3-1), glib, gtk+2, freeglut, 
gtkglarea, guile16, guile16-dev, gsl, libglade2,  gtk-canvas (= 0.1.1-20), 
libart2 (= 2.3.16-2), libart2-shlibs (= 2.3.16-2), guile16-net-http, 
clipper-dev,  ssmlib (= 0.1)
+Depends: clipper(= cvs-14-nov-2003-3-1), guile16-shlibs, gtk-canvas (= 
0.1.1-20), gsl-shlibs, libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, 
guile16-goosh (= 1.3-2), ssmlib (= 0.1), guile16, guile16-net-http, 
freeglut-shlibs, libart2-shlibs (= 2.3.16-2)
 BuildDependsOnly: false
 NoSetLDFLAGS: true
-Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 22b87da19a1156f281844c84cd9b8375 
+Source: http://chemistry.ucsc.edu/~wgscott/xtal/coot/%n-%v.tar.gz
+Source-MD5: ee3edc81eb3e4982affabf4caaaf4c36 
+SourceDirectory: %n-%v-pre-1
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: c7aa4ee8861d7e82df985fe2eb39c289
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz



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dists/10.4-transitional/unstable/main/finkinfo/sci clipper.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16048

Modified Files:
clipper.info 
Log Message:
newer clipper version I forgot to add

Index: clipper.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- clipper.info22 Jun 2005 12:23:14 -  1.3
+++ clipper.info27 Dec 2005 05:31:51 -  1.4
@@ -1,11 +1,11 @@
 Package:clipper
-Version: cvs-14-nov-2003
-Revision: 10
+Version: cvs-14-nov-2003-3
+Revision: 1
 GCC: 3.3
-BuildDepends: fftw | fftw-mpi, mmdb (= 1.0.8-ysbl), mccp4  
-Depends: mmdb (= 1.0.8-ysbl), mccp4, fftw-shlibs | fftw-mpi-shlibs
-Source: http://www.ysbl.york.ac.uk/~emsley/software/extras/%n.%v.tar.gz
-Source-MD5: 8a2eceb75d7aa149ca9d02b2708acac3
+BuildDepends: fftw | fftw-mpi, mmdb (= 1.0.8-ysbl), mccp4 , ssmlib (= 0.1) 
+Depends: mmdb (= 1.0.8-ysbl), mccp4, fftw-shlibs | fftw-mpi-shlibs, ssmlib 
(= 0.1)
+Source: http://www.ysbl.york.ac.uk/~emsley/software/extras/%n-%v.tar.gz
+Source-MD5: fd6ca97bcf9e5e6a8104ef69b74b11c2
 SourceDirectory: %n
 DocFiles: README AUTHORS NEWS COPYING 
 Description: Object-oriented crystallographic libraries



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dists/10.4-transitional/unstable/main/finkinfo/games mathwar.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/games
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18707

Added Files:
mathwar.info 
Log Message:
mathwar is a cheesy arithmetic flashcard game for kids

--- NEW FILE: mathwar.info ---
Package: mathwar
Version: 0.2.4
Revision: 1
Source: http://webpages.charter.net/stuffle/%n/download/files/MathWar-%v.tar.gz
Source-MD5: 2acd3214ec458c555f559b78b83cbf31  
SourceDirectory: MathWar-%v
Depends: x11-shlibs, gnome-libs-shlibs, orbit-shlibs, glib-shlibs (= 1.2.0), 
gtk+-shlibs, gdk-pixbuf-shlibs, imlib-shlibs, libexif-shlibs, 
libgettext3-shlibs, audiofile-shlibs, esound-shlibs, libiconv
BuildDepends: x11-dev, gnome-libs-dev, orbit-dev, glib (= 1.2.0), gtk+ (= 
1.2.0), gettext-tools, gdk-pixbuf, imlib, libexif-dev, libgettext3-dev, esound, 
audiofile, libiconv-dev
License: GPL
Maintainer: W. G. Scott [EMAIL PROTECTED]
Description: Simple flash-card type math game for kids
DescDetail:  
MathWar is a stand-alone, gnome-based, math flash card game for children,
originally developed for the Linux platform. To read the manual, type

open %p/share/gnome/help/MathWar/C/manual.html

MathWar is more or less like playing with flash cards, with the exception
that there is a computer player who can attempt to answer if the human
player is too slow. A game of MathWar consists of a set number of rounds. A
round consists of two cards and a mathematical operator (add, subtract, or
multiplication). The first player to guess an answer for a round gets that
rounds point if the guess is correct. Otherwise, the correct answer is
displayed, and no points are awarded. 

HomePage: http://webpages.charter.net/stuffle/mathwar/MathWar.html



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dists/10.4-transitional/unstable/main/finkinfo/sci gromacs.patch,NONE,1.1 gromacs.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17105a

Modified Files:
gromacs.info 
Added Files:
gromacs.patch 
Log Message:
gromacs version update and info file corrections

Index: gromacs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- gromacs.info20 Nov 2005 19:42:30 -  1.2
+++ gromacs.info1 Jan 2006 17:45:37 -   1.3
@@ -1,6 +1,6 @@
 Package: gromacs
 Version: 3.3
-Revision: 1
+Revision: 2
 Depends: %N-shlibs (= %v-%r), fftw3-shlibs, x11, openmotif3-shlibs
 BuildDepends: fftw3, x11-dev
 BuildDependsOnly: false
@@ -9,13 +9,17 @@
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
 Source-MD5: 99ea6f25a89f1511f51c350a66a2fdc4
-ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share 
+Patch: %n.patch
+ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share --with-external_lapack --with-external_blas
 DocFiles: AUTHORS COPYING README
 PatchScript: 
 #!/bin/zsh -f
 perl -pi.bak -e 's|/bin/csh|/bin/csh -f|g' share/**/* 2/dev/null
 perl -pi.bak -e 's|/lib/cpp|/usr/bin/cpp|g' share/**/* 2/dev/null
 
+CompileScript: 
+LIBS='/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib' 
./configure %c
+
 InstallScript: 
 mkdir -p %i/include/%n
 make install DESTDIR=%d 

--- NEW FILE: gromacs.patch ---
--- gromacs-3.3/configure.org   2005-12-16 21:31:28.0 -0500
+++ gromacs-3.3/configure   2005-12-16 21:32:55.0 -0500
@@ -2357,19 +2357,13 @@
 # Check whether --with-external_blas or --without-external_blas was given.
 if test ${with_external_blas+set} = set; then
   withval=$with_external_blas
-
-else
-  with_external_blas=no
-fi;
-
-
-if test with_external_blas = yes; then
   GMX_EXTERNAL_BLAS_TRUE=
   GMX_EXTERNAL_BLAS_FALSE='#'
 else
+  with_external_blas=no
   GMX_EXTERNAL_BLAS_TRUE='#'
   GMX_EXTERNAL_BLAS_FALSE=
-fi
+fi;
 
 
 
@@ -2377,19 +2371,13 @@
 # Check whether --with-external_lapack or --without-external_lapack was given.
 if test ${with_external_lapack+set} = set; then
   withval=$with_external_lapack
-
-else
-  with_external_lapack=no
-fi;
-
-
-if test with_external_lapack = yes; then
   GMX_EXTERNAL_LAPACK_TRUE=
   GMX_EXTERNAL_LAPACK_FALSE='#'
 else
+  with_external_lapack=no
   GMX_EXTERNAL_LAPACK_TRUE='#'
   GMX_EXTERNAL_LAPACK_FALSE=
-fi
+fi;
 
 
 



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dists/10.4-transitional/unstable/main/finkinfo/sci gromacs-mpi.info,1.2,1.3 gromacs-mpi.patch,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12084

Modified Files:
gromacs-mpi.info gromacs-mpi.patch 
Log Message:
gromacs mpi version upgrade

Index: gromacs-mpi.patch
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs-mpi.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gromacs-mpi.patch   20 Nov 2005 19:42:30 -  1.1
+++ gromacs-mpi.patch   4 Jan 2006 05:20:55 -   1.2
@@ -9,3 +9,49 @@
  LIBSUFFIX = @LIBSUFFIX@
  LIBTOOL = @LIBTOOL@
  LN_S = @LN_S@
+--- gromacs-3.3/configure.org  2005-12-16 21:31:28.0 -0500
 gromacs-3.3/configure  2005-12-16 21:32:55.0 -0500
+@@ -2357,19 +2357,13 @@
+ # Check whether --with-external_blas or --without-external_blas was given.
+ if test ${with_external_blas+set} = set; then
+   withval=$with_external_blas
+-
+-else
+-  with_external_blas=no
+-fi;
+-
+-
+-if test with_external_blas = yes; then
+   GMX_EXTERNAL_BLAS_TRUE=
+   GMX_EXTERNAL_BLAS_FALSE='#'
+ else
++  with_external_blas=no
+   GMX_EXTERNAL_BLAS_TRUE='#'
+   GMX_EXTERNAL_BLAS_FALSE=
+-fi
++fi;
+ 
+ 
+ 
+@@ -2377,19 +2371,13 @@
+ # Check whether --with-external_lapack or --without-external_lapack was given.
+ if test ${with_external_lapack+set} = set; then
+   withval=$with_external_lapack
+-
+-else
+-  with_external_lapack=no
+-fi;
+-
+-
+-if test with_external_lapack = yes; then
+   GMX_EXTERNAL_LAPACK_TRUE=
+   GMX_EXTERNAL_LAPACK_FALSE='#'
+ else
++  with_external_lapack=no
+   GMX_EXTERNAL_LAPACK_TRUE='#'
+   GMX_EXTERNAL_LAPACK_FALSE=
+-fi
++fi;
+ 
+ 
+ 

Index: gromacs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs-mpi.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- gromacs-mpi.info20 Nov 2005 19:42:30 -  1.2
+++ gromacs-mpi.info4 Jan 2006 05:20:55 -   1.3
@@ -1,8 +1,8 @@
 Package: gromacs-mpi
 Version: 3.3
-Revision: 1
+Revision: 2
 Depends: gromacs (= %v-%r), %N-shlibs (= %v-%r), fftw3-shlibs, x11, 
openmotif3-shlibs, lammpi (= 7.0.6-11)
-BuildDepends: fftw3, x11-dev, lammpi-dev (= 7.0.6-11)
+BuildDepends: fftw3, x11-dev, lammpi-dev (= 7.0.6-11), gromacs-dev (= %v-%r)
 BuildDependsOnly: false
 Source: mirror:custom:gromacs-%v.tar.gz
 Patch: %n.patch
@@ -10,10 +10,10 @@
  Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
 Source-MD5: 99ea6f25a89f1511f51c350a66a2fdc4
-ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share  --enable-mpi --program-suffix=_mpi
+ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share  --enable-mpi --program-suffix=_mpi --with-external-blas 
--with-external-lapack
 DocFiles: AUTHORS COPYING README
 CompileScript: 
-  ./configure %c
+  LIBS='/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib' 
./configure %c
   make mdrun
 
 InstallScript: 



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dists/10.4-transitional/unstable/main/finkinfo/sci eden.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12224

Modified Files:
eden.info 
Log Message:
eden packaging revision to use system python

Index: eden.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/eden.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- eden.info   14 Jun 2005 21:46:52 -  1.3
+++ eden.info   4 Jan 2006 05:22:04 -   1.4
@@ -1,12 +1,12 @@
 Package: eden
 Version: 5.3
-Revision: 4
+Revision: 5
 Source: http://www.edencrystallography.org/%n_V%v.tar.gz
 SourceRename: %n-%v.tar.gz
 Source-MD5: 17f4908db1944d788bac44e59c8a5cb5 
 SourceDirectory: eden
-Depends: x11, fftw-shlibs | fftw-mpi-shlibs, tcltk, grace, python, gsl-shlibs
-BuildDepends: tcltk-dev, x11-dev, gsl, fftw | fftw-mpi, gsl
+Depends: x11, fftw-shlibs | fftw-mpi-shlibs, grace, gsl-shlibs
+BuildDepends: x11-dev, gsl, fftw | fftw-mpi, gsl
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 Patch: %n.patch
@@ -17,20 +17,20 @@
 perl -pi.bak -e 's|mozilla|open|g' python/eden.py
 
 CompileScript:  
- cd source; make
+PATH=/usr/bin:$PATH ; cd source; make
 
 InstallScript: 
 #!/bin/zsh -f
- mkdir -p %i/bin
-cd source; make install
+mkdir -p %i/bin
+PATH=/usr/bin:$PATH ; cd source; make install
 make clean
 perl -pi.bak -e 's|DOUBLESWITCH = ON|DOUBLESWITCH  = OFF|g' Makefile
-make; make install; make clean
+PATH=/usr/bin:$PATH ; make; make install; make clean
 cd ..
- mkdir -p %i/share/xtal/%n
- cp -R * %i/share/xtal/%n/.
- mkdir -p %i/share/doc/%n
- cp manual/UserManual.pdf %i/share/doc/%n/EdenUserManual.pdf
+mkdir -p %i/share/xtal/%n
+cp -R * %i/share/xtal/%n/.
+mkdir -p %i/share/doc/%n
+cp manual/UserManual.pdf %i/share/doc/%n/EdenUserManual.pdf
 rm -f %i/bin/eden
 rm -f %i/bin/ieden
 ln -s %p/share/xtal/%n/python/%n.py %i/bin/ieden
@@ -48,7 +48,7 @@
 eden or seden to invoke single-precision eden, ieden for the GUI,
 and deden for double-precision eden.  GUI users need to define the
 environment variable EDITOR, eg:  export EDITOR='see'
-or setenv EDITOR vim .
+or setenv EDITOR vim.
 
 License: GPL  
 Homepage: http://www.edencrystallography.org



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dists/10.4-transitional/unstable/main/finkinfo/sci ccp4-onlylibs-dev.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13779

Added Files:
ccp4-onlylibs-dev.info 
Log Message:
package to permit replacing clipper, mccp4, mmdb, ssmlib as coot dependencies

--- NEW FILE: ccp4-onlylibs-dev.info ---
Package: ccp4-onlylibs-dev
# Use version numbering to sync with the current CCP4 release:
Version: 5.99.5
Revision: 1
Source: ftp://ftp.ccp4.ac.uk/prerelease/%n.tar.gz
Source-MD5: 2346cd87b1a3480d048221e2a41606c7   
SourceRename: %n-%v.tar.gz
SourceDirectory: %n
Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
Source2-MD5: ea307964e3786bef0868ea560471
Depends:  
BuildDepends: g77 (= 3.4.0-2), f2c, fort77 
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
###
PatchScript: 
#!/bin/zsh -ef
umask 0022
# Use my patched configure and ccp4.setup-zsh files
cp ../ccp4.setup-zsh include/.
cp ../configure .
# setup scripts for tcsh, zsh and bash users
export TEMPXTAL=$PWD:h
#
perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup*   
# build prefix (changed in install)
perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*
# location of tcktk, blt (not needed here, but doesn't hurt).
perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*   
# same
# make copy for tcsh users (CCP4 convention is no suffix)
cp include/ccp4.setup-dist include/ccp4.setup
#
# We need the mmdbold clipper libraries built for COOT:
perl -pi.bak -e 's|enable_mmdbold=no|enable_mmdbold=yes|g' 
lib/clipper/configure*
# clean up:
rm -f  include/*.bak lib/clipper/*.bak

###
CompileScript: 
#!/bin/zsh -f
umask 0022
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
#
FLIBS=-L%p/lib -lg2c LDFLAGS=-L/usr/lib -lg2c -lSystemStubs -L%p/lib 
FC=%p/bin/g77 CXX=/usr/bin/g++-3.3 CC=/usr/bin/gcc configure --onlylibs 
Darwin
#
#  fix some post-configure bugs
#
make -i 2../make.log  |tee ../make.log  
make -i install 2../makeinst.log  |tee ../makeinst.log  
#
echo Ignoring error messages.  They are harmless
#
command ls -1 lib/*.a
sleep 10
#
# Check to make sure all the libraries we need were built:
# (Sort real errors from the bogus ones we suppressed.)

if (( $(command ls -1 lib/*.a | command wc -l) == 15 ));then 
print Build appears to have succeeded.
else
print *
print   Build has failed:
print *
sleep 3
cat ../make.log  ../makeinst.log
return 1
fi

#
make realclean

###
InstallScript: 
#!/bin/zsh -f
umask 0022
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
ORIGDIR=$(dirname $PWD)
#
# Change environment scripts to match final installation install prefix:
 perl -pi.bak -e 's|\$TEMPXTAL|%p/share/xtal|g' include/ccp4.setup* 
 
 perl -pi.bak -e 's|CCP4_MASTER/%n|CCP4_MASTER/%n-%v|g' include/ccp4.setup-zsh
 perl -pi.bak -e 's|ccp4-5.99.5|%n-%v|g'include/ccp4.setup*
 rm -f include/*.bak
 perl -pi.bak -e 's|src/fink.build/%n-%v-%r/%n|share/xtal/%n-%v|g' 
bin/clipper-config 
 rm -f bin/clipper-config.bak   
   
 perl -pi.bak -e 's|/src/fink.build/%n-%v-%r/%n/lib|/share/xtal/%n-%v/lib|g' 
lib/*.la
 rm -f lib/*.la.bak
#
# Now install:
 mkdir -p %i/share/xtal/%n-%v
 cp -R * %i/share/xtal/%n-%v/.
 ranlib %i/share/xtal/%n-%v/lib/**/*.a

###
Description: CCP4 Libraries
DescDetail: 
This package installs CCP4 libraries, only.  If you need all 
of CCP4, install the self-contained CCP4 package instead of this.
The licensing for the CCP4 library loosely conforms to the LGPL,
unlike the more restrictive CCP4 license.

This version compiles with the Apple Lapack/Blas framework

CCP4lib files will be installed under 
%p/share/xtal/ccp4-onlylibs-dev-5.99.5.

Programs requiring these libraries to build or run need to
source the appropriate
%p/share/xtal/ccp4-onlylibs-dev-5.99.5/include/ccp4.setup
file for the shell, as is done in the coot.info file.

The primary use for this package, currently, is for compiling COOT.

DocFiles: conditions.txt 
Homepage: http://www.ccp4.ac.uk  
License: Restrictive
Maintainer: W. G. Scott [EMAIL PROTECTED]



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dists/10.4-transitional/unstable/main/finkinfo/sci ccp4-onlylibs-dev.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6571

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
added GCC: 3.3 field that I had inadvertantly omitted

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- ccp4-onlylibs-dev.info  4 Jan 2006 07:32:06 -   1.2
+++ ccp4-onlylibs-dev.info  4 Jan 2006 22:53:22 -   1.3
@@ -8,6 +8,7 @@
 SourceDirectory: %n
 Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
 Source2-MD5: ea307964e3786bef0868ea560471
+GCC: 3.3
 Depends:  
 BuildDepends: g77 (= 3.4.0-2), f2c, fort77 
 NoSetCPPFLAGS: true
@@ -38,7 +39,7 @@
 
 ###
 CompileScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -f
 umask 0022
 export TEMPXTAL=$PWD:h
 source include/ccp4.setup-zsh
@@ -75,7 +76,7 @@
 
 ###
 InstallScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -f
 umask 0022
 export TEMPXTAL=$PWD:h
 source include/ccp4.setup-zsh



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dists/10.4-transitional/unstable/main/finkinfo/sci ccp4-onlylibs-dev.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9344

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
re-restore the -e flags

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- ccp4-onlylibs-dev.info  4 Jan 2006 22:53:22 -   1.3
+++ ccp4-onlylibs-dev.info  4 Jan 2006 23:02:08 -   1.4
@@ -39,7 +39,7 @@
 
 ###
 CompileScript: 
-#!/bin/zsh -f
+#!/bin/zsh -ef
 umask 0022
 export TEMPXTAL=$PWD:h
 source include/ccp4.setup-zsh
@@ -76,7 +76,7 @@
 
 ###
 InstallScript: 
-#!/bin/zsh -f
+#!/bin/zsh -ef
 umask 0022
 export TEMPXTAL=$PWD:h
 source include/ccp4.setup-zsh



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dists/10.4-transitional/unstable/main/finkinfo/sci coot.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2952

Modified Files:
coot.info 
Log Message:
coot version upgrade

Index: coot.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- coot.info   14 Jan 2006 00:42:19 -  1.10
+++ coot.info   16 Jan 2006 05:40:42 -  1.11
@@ -1,53 +1,67 @@
 Package:coot
-Version: 0.0.34
+Version: 0.1.0-pre-1
 Revision: 1
-GCC: 3.3
-BuildDepends: clipper (= cvs-14-nov-2003-3-1), glib, gtk+2, freeglut, 
gtkglarea, guile16, guile16-dev, gsl, libglade2,  gtk-canvas (= 0.1.1-20), 
libart2 (= 2.3.16-2), libart2-shlibs (= 2.3.16-2), guile16-net-http, 
clipper-dev,  ssmlib (= 0.1), gtk+2-dev, libgettext3-dev, imlib, libjpeg, 
giflib, libpng3, gnome-libs-dev, fftw, libiconv-dev
-Depends: clipper(= cvs-14-nov-2003-3-1), guile16-shlibs, gtk-canvas (= 
0.1.1-20), gsl-shlibs, libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, 
guile16-goosh (= 1.3-2), ssmlib (= 0.1), guile16, guile16-net-http, 
freeglut-shlibs, libart2-shlibs (= 2.3.16-2)
-BuildDependsOnly: false
-NoSetLDFLAGS: true
+GCC: 3.3 
+#Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz
 Source: http://chemistry.ucsc.edu/~wgscott/xtal/coot/%n-%v.tar.gz
-Source-MD5: ee3edc81eb3e4982affabf4caaaf4c36 
-SourceDirectory: %n-%v-pre-1
+Source-MD5: 94fe4c4af6ae1acfa59f36393fa34aa9
+SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: c7aa4ee8861d7e82df985fe2eb39c289
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e
-DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
+###
+BuildDepends: ccp4-onlylibs-dev, glib, gtk+2, freeglut, gtkglarea, guile16, 
guile16-dev, gsl, libglade2,  gtk-canvas (= 0.1.1-20), libart2 (= 2.3.16-2), 
libart2-shlibs (= 2.3.16-2), guile16-net-http, gtk+2-dev, libgettext3-dev, 
imlib, libjpeg, giflib, libpng3, gnome-libs-dev, fftw, libiconv-dev
+#
+Depends: guile16-shlibs, gtk-canvas (= 0.1.1-20), gsl-shlibs, 
libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, guile16-goosh (= 
1.3-2), guile16, guile16-net-http, freeglut-shlibs, libart2-shlibs (= 2.3.16-2)
+#
+BuildDependsOnly: false
+NoSetLDFLAGS: true
+###
 Description: Crystallographic molecular graphics
 DescDetail: 
-Coot stands for Crystallograhic Object Oriented Toolkit.  
-It is a testbest toolkit for (Protein) Crystallography.  
-Coot uses professional (and free) widgets (with
-the gui builder glade), mmdb, clipper, and OpenGL, together with a new
-approach to map contouring and importing/creation and other
-(modelling) operations.
+Coot stands for Crystallograhic Object Oriented Toolkit. It is a testbest 
+toolkit for (Protein) Crystallography. Coot uses professional (and free) 
+widgets (with the gui builder glade), mmdb, clipper, and OpenGL, together 
+with a new approach to map contouring and importing/creation and other
+(modelling) operations. The mmdb, clipper, ssm and mccp4 libraries are now
+provided in the ccp4-onlylibs-dev fink package.
 
+###
 PatchScript:  
 #!/bin/zsh -ef
 perl -pi.bak -e 's|use-modules \(goosh\)|use-modules \(goosh goosh\)|g' 
scheme/coot-utils.scm
-#
 perl -pi.bak -e 's/include malloc.h//g' **/*.c
-#
-# Fix configure file lines 10619 and 10626
-#
-perl -pi.bak -e 's|core -lmccp4 \$MMDB_LIBS -lrfftw -lfftw -lz -lm|core 
-lmccp4 \$MMDB_LIBS -lsrfftw -lsfftw -lz -lm|g' configure
 
-ConfigureParams: --with-mmdb-prefix=%p --with-clipper-prefix=%p 
--with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 --with-gtkcanvas-prefix=%p 
--with-ssmlib-prefix=%p --with-imlib-prefix=%p --with-gtkgl-prefix=%p 
--with-glib-prefix=%p --with-gsl-prefix=%p --with-guile
+###
+ConfigureParams:  --with-mmdb-prefix=$CCP4  --with-clipper-prefix=$CCP4 
--with-fftw=$CCP4 --with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 
--with-gtkcanvas-prefix=%p --with-ssmlib-prefix=$CCP4  --with-imlib-prefix=%p 
--with-gtkgl-prefix=%p --with-glib-prefix=%p --with-gsl-prefix=%p --with-guile
+###
 CompileScript: 
 #!/bin/zsh -ef
-export LD_LIBRARY_PATH=
-export DYLD_LIBRARY_PATH=
+source %p/share/xtal/ccp4-onlylibs-dev-5.99.5/include/ccp4.setup-zsh
 export PATH=%p/share/guile/1.6/scripts/binoverride:$PATH
+FLIBS=-L%p/lib \
+CPPFLAGS=-I$CCP4/lib/clipper/clipper/mmdbold \
+LDFLAGS=-L$CLIB -L/usr/lib -lSystemStubs 

dists/10.4-transitional/unstable/main/finkinfo/sci clipper.info,1.4,NONE clipper.patch,1.1,NONE ssmlib.info,1.3,NONE mccp4.info,1.1,NONE mmdb.info,1.3,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3550

Removed Files:
clipper.info clipper.patch ssmlib.info mccp4.info mmdb.info 
Log Message:
removing obsolete dependency packages for coot

--- clipper.info DELETED ---

--- clipper.patch DELETED ---

--- mmdb.info DELETED ---

--- mccp4.info DELETED ---

--- ssmlib.info DELETED ---



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dists/10.4-transitional/unstable/main/finkinfo/sci coot.info,1.11,1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14783

Modified Files:
coot.info 
Log Message:
fixed missing dependency on coot-shlibs

Index: coot.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- coot.info   16 Jan 2006 05:40:42 -  1.11
+++ coot.info   17 Jan 2006 23:32:36 -  1.12
@@ -13,7 +13,7 @@
 ###
 BuildDepends: ccp4-onlylibs-dev, glib, gtk+2, freeglut, gtkglarea, guile16, 
guile16-dev, gsl, libglade2,  gtk-canvas (= 0.1.1-20), libart2 (= 2.3.16-2), 
libart2-shlibs (= 2.3.16-2), guile16-net-http, gtk+2-dev, libgettext3-dev, 
imlib, libjpeg, giflib, libpng3, gnome-libs-dev, fftw, libiconv-dev
 #
-Depends: guile16-shlibs, gtk-canvas (= 0.1.1-20), gsl-shlibs, 
libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, guile16-goosh (= 
1.3-2), guile16, guile16-net-http, freeglut-shlibs, libart2-shlibs (= 2.3.16-2)
+Depends: guile16-shlibs, gtk-canvas (= 0.1.1-20), gsl-shlibs, 
libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, guile16-goosh (= 
1.3-2), guile16, guile16-net-http, freeglut-shlibs, libart2-shlibs (= 
2.3.16-2), coot-shlibs (= %v-%r)
 #
 BuildDependsOnly: false
 NoSetLDFLAGS: true
@@ -89,7 +89,7 @@
 
 Shlibs: 
 %p/lib/libccp4mg-surface.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1)
-%p/lib/libccp4mg-utils.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1) 
+%p/lib/libccp4mg-utils.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1)
 %p/lib/libcoot-analysis.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1)
 %p/lib/libcoot-AngleInfo.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1)
 %p/lib/libcoot-atomutils.0.0.0.dylib 0.1.0 %n (= 0.1.0-pre-1-1)



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dists/10.4-transitional/unstable/main/finkinfo/sci gromacs-mpi.info,1.3,1.4 gromacs.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7471

Modified Files:
gromacs-mpi.info gromacs.info 
Log Message:
gromacs fixes to info and patch files

Index: gromacs.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- gromacs.info4 Jan 2006 07:32:06 -   1.4
+++ gromacs.info19 Jan 2006 20:21:15 -  1.5
@@ -1,8 +1,9 @@
 Package: gromacs
 Version: 3.3
-Revision: 2
+Revision: 3
 Depends: %N-shlibs (= %v-%r), fftw3-shlibs, x11, openmotif3-shlibs
 BuildDepends: fftw3, x11-dev
+BuildConflicts: gromacs-dev ( %v-%r)
 BuildDependsOnly: false
 Source: mirror:custom:%n-%v.tar.gz
 CustomMirror: 

Index: gromacs-mpi.info
===
RCS file: 
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gromacs-mpi.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- gromacs-mpi.info4 Jan 2006 05:20:55 -   1.3
+++ gromacs-mpi.info19 Jan 2006 20:21:15 -  1.4
@@ -1,6 +1,6 @@
 Package: gromacs-mpi
 Version: 3.3
-Revision: 2
+Revision: 3
 Depends: gromacs (= %v-%r), %N-shlibs (= %v-%r), fftw3-shlibs, x11, 
openmotif3-shlibs, lammpi (= 7.0.6-11)
 BuildDepends: fftw3, x11-dev, lammpi-dev (= 7.0.6-11), gromacs-dev (= %v-%r)
 BuildDependsOnly: false
@@ -13,6 +13,8 @@
 ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share  --enable-mpi --program-suffix=_mpi --with-external-blas 
--with-external-lapack
 DocFiles: AUTHORS COPYING README
 CompileScript: 
+#! /bin/sh -v
+  unset MACOSX_DEPLOYMENT_TARGET
   LIBS='/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib' 
./configure %c
   make mdrun
 



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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.84,1.85

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv26237

Modified Files:
coot.info 
Log Message:
coot with fix to avoid what is in coot.patch

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -d -r1.84 -r1.85
--- coot.info   26 Aug 2008 23:47:04 -  1.84
+++ coot.info   8 Sep 2008 17:03:09 -   1.85
@@ -1,10 +1,10 @@
 Package: coot
-Version: 0.5-pre-1-1372
+Version: 0.5-pre-1-1377
 Revision: 1
 GCC: 4.0 
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1372.tar.gz
  
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1377.tar.gz
  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 6ffc2902e794cef7de3888283982333b
+Source-MD5: f857261f25fe719ea5b309ddbd260078
 SourceDirectory: %n-0.5-pre-1
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
@@ -116,7 +116,7 @@
 ###
 BuildDependsOnly: false
 NoSetLDFLAGS: true
-Patch: %n.patch
+# Patch: %n.patch
 PatchScript:  
 #!/bin/zsh -exf
 if [[ $(sw_vers -productVersion)  10.5 ]]; then
@@ -159,6 +159,7 @@
 # set -x
 export 
PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH:%p/share/guile/1.8/goosh
 export SED=/usr/bin/sed
+export GDK_USE_XFT='1'
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 export 
PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:${PKG_CONFIG_PATH}
 FLIBS=-L%p/lib \
@@ -237,35 +238,35 @@
 lib/libcootaneer*.dylib
 
 Shlibs: 
-%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-map-heavy.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-map-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-mmtz-extras.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-sequence-view.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-shelx.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-surface.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-wrap-guile.0.dylib   1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcoot-wrap-python.0.dylib  1.0.0 %n (= 
0.5-pre-1-1372-1)
-%p/lib/libcootaneer.0.dylib 1.0.0 %n (= 
0.5-pre-1-1372-1)
+%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1377-1)
+%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.patch,1.4,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv26778

Removed Files:
coot.patch 
Log Message:
coot with fix to avoid what is in coot.patch

--- coot.patch DELETED ---


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-multibyte.info, 1.8, 1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18630

Modified Files:
zsh-multibyte.info 
Log Message:
fixed misnaming of dylib to agree with change made in zsh.info

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- zsh-multibyte.info  2 Apr 2008 13:25:29 -   1.8
+++ zsh-multibyte.info  8 Sep 2008 19:12:44 -   1.9
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
 Version: 4.3.6
-Revision: 1
+Revision: 2
 Conflicts: zsh
 Replaces: zsh
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -39,7 +39,7 @@
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
-perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
+# perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
  ./configure %c
 perl -pi.bak -e s;-ldl -ltinfo -lm  -lc;-L%p/lib -lpcre -L%p/lib -lncurses 
-L%p/lib -liconv -ltinfo -ldl -lm -lc; Makefile
 perl -pi.bak -e s;-bundle -flat_namespace -undefined suppress;-bundle 
-twolevel_namespace -undefined dynamic_lookup; Makefile


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[cvs] dists/10.4/unstable/main/finkinfo/sci clipper.info, NONE, 1.1 ssm.info, NONE, 1.1 gpp4.info, NONE, 1.1 coot.info, 1.85, 1.86 mmdb.info, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv12584

Modified Files:
coot.info mmdb.info 
Added Files:
clipper.info ssm.info gpp4.info 
Log Message:
upgrade coot and add streamlined dependencies

--- NEW FILE: gpp4.info ---
Package: gpp4
Version: 1.0.4
Revision: 5
Maintainer: W. G. Scott [EMAIL PROTECTED] 
# Maintainer: Morten Kjeldgaard [EMAIL PROTECTED]
DescPackaging: 
 Based on package created by Morten Kjeldgaard [EMAIL PROTECTED] with minor
 edits to conform to standard Fink packaging requirements.

Description: Library providing CCP4 functionality 
License: LGPL
Source: ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-%v.tar.gz
Source-MD5: 48931781425a5b79a8255ebefaed24b3
NoSourceDirectory: false
Depends: %N-shlibs (= %v-%r)
BuildDependsOnly: true
HomePage: http://www.bioxray.dk/~mok/gpp4
DocFiles: README AUTHORS NEWS COPYING
DescDetail:  
The CCP4 software suite is based around a library of routines that
cover common tasks, such as file opening, parsing keyworded input,
reading and writing of standard data formats, applying symmetry
operations, etc. Programs in the suite call these routines which, as
well as saving the programmer some effort, ensure that the varied
programs in the suite have a similar look-and-feel.

The library contains several subcomponents: 
  * CMTZ library -- Contains a variety of functions for manipulating 
the data structure, for example adding crystals, datasets or columns. 
The data structure can be dumped to an output MTZ data file.
  * CMAP library -- Functions defining the C-level API for accessing 
CCP4 map files.
  * CSYM library -- a collection of functions centred around a data file 
syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox 
of cctbx).
  * CCP4 utility library -- many utility functions which either give 
specific CCP4 or platform independent functionality.
  * CCP4 Parser library -- provides CCP4-style parsing, as used for 
processing keywords of CCP4 programs, MTZ header records, etc.
  * CCP4 resizable arrays -- defines an object and methods which looks 
just like a simple C array, but can be resized at will without 
incurring excessive overheads.

CompileScript: 
  ./configure --prefix=%p
  make

InstallScript: 
  make install DESTDIR=%d

SplitOff: 
  Package: %N-shlibs
  Files: 
lib/libgpp4.0.dylib
lib/libgpp4.0.0.0.dylib
  
  Shlibs: 
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.0.4-2)
  

SplitOff2: 
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev  
Replaces: ccp4-onlylibs-dev
 Files:
  lib/*.a
  lib/*.la
  include/gpp4/ccp4/*.h
  share/gpp4/default.def
  share/gpp4/environ.def
  share/gpp4/syminfo.lib
 


 

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- mmdb.info   26 Aug 2008 23:46:08 -  1.1
+++ mmdb.info   10 Sep 2008 08:14:02 -  1.2
@@ -1,6 +1,6 @@
 Package: mmdb
 Version: 1.12
-Revision: 1
+Revision: 5 
 # Maintainer: Morten Kjeldgaard [EMAIL PROTECTED]
 Maintainer: W. G. Scott [EMAIL PROTECTED] 
 DescPackaging: 
@@ -43,12 +43,14 @@
 SplitOff: 
   Package: %N-shlibs
   Files: lib/libmmdb.0.dylib lib/libmmdb.0.0.0.dylib
-  Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (= 1.12-1)
+  Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (= 1.12-2)
 
 SplitOff2: 
 Package: %N-dev
 Depends: %N (= %v-%r)
 BuildDependsOnly: True
+Conflicts: ccp4-onlylibs-dev  
+Replaces: ccp4-onlylibs-dev
 Files:
 include/mmdb/*.h
 lib/*.a

--- NEW FILE: clipper.info ---
Package: clipper
Epoch: 1
Version: 2.0.3
Revision: 5
BuildDepends: fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), mmdb-dev (= 
1.12-5), ssm-dev (= 0.1-5), gpp4-dev (= 1.0.4-5)
Depends: %n-shlibs (= 1:%v-%r), fftw-shlibs (= 2.1.5-1010) | fftw-mpi-shlibs 
(= 2.1.5-1010), mmdb-shlibs (= 1.0.10-5), ssm-shlibs (= 0.1-5), gpp4-shlibs 
(= 1.0.4-5)
Maintainer: W. G. Scott [EMAIL PROTECTED] 
Homepage: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html 
Source: http://www.ysbl.york.ac.uk/~cowtan/%n/%n20ac.latest.tar.gz
Source-MD5: cf5746cd7e040180c1e4cb429c7b2ac1
NoSourceDirectory: true
DocFiles: README AUTHORS NEWS COPYING 
Description: Object-oriented crystallographic libraries
DescDetail: 
The aim of the project is to produce a set of object-oriented libraries 
for the organisation of crystallographic data and the performance of
crystallographic computation. The libraries are designed as a framework 
for new crystallographic software, which will allow the full power of 
modern programming techniques to be exploited by the developer. 

SetCFLAGS: -fno-strict-aliasing  -I%p/include -I%p/include/mmdb 
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I/usr/include -I/usr/include/sys
SetLDFLAGS: -L/usr/lib
License: LGPL
CompileScript: 
  LDFLAGS=-L%p/lib 
  

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.86,1.87

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv3368

Modified Files:
coot.info 
Log Message:
cleaned up info file and have latest version

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.86
retrieving revision 1.87
diff -u -d -r1.86 -r1.87
--- coot.info   10 Sep 2008 08:14:02 -  1.86
+++ coot.info   10 Sep 2008 15:30:14 -  1.87
@@ -1,10 +1,10 @@
 Package: coot
-Version: 0.5-pre-1-1382
-Revision: 2
+Version: 0.5-pre-1-1391
+Revision: 1
 GCC: 4.0 
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1382.tar.gz
  
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1391.tar.gz
  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: bf54db93380c1e2d23515fa4ea46cf4f
+Source-MD5: fed9229e285e3ede30f7d3f9798e4d11
 SourceDirectory: %n-0.5-pre-1
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
@@ -20,8 +20,9 @@
 widgets (with the gui builder glade), mmdb, clipper, and OpenGL, together 
 with a new approach to map contouring and importing/creation and other
 (modelling) operations. The mmdb, clipper, ssm and mccp4 libraries are now
-provided in the ccp4-onlylibs-dev fink package. On-line documentation is 
-available from the coot Web site (see below) and is updated regularly.
+provided in separate fink packages that replace the ccp4-onlylibs-dev fink 
+package. On-line documentation is available from the coot Web via the help
+menu or via the web site (see below) and is updated regularly.
 .
 To have an Aqua-like Coot gtk+2 environment, issue the following command:
  echo include \%p/share/themes/Glossy_P/gtk-2.0/gtkrc\~/.gtkrc-2.0
@@ -130,26 +131,15 @@
 # Patch: %n.patch
 PatchScript:  
 #!/bin/zsh -exf
-if [[ $(sw_vers -productVersion)  10.5 ]]; then
-:
-else
-:
-# patch -p1  %a/%n-10.5.patch
-fi
 perl -pi.bak -e 's|use-modules \(goosh\)|use-modules \(goosh goosh\)|g' 
scheme/coot-utils.scm
-#perl -pi.bak -e 's/include malloc.h//g' **/*.c
 # Use the correct povray directory
 perl -pi.bak -e 's|povray-3.5|povray-3.6|g' scheme/povray.scm
 # Use open to display the png snapshot in Preview.app (or the user's default 
application)
 perl -pi.bak -e 's|coot-png-display-program 
\display\|coot-png-display-program \open\|g' scheme/raster3d.scm
 # This is required to get the map displayed on both sides of side-by-side 
stereo
 echo (set-display-lists-for-maps 0)  | scheme/group-settings.scm
-# Fix configure to work with gpp4 library instead of ccp4c
-# perl -pi -e 's|ccp4c|gpp4|g' configure
-#perl -pi.bak -e 's|2.8.0|2.6.0|g' configure
-# perl -pi.bak -e 's|have_glut=no|have_glut=yes|g' configure
+# Hopefully temporary hacks to configure
 perl -pi.bak -e 's|have_goosh=no|have_goosh=yes|g' configure
-# perl -pi.bak -e 's|have_guile_gui=no|have_guile_gui=yes|g' configure
 perl -pi -e s|guile-config|guile-1.8-config|g configure
 perl -pi -e 's|\(goosh\)|\(goosh goosh\)|g' configure
 perl -pi -e 's|lccp4c|lgpp4|g' configure
@@ -157,19 +147,15 @@
 
 ###
 ConfigureParams:   
---with-gpp4=%p --with-mmdb=%p   \
---with-clipper-prefix=%p  \
---with-fftw=%p \
---with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 --with-gtk2 \
---with-gnomecanvas-prefix=%p --with-ssmlib-prefix=%p  \
---with-imlib-prefix=%p --with-gtkgl-prefix=%p --with-glib-prefix=%p \
---with-guile-gtk --with-guile-gtk-prefix=%p  \
+--with-gpp4=%p --with-mmdb=%p --with-ssmlib-prefix=%p --with-clipper-prefix=%p 
 \
+--with-fftw=%p --with-gnomecanvas-prefix=%p  --with-gtk2 --with-glut-prefix=%p 
 \
+--with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
 \
+--with-imlib-prefix=%p --with-gtkgl-prefix=%p --with-glib-prefix=%p
 \
 --with-gsl-prefix=%p --with-guile --with-python 
 
 ###
 CompileScript: 
 #!/bin/zsh -efv
-# set -x
 export 
PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH:%p/share/guile/1.8/goosh
 export SED=/usr/bin/sed
 export GDK_USE_XFT='1'
@@ -184,12 +170,12 @@
 DYLD_LIBRARY_PATH= \
 ./configure %c
 #
+# Force coot to link to single-precision fftw libraries.  The double-precision 
libraries
+# cause coot to crash.
 perl -pi -e 's|lrfftw |lsrfftw |g'   **/Makefile
 perl -pi -e 's|lfftw |lsfftw |g' **/Makefile
 perl -pi -e 's|include rfftw.h|include srfftw.h|g'   
surface/CXXFFTSolventMap.h
 #
-# py_path=%p/bin/python2.5 \
-#
 #remake the  src/coot_wrap_python.cc and src/coot_wrap_guile.cc files
/bin/rm -f **/coot_wrap_**.cc
cd src
@@ -226,7 +212,6 @@
 # This installs the refmac monomer library
 mkdir 

[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.35,1.36

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv29097

Modified Files:
ccp4.info 
Log Message:
fixed validation problems with shlibs and added BuildConflicts with the new 
alternate packages. Verified everything works with latest Deve tools.

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.35
retrieving revision 1.36
diff -u -d -r1.35 -r1.36
--- ccp4.info   29 Aug 2008 19:52:57 -  1.35
+++ ccp4.info   10 Sep 2008 21:47:57 -  1.36
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.99e
-Revision: 4
+Revision: 6
 Distribution: 10.5
 GCC: 1
 Source: ftp://ftp.%n.ac.uk/%n/6.1/%n-%v-core-src.tar.gz
@@ -42,24 +42,16 @@
 are issued by CCP4 are now downloaded and applied individually, helping
 to keep the ccp4.patch file from growing metastatically and also to
 permit the user to verify that the latest patches have been applied.
-These start with Source5 (above) and are applied individually at the
+These start with Source2 (above) and are applied individually at the
 end of the PatchScript field.
+
+Clipper libraries are not behaving properly when linked to fink fftw
+so we return to the option of having ccp4 build its own private fftw.
+Yes, I hate it too, but now all the examples pass the run-all test.
 
-Depends: 
-x11, 
-fftw-shlibs | fftw-mpi-shlibs,
-tcltk,
-blt,
-gcc43-shlibs,
-%N-shlibs (= %v-%r)
-
-BuildDepends: 
-gcc43, 
-fftw | fftw-mpi,
-f2c, 
-fort77, 
-tcltk-dev
-
+Depends:  x11, tcltk, blt, gcc43-shlibs, %N-shlibs (= %v-%r)
+BuildDepends: gcc43, f2c, fort77, tcltk-dev
+BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev
 Replaces: phaser (= 2.1.4-1), pointless (= 1.2.18-1), mosflm (= 7.0.3-3), 
mosflm-small (= 7.0.3-3), refmac (= 5.4-4), ccp4-shlibs (= 6.0.2-), ccp4 
(= 6.0.2-), ccp4-dev (= 6.0.2-), bundle-ccp4-intel, clipper-bin, 
ccp4-gfortran, ccp4-gfortran-dev, bundle-ccp4-powerpc
 Conflicts: 
mosflm (= 7.0.3-3), 
@@ -140,23 +132,11 @@
   export RPATH=%p/lib/ccp4-%v
 
 # === CONFIGURE === 
-FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib ./configure  
--with-shared-libs  --with-x --with-fftw=%p  Darwin
-# FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib ./configure 
--disable-pdb_extract --disable-cctbx --disable-phaser  --with-shared-libs  
--with-x --with-fftw=%p  Darwin
- 
+# FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib ./configure  
--with-shared-libs  --with-x --with-fftw=%p  Darwin
+FC=%p/lib/gcc4.3/bin/gfortran F_LIBS=-L%p/lib/gcc4.3/lib ./configure  
--with-shared-libs  --with-x   Darwin 
+#
 #  fix some post-configure bugs by getting rid of -lg2c
   perl -pi.bak -e 's|-lg2c||g' x-windows/**/*akefile*
-
-
-
-# if [[ $(uname -p) != powerpc ]];then 
-# perl -pi.bak -e 's|%p/lib/gcc4.3/bin/||g' lib/clipper/**/Makefile*
-#   # Replace the ccp4 libtool file with one that works and compiles 
cpirate:
-# cp ../ccp4_i686-apple-darwin8.6.1_libtool.gz  lib/clipper/libtool.gz 
-# mv -f lib/clipper/libtool lib/clipper/libtool-dist
-# gunzip lib/clipper/libtool.gz
-# chmod a+x lib/clipper/libtool
-# fi
-
   ( cd x-windows/XCCPJIFFY; perl -pi.bak -e 's|-lgfortran|-lgfortran 
-L%p/lib/gcc4.3/lib |g' *akefile* ) || exit 1
 if [[ $(sw_vers -productVersion)  10.5 ]]; then
  :
@@ -195,8 +175,6 @@
   echo 
**
   echo 
 #
-  #perl -pi.bak -e 's|FC = g77 -fno-second-underscore||g' Makefile
-  #make -i xloggraph  2/dev/null
   cd  XCCPJIFFY
   fort77 -o xloggraph msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o 
xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o -g 
-Os -I/usr/include/X11R6 -L/usr/X11R6/lib -lXaw -lXmu -lXt -lSM -lICE -lXpm 
-lXext -lX11 -lm -lgfortran -L%p/lib/gcc4.3/lib
 
@@ -231,9 +209,6 @@
  /bin/rm -f **/*.c 
  /bin/rm -f **/*.f 
  /bin/rm -f **/*.cpp
-# echo Compile Phase Completed!
-# echo There are $(command ls -1 $CBIN | wc -l) programs in $CBIN; 
-# echo there should be 200
 
 

 InstallScript: 
@@ -322,61 +297,34 @@
 Package: %N-shlibs
 Description: CCP4 dynamic libraries
 Files:
-lib/ccp4-%v/*.dylib  
+lib/ccp4-%v/*.*.dylib  
+lib/ccp4-%v/libccif.dylib   
+lib/ccp4-%v/libccp4c.dylib
+lib/ccp4-%v/libmmdb.dylib
 
 Shlibs: 
-%p/lib/ccp4-%v/libDiffractionImage.0.0.0.dylib   1.0.0  %n 
  (= 6.0.99e-1)
 %p/lib/ccp4-%v/libDiffractionImage.0.dylib   1.0.0  %n 
  (= 6.0.99e-1)
-

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.88,1.89

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv31897

Modified Files:
coot.info 
Log Message:
coot version update and added missing dependency for fftw

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.88
retrieving revision 1.89
diff -u -d -r1.88 -r1.89
--- coot.info   11 Sep 2008 21:54:04 -  1.88
+++ coot.info   14 Sep 2008 16:10:54 -  1.89
@@ -1,10 +1,10 @@
 Package: coot
-Version: 0.5-pre-1-1391
+Version: 0.5-pre-1-1406
 Revision: 1
 GCC: 4.0 
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1391.tar.gz
  
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1406.tar.gz
  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: fed9229e285e3ede30f7d3f9798e4d11
+Source-MD5: 1287ea3d2efc3f9eba9351456c37a244
 SourceDirectory: %n-0.5-pre-1
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
@@ -37,7 +37,6 @@
 BuildDepends: 
  clipper-dev (= 1:2.0.3-5)  ,
  clipper (= 1:2.0.3-5)  ,
- fftw   ,
  gpp4-dev (= 1.0.4-5)   ,
  gpp4 (= 1.0.4-5)   ,
  mmdb-dev (= 1.12-5),
@@ -47,6 +46,7 @@
  atk1 (= 1.20.0-1)  ,
  cairo (= 1.6-1),
  expat1  ,
+ fftw | fftw-mpi ,
  fontconfig2-dev (= 2.4.1-1),
  freetype219 (= 2.3.5-1),
  freeglut,
@@ -91,6 +91,7 @@
  ssm-shlibs (= 0.1-5),
  atk1-shlibs (= 1.20.0-1),
  coot-shlibs (= %v-%r),
+ fftw-shlibs | fftw-mpi-shlibs,
  freeglut-shlibs  ,
  giflib-shlibs,
  glib2-shlibs (= 2.14.0-1)   ,
@@ -242,34 +243,34 @@
 lib/libcootaneer.0*.dylib
 
 Shlibs: 
-%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-map-heavy.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-map-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-sequence-view.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-shelx.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-surface.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-wrap-guile.0.dylib   1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcoot-wrap-python.0.dylib  1.0.0 %n (= 
0.5-pre-1-1391-1)
-%p/lib/libcootaneer.0.dylib 1.0.0 %n (= 
0.5-pre-1-1391-1)
+%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
+  

[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.24, 1.25

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv30907

Modified Files:
zsh-templates.info 
Log Message:
mystuff correction

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -d -r1.24 -r1.25
--- zsh-templates.info  11 Feb 2008 17:01:46 -  1.24
+++ zsh-templates.info  15 Sep 2008 05:02:17 -  1.25
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.3.3
+Version: 1.3.4
 Revision: 1
 Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
-Source-MD5: deee71a861dacfbda96f65b5c7ca7c75
+Source-MD5: e689cdb8d36fc3d10f2660c3f98614c1
 #SourceDirectory: zsh-templates-osx  
 SourceDirectory: %n-%v
 Depends: macosx, zsh (= 4.3.4-1) | zsh-multibyte (= 4.3.4-1)
@@ -11,8 +11,9 @@
 Description: Template files for zsh customization 
 PatchScript: 
 #!/bin/zsh -efx
+perl -pi.bak -e 's|/sw|%p|g' **/*
 perl -pi.bak -e 's|ALT_SWPREFIX|%p|g' etc/zshenv
-rm -f etc/*.bak
+rm -f **/*.bak
 
 CompileScript:
 


-
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[cvs] dists/10.4/stable/main/finkinfo/sci clipper.info, NONE, 1.1 gpp4.info, NONE, 1.1 mmdb.info, NONE, 1.1 ssm.info, NONE, 1.1 coot.info, 1.15, 1.16

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv27367

Modified Files:
coot.info 
Added Files:
clipper.info gpp4.info mmdb.info ssm.info 
Log Message:
a version of coot that builds and runs in stable and its new dependencies

--- NEW FILE: gpp4.info ---
Package: gpp4
Version: 1.0.4
Revision: 5
Maintainer: W. G. Scott [EMAIL PROTECTED] 
# Maintainer: Morten Kjeldgaard [EMAIL PROTECTED]
DescPackaging: 
 Based on package created by Morten Kjeldgaard [EMAIL PROTECTED] with minor
 edits to conform to standard Fink packaging requirements.

Description: Library providing CCP4 functionality 
License: LGPL
Source: ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-%v.tar.gz
Source-MD5: 48931781425a5b79a8255ebefaed24b3
NoSourceDirectory: false
Depends: %N-shlibs (= %v-%r)
BuildDependsOnly: true
HomePage: http://www.bioxray.dk/~mok/gpp4
DocFiles: README AUTHORS NEWS COPYING
DescDetail:  
The CCP4 software suite is based around a library of routines that
cover common tasks, such as file opening, parsing keyworded input,
reading and writing of standard data formats, applying symmetry
operations, etc. Programs in the suite call these routines which, as
well as saving the programmer some effort, ensure that the varied
programs in the suite have a similar look-and-feel.

The library contains several subcomponents: 
  * CMTZ library -- Contains a variety of functions for manipulating 
the data structure, for example adding crystals, datasets or columns. 
The data structure can be dumped to an output MTZ data file.
  * CMAP library -- Functions defining the C-level API for accessing 
CCP4 map files.
  * CSYM library -- a collection of functions centred around a data file 
syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox 
of cctbx).
  * CCP4 utility library -- many utility functions which either give 
specific CCP4 or platform independent functionality.
  * CCP4 Parser library -- provides CCP4-style parsing, as used for 
processing keywords of CCP4 programs, MTZ header records, etc.
  * CCP4 resizable arrays -- defines an object and methods which looks 
just like a simple C array, but can be resized at will without 
incurring excessive overheads.

CompileScript: 
  ./configure --prefix=%p
  make

InstallScript: 
  make install DESTDIR=%d

SplitOff: 
  Package: %N-shlibs
  Files: 
lib/libgpp4.0.dylib
lib/libgpp4.0.0.0.dylib
  
  Shlibs: 
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.0.4-2)
  

SplitOff2: 
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev  
Replaces: ccp4-onlylibs-dev
 Files:
  lib/*.a
  lib/*.la
  include/gpp4/ccp4/*.h
  share/gpp4/default.def
  share/gpp4/environ.def
  share/gpp4/syminfo.lib
 


 

--- NEW FILE: mmdb.info ---
Package: mmdb
Version: 1.12
Revision: 5 
# Maintainer: Morten Kjeldgaard [EMAIL PROTECTED]
Maintainer: W. G. Scott [EMAIL PROTECTED] 
DescPackaging: 
 Based on package created by Morten Kjeldgaard [EMAIL PROTECTED] with minor
 edits to conform to standard Fink packaging requirements.

Description: Macromolecular coordinate library
License: LGPL
HomePage: http://www.ebi.ac.uk/~keb/cldoc/
Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
Source-MD5: b46e31159b85d6742f4014822f2240f4
Depends: %N-shlibs (= %v-%r)
BuildDependsOnly: true
DescDetail:  
MMDB is CCP4's macromolecular coordinate library, written by Eugene
Krissinel of the EBI.  The Coordinate Library is designed to assist
CCP4 developers in working with coordinate files. The major source of
coordinate information remains the PDB files, although more
information becomes available in mmCIF format.

The Library features working with both file formats plus an internal
binary format portable between different platforms. This is achieved
at uniformity of the Library's interface functions, so that there is
no difference in handling different formats.

The Library provides various high-level tools for working with
coordinate files, which include not only reading and writing, but also
orthogonal-fractional coordinate transforms, generation of symmetry
mates, editing the molecular structure and some others. The Library is
supposed as a general low-level tool for unifying the
coordinate-related operations.

CompileScript: 
  ./configure --prefix=%p
  make

InstallScript: 
  make install DESTDIR=%d

SplitOff: 
  Package: %N-shlibs
  Files: lib/libmmdb.0.dylib lib/libmmdb.0.0.0.dylib
  Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (= 1.12-2)

SplitOff2: 
Package: %N-dev
Depends: %N (= %v-%r)
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev  
Replaces: ccp4-onlylibs-dev
Files:
include/mmdb/*.h
lib/*.a
lib/*.la



--- NEW FILE: clipper.info ---
Package: clipper
Epoch: 1
Version: 2.0.3
Revision: 5
BuildDepends: fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), mmdb-dev (= 
1.12-5), ssm-dev (= 0.1-5), gpp4-dev (= 1.0.4-5)
Depends: %n-shlibs (= 1:%v-%r), fftw-shlibs (= 

[cvs] dists/10.4/stable/main/finkinfo/sci ccp4-onlylibs-dev.info, 1.7, NONE ccp4-onlylibs-dev.patch, 1.2, NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28159

Removed Files:
ccp4-onlylibs-dev.info ccp4-onlylibs-dev.patch 
Log Message:
removing obsolete dependency for coot.  This is replaced by clipper, gpp4, 
mmdb, ssm

--- ccp4-onlylibs-dev.patch DELETED ---

--- ccp4-onlylibs-dev.info DELETED ---


-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
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http://news.gmane.org/gmane.os.apple.fink.cvs

[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.16,1.17

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv27557

Modified Files:
coot.info 
Log Message:
fixed bug in one of the internal python scripts

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- coot.info   16 Sep 2008 16:28:00 -  1.16
+++ coot.info   17 Sep 2008 03:01:38 -  1.17
@@ -1,10 +1,10 @@
 Package: coot
-Version: 0.5-pre-1-1406
+Version: 0.5-pre-1-1412
 Revision: 1
 GCC: 4.0 
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1406.tar.gz
  
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1412.tar.gz
  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 1287ea3d2efc3f9eba9351456c37a244
+Source-MD5: 213d2bf18939723bfe204387d50d586c
 SourceDirectory: %n-0.5-pre-1
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
@@ -243,34 +243,34 @@
 lib/libcootaneer.0*.dylib
 
 Shlibs: 
-%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-map-heavy.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-map-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-sequence-view.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-shelx.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-surface.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-wrap-guile.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-wrap-python.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcootaneer.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-map-heavy.0.dylib

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.89,1.90

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv27589

Modified Files:
coot.info 
Log Message:
fixed bug in one of the internal python scripts

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.89
retrieving revision 1.90
diff -u -d -r1.89 -r1.90
--- coot.info   14 Sep 2008 16:10:54 -  1.89
+++ coot.info   17 Sep 2008 03:02:00 -  1.90
@@ -1,10 +1,10 @@
 Package: coot
-Version: 0.5-pre-1-1406
+Version: 0.5-pre-1-1412
 Revision: 1
 GCC: 4.0 
-Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1406.tar.gz
  
+Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1412.tar.gz
  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 1287ea3d2efc3f9eba9351456c37a244
+Source-MD5: 213d2bf18939723bfe204387d50d586c
 SourceDirectory: %n-0.5-pre-1
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
@@ -243,34 +243,34 @@
 lib/libcootaneer.0*.dylib
 
 Shlibs: 
-%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-map-heavy.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-map-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-sequence-view.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-shelx.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-surface.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-utils.0.dylib1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-wrap-guile.0.dylib   1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcoot-wrap-python.0.dylib  1.0.0 %n (= 
0.5-pre-1-1406-1)
-%p/lib/libcootaneer.0.dylib 1.0.0 %n (= 
0.5-pre-1-1406-1)
+%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-atomutils.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 
0.5-pre-1-1412-1)
+%p/lib/libcoot-map-heavy.0.dylib

[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.36,1.37

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv9296

Modified Files:
ccp4.info 
Log Message:
fixed conflict with xml2 and no longer puts itself at the front of the path 
ahead of /sw/bin

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.36
retrieving revision 1.37
diff -u -d -r1.36 -r1.37
--- ccp4.info   10 Sep 2008 21:47:57 -  1.36
+++ ccp4.info   18 Sep 2008 15:09:33 -  1.37
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.99e
-Revision: 6
+Revision: 7
 Distribution: 10.5
 GCC: 1
 Source: ftp://ftp.%n.ac.uk/%n/6.1/%n-%v-core-src.tar.gz
@@ -85,6 +85,11 @@
   perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*   # 
location of tcktk, blt
   perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*# same
   perl -pi.bak -e 's|limit stacksize 65536|limit stacksize unlimited|g' 
include/ccp4.setup* # same
+  perl -pi.bak -e 's|ccp4_first_in_path=1|ccp4_first_in_path=0|g'  
include/ccp4.setup*
+  perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g'  
include/ccp4.setup*
+  perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv 
GFORTRAN_UNBUFFERED_ALL Y|g'   include/ccp4.setup*
+  perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export 
GFORTRAN_UNBUFFERED_ALL|g'   include/ccp4.setup*
+
 #
   cp include/ccp4.setup-dist include/ccp4.setup
   rm -f include/ccp4.setup-sh   include/ccp4.setup*.bak
@@ -128,6 +133,7 @@
   source $PWD/include/ccp4.setup-zsh
   [[ -d $CCP4 ]] || exit 1
   export DYLD_LIBRARY_PATH=$CLIB
+  export GFORTRAN_UNBUFFERED_ALL=Y
   export rpath=%p/lib/ccp4-%v
   export RPATH=%p/lib/ccp4-%v
 
@@ -188,7 +194,13 @@
   cd ../..
 #
# Cleanup:
+
+   # Get rid of the corrupting influence of ccp4's own xml2-config:
+ if [[ -x $CBIN/xml2-config ]];then
+/bin/rm -f $CBIN/xml2-config
+ fi
#
+
# make realclean
  /bin/rm -f **/*.o
  /bin/rm -f **/*.bak


-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh.info, 1.15, 1.16 zsh-multibyte.info, 1.9, 1.10 zsh-helpfiles.info, 1.9, 1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv18176

Modified Files:
zsh.info zsh-multibyte.info zsh-helpfiles.info 
Log Message:
zsh version update to 4.3.8

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- zsh-helpfiles.info  2 Apr 2008 13:29:06 -   1.9
+++ zsh-helpfiles.info  29 Oct 2008 14:54:28 -  1.10
@@ -1,5 +1,5 @@
 Package: zsh-helpfiles
-Version: 4.3.6
+Version: 4.3.8
 Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
@@ -26,7 +26,7 @@
 
 Source: mirror:custom:/zsh-%v.tar.bz2
 Source2: 
http://code.google.com/p/zsh-templates-osx/source/browse/trunk/Library/init/zsh/local-functions/general/run-help
-Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
+Source-MD5: 6025f234700eba57746df765b2415ad3
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:
 #!/bin/zsh -efv
@@ -86,9 +86,9 @@
 
 DescUsage: 
 Fink automatically issues the command autoload -U run-help upon z-shell 
-startup. Then, for example, issuing run-help zargs will enable you to 
+startup. Then, for example, issuing run-help echo will enable you to 
 view a formatted helpfile extracted from the zsh man pages for the zsh 
-function zargs.  The environment variable $HELPDIR should point to
+builtin function echo.  The environment variable $HELPDIR should point to
 /sw/share/zsh/zsh_help; this too is set up automatically by fink.
 
 License: GPL

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- zsh.info7 Sep 2008 01:12:35 -   1.15
+++ zsh.info29 Oct 2008 14:54:28 -  1.16
@@ -1,6 +1,6 @@
 Package: zsh 
-Version: 4.3.6
-Revision: 2
+Version: 4.3.8
+Revision: 1
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/%n-%v.tar.bz2
-Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
+Source-MD5: 6025f234700eba57746df765b2415ad3
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: cab29228a90f58b1431a66ab24a0a0c2
+Source2-MD5: 98c1367575d1ba75273d6243370ea790
 ConfigureParams:
 --mandir=%p/share/man --infodir=%p/share/info --enable-etcdir=%p/etc/%n   \
 --enable-maildir-support --enable-pcre --enable-zsh-secure-free   \

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- zsh-multibyte.info  8 Sep 2008 19:12:44 -   1.9
+++ zsh-multibyte.info  29 Oct 2008 14:54:28 -  1.10
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
-Version: 4.3.6
-Revision: 2
+Version: 4.3.8
+Revision: 1
 Conflicts: zsh
 Replaces: zsh
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source-MD5: 16f399af1081ad3c303a794c9c7dc47e
+Source-MD5: 6025f234700eba57746df765b2415ad3
 Source2: mirror:custom:zsh-%v-doc.tar.bz2
-Source2-MD5: cab29228a90f58b1431a66ab24a0a0c2
+Source2-MD5: 98c1367575d1ba75273d6243370ea790
 ConfigureParams: 
 --mandir=%p/share/man --infodir=%p/share/info \
 --enable-etcdir=%p/etc/zsh --enable-maildir-support \
@@ -39,8 +39,13 @@
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
+ zsh-multibyte.info
+perl -pi.bak -e s|ypcat|false|g configure
+./configure %c
+===
 # perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
  ./configure %c
+ 1.9
 perl -pi.bak -e s;-ldl -ltinfo -lm  -lc;-L%p/lib -lpcre -L%p/lib -lncurses 
-L%p/lib -liconv -ltinfo -ldl -lm -lc; Makefile
 perl -pi.bak -e s;-bundle -flat_namespace -undefined suppress;-bundle 
-twolevel_namespace -undefined dynamic_lookup; Makefile
 /bin/rm -f *.bak 


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This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.92,1.93

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv23919

Modified Files:
coot.info 
Log Message:
coot version update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.92
retrieving revision 1.93
diff -u -d -r1.92 -r1.93
--- coot.info   24 Sep 2008 14:51:59 -  1.92
+++ coot.info   29 Oct 2008 15:38:33 -  1.93
@@ -1,13 +1,12 @@
 Package: coot
-Version: 0.5.0
+Version: 0.5.1-pre-1-revision-1526
 Revision: 1
+SourceDirectory: %n-0.5.1-pre-1
+#SourceDirectory: %n-%v
 GCC: 4.0 
-# Source: 
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1441.tar.gz
  
+Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-0.5.tar.gz
-Source-MD5: c9574cb95b130c3803d6158b6a08f3e8
-#SourceDirectory: %n-%v 
-SourceDirectory: %n-0.5 
+Source-MD5: a6a4061b8864ac2207b660f35001bfcd
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -147,7 +146,6 @@
 perl -pi -e s|guile-config|guile-1.8-config|g configure
 perl -pi -e 's|\(goosh\)|\(goosh goosh\)|g' configure
 perl -pi -e 's|lccp4c|lgpp4|g' configure
-###
 
 ###
 ConfigureParams:   
@@ -171,6 +169,7 @@
 CXX=/usr/bin/g++ \
 CC=/usr/bin/gcc \
 PYTHON=%p/bin/python2.5 \
+python=%p/bin/python2.5 \
 DYLD_LIBRARY_PATH= \
 ./configure %c
 #
@@ -229,7 +228,10 @@
 /bin/rm -rf %i/include
 /bin/rm -rf %i/**/.libs
 
-RuntimeVars: COOT_REFMAC_LIB_DIR: %p/share/coot/lib
+RuntimeVars: 
+COOT_REFMAC_LIB_DIR: %p/share/coot/lib
+COOT_PYTHON_DIR: %p/share/coot/python
+
 ###
 DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
 License: GPL


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-multibyte.info, 1.10, 1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv28299

Modified Files:
zsh-multibyte.info 
Log Message:
fix corrupted file

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- zsh-multibyte.info  29 Oct 2008 14:54:28 -  1.10
+++ zsh-multibyte.info  31 Oct 2008 23:30:56 -  1.11
@@ -39,16 +39,11 @@
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
- zsh-multibyte.info
 perl -pi.bak -e s|ypcat|false|g configure
 ./configure %c
-===
-# perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
- ./configure %c
- 1.9
 perl -pi.bak -e s;-ldl -ltinfo -lm  -lc;-L%p/lib -lpcre -L%p/lib -lncurses 
-L%p/lib -liconv -ltinfo -ldl -lm -lc; Makefile
 perl -pi.bak -e s;-bundle -flat_namespace -undefined suppress;-bundle 
-twolevel_namespace -undefined dynamic_lookup; Makefile
-/bin/rm -f *.bak 
+/bin/rm -f *.bak
 make
 
 InstallScript:


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.93,1.94

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv27035

Modified Files:
coot.info 
Log Message:
coot version update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.93
retrieving revision 1.94
diff -u -d -r1.93 -r1.94
--- coot.info   29 Oct 2008 15:38:33 -  1.93
+++ coot.info   2 Nov 2008 20:37:06 -   1.94
@@ -1,12 +1,12 @@
 Package: coot
-Version: 0.5.1-pre-1-revision-1526
+Version: 0.5.1-pre-1-revision-1541
 Revision: 1
 SourceDirectory: %n-0.5.1-pre-1
 #SourceDirectory: %n-%v
 GCC: 4.0 
 Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: a6a4061b8864ac2207b660f35001bfcd
+Source-MD5: 1dc9cdeda143f0afe63577c87633b65c
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh.info, 1.16, 1.17 zsh-multibyte.info, 1.11, 1.12 zsh-helpfiles.info, 1.10, 1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv10719

Modified Files:
zsh.info zsh-multibyte.info zsh-helpfiles.info 
Log Message:
zsh version update to 4.3.9 upstream completion bug fix

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- zsh-helpfiles.info  29 Oct 2008 14:54:28 -  1.10
+++ zsh-helpfiles.info  3 Nov 2008 15:53:01 -   1.11
@@ -1,5 +1,5 @@
 Package: zsh-helpfiles
-Version: 4.3.8
+Version: 4.3.9
 Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
@@ -26,7 +26,7 @@
 
 Source: mirror:custom:/zsh-%v.tar.bz2
 Source2: 
http://code.google.com/p/zsh-templates-osx/source/browse/trunk/Library/init/zsh/local-functions/general/run-help
-Source-MD5: 6025f234700eba57746df765b2415ad3
+Source-MD5: 0539d0a590e545ad8c40ff8c97e94538
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:
 #!/bin/zsh -efv

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- zsh.info29 Oct 2008 14:54:28 -  1.16
+++ zsh.info3 Nov 2008 15:53:01 -   1.17
@@ -1,5 +1,5 @@
 Package: zsh 
-Version: 4.3.8
+Version: 4.3.9
 Revision: 1
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/%n-%v.tar.bz2
-Source-MD5: 6025f234700eba57746df765b2415ad3
+Source-MD5: 0539d0a590e545ad8c40ff8c97e94538
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 98c1367575d1ba75273d6243370ea790
+Source2-MD5: b3a026cf02471b66454a2b241a4d92a4
 ConfigureParams:
 --mandir=%p/share/man --infodir=%p/share/info --enable-etcdir=%p/etc/%n   \
 --enable-maildir-support --enable-pcre --enable-zsh-secure-free   \

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- zsh-multibyte.info  31 Oct 2008 23:30:56 -  1.11
+++ zsh-multibyte.info  3 Nov 2008 15:53:01 -   1.12
@@ -1,5 +1,5 @@
 Package: zsh-multibyte
-Version: 4.3.8
+Version: 4.3.9
 Revision: 1
 Conflicts: zsh
 Replaces: zsh
@@ -26,9 +26,9 @@
   eur-UK: ftp://ftp.lysator.liu.se/pub/unix/zsh/ 
 
 Source: mirror:custom:/zsh-%v.tar.bz2
-Source-MD5: 6025f234700eba57746df765b2415ad3
+Source-MD5: 0539d0a590e545ad8c40ff8c97e94538
 Source2: mirror:custom:zsh-%v-doc.tar.bz2
-Source2-MD5: 98c1367575d1ba75273d6243370ea790
+Source2-MD5: b3a026cf02471b66454a2b241a4d92a4
 ConfigureParams: 
 --mandir=%p/share/man --infodir=%p/share/info \
 --enable-etcdir=%p/etc/zsh --enable-maildir-support \


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[cvs] dists/10.4/unstable/main/finkinfo/sci mmdb.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv1070

Modified Files:
mmdb.info 
Log Message:
version update with mmdb and official URL

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- mmdb.info   10 Sep 2008 08:14:02 -  1.2
+++ mmdb.info   12 Nov 2008 22:56:29 -  1.3
@@ -1,6 +1,6 @@
 Package: mmdb
-Version: 1.12
-Revision: 5 
+Version: 1.19
+Revision: 1
 # Maintainer: Morten Kjeldgaard [EMAIL PROTECTED]
 Maintainer: W. G. Scott [EMAIL PROTECTED] 
 DescPackaging: 
@@ -10,8 +10,9 @@
 Description: Macromolecular coordinate library
 License: LGPL
 HomePage: http://www.ebi.ac.uk/~keb/cldoc/
-Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: b46e31159b85d6742f4014822f2240f4
+Source: http://www.ebi.ac.uk/~keb/cldoc/downloads/%n-%v.tar.gz
+#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
+Source-MD5: cd6d1439b0c31d46643e3aff6c7b49e9
 Depends: %N-shlibs (= %v-%r)
 BuildDependsOnly: true
 DescDetail:  


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[cvs] dists/10.4/unstable/main/finkinfo/sci ssm.info, 1.1, 1.2 clipper.info, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv1132

Modified Files:
ssm.info clipper.info 
Log Message:
revision bump due to update of mmdb dependency

Index: ssm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ssm.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- ssm.info10 Sep 2008 08:14:02 -  1.1
+++ ssm.info12 Nov 2008 22:57:04 -  1.2
@@ -1,6 +1,6 @@
 Package: ssm
 Version: 0.1
-Revision: 5
+Revision: 6
 Maintainer: W. G. Scott [EMAIL PROTECTED] 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard [EMAIL PROTECTED] with minor
@@ -15,7 +15,7 @@
 Source-MD5: 317d9cc78a88fa5652a4a4b06f329823
 NoSourceDirectory: false
 Depends: %n-shlibs (= %v-%r)
-BuildDepends: mmdb-dev (= 1.0.10-5)
+BuildDepends: mmdb-dev (= 1.19-1)
 BuildDependsOnly: true
 DocFiles: README AUTHORS NEWS COPYING 
 DescDetail:  

Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- clipper.info10 Sep 2008 08:14:02 -  1.1
+++ clipper.info12 Nov 2008 22:57:04 -  1.2
@@ -1,9 +1,9 @@
 Package: clipper
 Epoch: 1
 Version: 2.0.3
-Revision: 5
-BuildDepends: fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), mmdb-dev (= 
1.12-5), ssm-dev (= 0.1-5), gpp4-dev (= 1.0.4-5)
-Depends: %n-shlibs (= 1:%v-%r), fftw-shlibs (= 2.1.5-1010) | fftw-mpi-shlibs 
(= 2.1.5-1010), mmdb-shlibs (= 1.0.10-5), ssm-shlibs (= 0.1-5), gpp4-shlibs 
(= 1.0.4-5)
+Revision: 6
+BuildDepends: fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), mmdb-dev (= 
1.19-1), ssm-dev (= 0.1-6), gpp4-dev (= 1.0.4-5)
+Depends: %n-shlibs (= 1:%v-%r), fftw-shlibs (= 2.1.5-1010) | fftw-mpi-shlibs 
(= 2.1.5-1010), mmdb-shlibs (= 1.19-1), ssm-shlibs (= 0.1-6), gpp4-shlibs 
(= 1.0.4-5)
 Maintainer: W. G. Scott [EMAIL PROTECTED] 
 Homepage: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html 
 Source: http://www.ysbl.york.ac.uk/~cowtan/%n/%n20ac.latest.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.94,1.95

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv1188

Modified Files:
coot.info 
Log Message:
new version coot with dependencies on newer ssm mmdb clipper

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.94
retrieving revision 1.95
diff -u -d -r1.94 -r1.95
--- coot.info   2 Nov 2008 20:37:06 -   1.94
+++ coot.info   12 Nov 2008 22:57:42 -  1.95
@@ -1,12 +1,12 @@
 Package: coot
-Version: 0.5.1-pre-1-revision-1541
+Version: 0.5.1-pre-1-revision-1563
 Revision: 1
 SourceDirectory: %n-0.5.1-pre-1
 #SourceDirectory: %n-%v
 GCC: 4.0 
 Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz  
 # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 1dc9cdeda143f0afe63577c87633b65c
+Source-MD5: 5b5faba878123d747b4c8aede180753c
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
 Source2-MD5: 14b965dc5ab9762c819f632c133998b9
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -36,14 +36,14 @@
 ###
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
- clipper-dev (= 1:2.0.3-5)  ,
- clipper (= 1:2.0.3-5)  ,
+ clipper-dev (= 1:2.0.3-6)  ,
+ clipper (= 1:2.0.3-6)  ,
  gpp4-dev (= 1.0.4-5)   ,
  gpp4 (= 1.0.4-5)   ,
- mmdb-dev (= 1.12-5),
- mmdb (= 1.12-5),
- ssm-dev (= 0.1-5)  ,
- ssm (= 0.1-5)  ,
+ mmdb-dev (= 1.19-1),
+ mmdb (= 1.19-1),
+ ssm-dev (= 0.1-6)  ,
+ ssm (= 0.1-6)  ,
  atk1 (= 1.20.0-1)  ,
  cairo (= 1.6-1),
  expat1  ,
@@ -86,10 +86,10 @@
 #
 # Note: gtkglext1 IS required at runtime for stereo functionality
 Depends: 
- clipper-shlibs (= 1:2.0.3-5),
+ clipper-shlibs (= 1:2.0.3-6),
  gpp4-shlibs (= 1.0.4-5) ,
- mmdb-shlibs (= 1.12-5)  ,
- ssm-shlibs (= 0.1-5),
+ mmdb-shlibs (= 1.19-1)  ,
+ ssm-shlibs (= 0.1-6),
  atk1-shlibs (= 1.20.0-1),
  coot-shlibs (= %v-%r),
  fftw-shlibs | fftw-mpi-shlibs,


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