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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv11394

Modified Files:
gromacs-mpi.info gromacs.info 
Log Message:
new version gromacs and compatible with new openmpi

Index: gromacs.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- gromacs.info14 May 2006 04:45:52 -  1.3
+++ gromacs.info7 Oct 2007 15:09:45 -   1.4
@@ -1,6 +1,6 @@
 Package: gromacs
-Version: 3.3.1
-Revision: 1001
+Version: 3.3.2
+Revision: 1000
 Depends: %N-shlibs (= %v-%r), fftw3-shlibs, x11, openmotif3-shlibs
 BuildDepends: fftw3, x11-dev
 BuildConflicts: gromacs-dev ( %v-%r)
@@ -9,7 +9,7 @@
 CustomMirror: 
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: 1af34a99950813ca7cf893253c447cd1
+Source-MD5: f25853fefdbfbe7f4e8667a16c495736
 ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p --mandir=%p/share
 DocFiles: AUTHORS COPYING README
 PatchScript: 
@@ -17,6 +17,15 @@
 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: 
+#!/bin/bash -ev
+if [ `uname -p` = powerpc ]; then
+./configure %c --enable-ppc-altivec
+else
+./configure %c
+fi
+make 
+
 InstallScript: 
 mkdir -p %i/include/%n
 make install DESTDIR=%d 

Index: gromacs-mpi.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/gromacs-mpi.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- gromacs-mpi.info9 Jul 2006 04:35:00 -   1.4
+++ gromacs-mpi.info7 Oct 2007 15:09:45 -   1.5
@@ -1,7 +1,7 @@
 Info2: 
 Package: gromacs-mpi-%type_pkg[handler]
-Version: 3.3.1
-Revision: 1002
+Version: 3.3.2
+Revision: 1000
 Type: handler (lammpi openmpi)
 Depends: gromacs (= %v), %N-shlibs (= %v-%r), fftw3-shlibs, x11, 
openmotif3-shlibs, (%type_pkg[handler] = lammpi) lammpi (= 7.1.2-1000), 
(%type_pkg[handler] = openmpi) openmpi 
 BuildDepends: fftw3, x11-dev, (%type_pkg[handler] = lammpi) lammpi-dev (= 
7.1.2-1000), (%type_pkg[handler] = openmpi) openmpi-dev, gromacs-dev (= %v)
@@ -13,13 +13,18 @@
 CustomMirror: 
  Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: 1af34a99950813ca7cf893253c447cd1
+Source-MD5: f25853fefdbfbe7f4e8667a16c495736
 ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share  --enable-mpi --program-suffix=_mpi
 DocFiles: AUTHORS COPYING README
 SetCPPFLAGS: -I%p/include/%type_raw[handler]
 SetLDFLAGS: -L%p/lib/%type_raw[handler] 
 CompileScript: 
-  ./configure %c
+#!/bin/bash -ev
+  if [ `uname -p` = powerpc ]; then
+./configure %c --enable-ppc-altivec
+  else
+./configure %c
+  fi
   make mdrun
 
 InstallScript: 
@@ -37,8 +42,8 @@
lib/libmd_mpi.4.dylib
 
 Shlibs: 
-   %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)
+   %p/lib/libgmx_mpi.4.dylib 5.0.0 %n (= 3.3-1)
+   %p/lib/libmd_mpi.4.dylib 5.0.0 %n (= 3.3-1)
 
 DocFiles: AUTHORS COPYING README
  
@@ -46,7 +51,7 @@
 Package: %N-dev
 Conflicts: gromacs-mpi-dev, gromacs-mpi-lammpi-dev, gromacs-mpi-openmpi-dev
 Replaces: gromacs-mpi-dev, gromacs-mpi-lammpi-dev, gromacs-mpi-openmpi-dev
-Depends: (%type_pkg[handler] = lammpi) lammpi-dev (= 7.1.2-1000), 
(%type_pkg[handler] = openmpi) openmpi-dev, fftw3-shlibs
+Depends: %N-shlibs, fftw3-shlibs
 Files: 
 lib/libgmx_mpi.dylib
 lib/libmd_mpi.dylib
@@ -69,6 +74,10 @@
 version has parallel processing support for the main
 GROMACS package.
 
+DescUsage: 
+Any package using gromacs-mpi-openmpi-dev or gromacs-mpi-lammpi-dev
+should BuildDepends either openmpi-dev or lammpi-dev as well.
+
 Homepage: http://www.gromacs.org
 License: GPL
 Maintainer: Jack Howarth [EMAIL PROTECTED]


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.14, 1.15

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv11759

Modified Files:
zsh-templates.info 
Log Message:
several bug fixes

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- zsh-templates.info  1 Oct 2007 04:48:52 -   1.14
+++ zsh-templates.info  14 Oct 2007 06:31:16 -  1.15
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.2
+Version: 1.2.1
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: cac284d995ce28d096cb3a673ca458bf 
+Source-MD5: 59b2e4659033d8d65a8d9eedc4ff7a1c 
 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/shells zsh-templates.info, 1.15, 1.16

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv17194

Modified Files:
zsh-templates.info 
Log Message:
new revision of zsh-templates

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- zsh-templates.info  14 Oct 2007 06:31:16 -  1.15
+++ zsh-templates.info  15 Oct 2007 07:51:24 -  1.16
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.2.1
+Version: 1.2.2
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: 59b2e4659033d8d65a8d9eedc4ff7a1c 
+Source-MD5: 199822f247d01278bc317d7de6a664f1
 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/shells zsh-templates.info, 1.16, 1.17

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv20459

Modified Files:
zsh-templates.info 
Log Message:
fixes for 10.5 compatibility

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- zsh-templates.info  15 Oct 2007 07:51:24 -  1.16
+++ zsh-templates.info  28 Oct 2007 21:07:22 -  1.17
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.2.2
+Version: 1.2.3
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: 199822f247d01278bc317d7de6a664f1
+Source-MD5: ce193f978a2f2f7f502d9f003fb5c45b
 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 ccp4.info,1.21,1.22

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv831

Modified Files:
ccp4.info 
Log Message:
ccp4 patch upgrade, added anti-norton-antivirus conditional test

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -d -r1.21 -r1.22
--- ccp4.info   29 Jan 2007 01:10:58 -  1.21
+++ ccp4.info   1 Mar 2007 01:52:30 -   1.22
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.2
-Revision: 4
+Revision: 5
 GCC: 4
 Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
 Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
@@ -21,6 +21,12 @@
 Source7-MD5: 52ac21688c047287d4fcbbd1aaaea774
 Source8: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/amore.f-r1.115-r1.116.diff
 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
 #
 DescPort: 
CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
@@ -129,6 +135,9 @@
/usr/bin/patchsrc/scala_/scala.f   
../scala.f-r1.101.2.3-r1.101.2.4.diff
/usr/bin/patchccp4i/src/util_windows.tcl   
../util_windows.tcl-r1.27-r1.27.2.1.diff
/usr/bin/patchsrc/amore.f  
../amore.f-r1.115-r1.116.diff
+   /usr/bin/patchsrc/bp3_/crystal.C   
../crystal.C-r1.5-r1.6.diff
+   cp../export-r1_12.tcl  
$CCP4/ccp4i/tasks/export.tcl
+   cp../export-r1_6.def   
$CCP4/ccp4i/tasks/export.def
#
 
 

@@ -136,6 +145,24 @@
#!/bin/zsh -efv
  umask 0022

+   # The build will fail if Norton Auto-Protect is running.
+   # Check to see if it is, and abort the installation with a
+   # warning to the user.
+   if  [[ $(ps axww | grep NortonAutoProtect | wc -l) -gt 1 ]];then
+   print 
\e[1m**
+   print 
**
+   print 
**
+   print 
+   print Norton AutoProtect must be suspended during CCP4 
installation. Please do so now and then try again.
+   print 
+   print 
**
+   print 
**
+   print 
**\e[0m
+   sleep 15
+   return 1000
+   fi
+   
+   
# These are required for the build environment
  export TEMPXTAL=$PWD:h
  source include/ccp4.setup-zsh
@@ -393,7 +420,7 @@
License agreement is part of configure file -- print out form and mail 
in,
additional comments at http://xanana.ucsc.edu/xtal/ccp4.html
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0.2
-   This revision includes all available CCP4 patches as of Dec 19, 2006. 
+   This revision includes all available CCP4 patches as of Feb 24, 2007. 
and new bash and zsh command completions specific to ccp4. 
 
 DocFiles: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.22,1.23

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv12594

Modified Files:
ccp4.info 
Log Message:
ccp4 bug fix and new patches

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -d -r1.22 -r1.23
--- ccp4.info   1 Mar 2007 01:52:30 -   1.22
+++ ccp4.info   13 Mar 2007 02:57:47 -  1.23
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.0.2
-Revision: 5
+Revision: 6
 GCC: 4
 Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
 Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
@@ -27,6 +27,12 @@
 Source10-MD5: 984f7305ba151d961bef2ac25b1b9925
 Source11: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/export-r1_6.def
 Source11-MD5: 3babc1ee652fed6d2bb976bde41450a8
+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
+Source13-MD5: fa9127eaceeb3e20328400a5add6b042
+#Source14: 
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various.f-r1.124.2.3-r1.124.2.4.diff
+#Source14-MD5: 9fde5290a42032916893cd9d0ffd5b15
 #
 DescPort: 
CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
@@ -136,8 +142,11 @@
/usr/bin/patchccp4i/src/util_windows.tcl   
../util_windows.tcl-r1.27-r1.27.2.1.diff
/usr/bin/patchsrc/amore.f  
../amore.f-r1.115-r1.116.diff
/usr/bin/patchsrc/bp3_/crystal.C   
../crystal.C-r1.5-r1.6.diff
-   cp../export-r1_12.tcl  
$CCP4/ccp4i/tasks/export.tcl
-   cp../export-r1_6.def   
$CCP4/ccp4i/tasks/export.def
+   cp../export-r1_12.tcl   ccp4i/tasks/export.tcl
+   cp../export-r1_6.defccp4i/tasks/export.def
+   cp../mtz2various-r1_132.f   src/mtz2various.f
+   cp../mtz2various-r1_40.html html/mtz2various.html
+   # /usr/bin/patchsrc/mtz2various.f 
../mtz2various.f-r1.124.2.3-r1.124.2.4.diff
#
 
 

@@ -420,7 +429,7 @@
License agreement is part of configure file -- print out form and mail 
in,
additional comments at http://xanana.ucsc.edu/xtal/ccp4.html
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0.2
-   This revision includes all available CCP4 patches as of Feb 24, 2007. 
+   This revision includes all available CCP4 patches as of March 12, 2007. 
and new bash and zsh command completions specific to ccp4. 
 
 DocFiles: 


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv13043

Modified Files:
coot.info 
Log Message:
coot prerelease version update in attempt to fix a bug

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -d -r1.29 -r1.30
--- coot.info   19 Feb 2007 17:55:11 -  1.29
+++ coot.info   13 Mar 2007 02:58:41 -  1.30
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.2.1-pre-3
+Version: 0.2.1-pre-5
 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: b98e7383085e1b641bb311025748acde
+Source-MD5: 7303aff67e72a1f6a69d41bf9362647f 
 SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6


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[cvs] dists/10.4/unstable/main/finkinfo/sci refmac.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv16878

Modified Files:
refmac.info 
Log Message:
refmac MD5sum and license corrections

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- refmac.info 29 Jan 2007 04:15:48 -  1.8
+++ refmac.info 29 Mar 2007 18:08:07 -  1.9
@@ -2,7 +2,7 @@
 Version: 5.3.0026
 Revision: 1
 Source: http://www.ysbl.york.ac.uk/refmac/data/refmac5.3_source.tar.gz
-Source-MD5: 0e9a688a15c62dccffaec61be245815d 
+Source-MD5: 5633e81f9efb36077aa6743b0e1da2ee 
 SourceRename: %n-%v.tar.gz
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.3_dictionary.tar.gz
 Source2-MD5: 296c773f701c7eda67babdac2875ac4d 
@@ -44,6 +44,6 @@
 makecif and tlsgroups reside in $CBIN with %v suffix and are symbolically
 linked to suffixless commands in %p/bin.
 
-License: Restrictive 
+License: LGPL 
 Homepage:  http://www.ysbl.york.ac.uk/refmac
 Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/unstable/main/finkinfo/sci pointless.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv29417

Modified Files:
pointless.info 
Log Message:
another pointless update

Index: pointless.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pointless.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- pointless.info  22 Nov 2006 19:57:21 -  1.4
+++ pointless.info  30 Mar 2007 02:42:29 -  1.5
@@ -1,14 +1,14 @@
 Package: pointless
-Version: 1.1.0.6
+Version: 1.1.1.c
 Revision: 1
 Source: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n-%v-src.tar.gz
-Source-MD5: bc261b31722836a2c5c67128c194eb41
+Source-MD5: b162fb106caa9d5f463361feda471913
 Source2: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n.html
 Source2-MD5: c5923f0c135f8434fb97781e91b93987
 Source3: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n-ccp4i-0.0.8.tar.gz
 Source3-MD5: e4d9a43059ad3981ea7eda165c5ba5aa
-Source4: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/source/phaser-1.3.2-cctbx-src.tar.gz
-Source4-MD5: e4eee45ca8a299242a1089e35e63c7a0
+Source4: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/source/phaser-1.3.3-cctbx-src.tar.gz
+Source4-MD5: edff4d201e7b6d987c05efcf965f6023
 NoSourceDirectory: yes
 Depends: ccp4 (= 6.0.2) | ccp4-g77 (= 6.0.2) , fftw-shlibs
 BuildDepends: ccp4-dev (= 6.0.2) | ccp4-g77-dev (= 6.0.2), fftw
@@ -18,7 +18,7 @@
 #!/bin/bash -efv
 mv pointless pointless-ccp4i
 cp Makefile.linux Makefile
-perl -pi -e 's|CCTBX \= \${CLIB}/cctbx|CCTBX \= ccp4-6.0/lib/cctbx|g' 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:  


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[cvs] dists/10.4/unstable/main/finkinfo/sci pdb2pqr.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv25722

Modified Files:
pdb2pqr.info 
Log Message:
update pdb2pqr version

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- pdb2pqr.info22 Nov 2006 17:16:40 -  1.4
+++ pdb2pqr.info1 Apr 2007 22:35:45 -   1.5
@@ -1,32 +1,42 @@
 Package: pdb2pqr
-Version: 1.0.2
-Revision: 40
+Version: 1.1.2
+Revision: 1
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
-Source-MD5: 4294713d22ae34079fcd4f652f2c793a 
+Source-MD5: 40386de56577ba6842076483327bc341 
 SourceDirectory: %n-%v
-BuildDepends: g77 | fort77
+BuildDepends: fort77
 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 -efv
+#!/bin/zsh -ef 
  PATH=/usr/bin:$PATH
  perl -pi -e 's|python2.2|python2.3|g' **/* 2/dev/null
  perl -pi -e 's|python2 |python2.3 |g' **/* 2/dev/null
  perl -pi -e s|/usr/bin/python2.3|/usr/bin/python|g **/*.py 2/dev/null
-FC=gfortran py_path=/usr/bin/python2.3 
LDFLAGS=-F/System/Library/Frameworks/Python.framework  ./configure  
--with-f77=gfortran
+#  
+FC=fort77 py_path=/usr/bin/python2.3 
LDFLAGS=-F/System/Library/Frameworks/Python.framework  ./configure  
--with-f77=fort77
 make
 rm -f **/*.o
 
 InstallScript: 
-#!/bin/zsh -efv
+#!/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
+echo #\!/bin/zsh -f   |   %i/bin/pdb2pqr
+echo %p/share/pdb2pqr/pdb2pqr.py \[EMAIL PROTECTED]  |   %i/bin/pdb2pqr
+chmod a+x%i/bin/pdb2pqr
+#
+echo #\!/bin/zsh -f   |   %i/bin/propka
+echo %p/share/pdb2pqr/propka/propka \[EMAIL PROTECTED]   |   
%i/bin/propka
+chmod a+x%i/bin/propka
+# Symbolic links are problematic in this version.
+#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: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci pdb2pqr.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv26480

Modified Files:
pdb2pqr.info 
Log Message:
forgot to put back the annoying verbosity flags

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pdb2pqr.info1 Apr 2007 22:35:45 -   1.5
+++ pdb2pqr.info1 Apr 2007 22:37:08 -   1.6
@@ -11,7 +11,7 @@
 SetLDFLAGS: -F/System/Library/Frameworks/Python.framework
 ConfigureParams: py_path=/usr/bin/python2.3
 CompileScript: 
-#!/bin/zsh -ef 
+#!/bin/zsh -efv 
  PATH=/usr/bin:$PATH
  perl -pi -e 's|python2.2|python2.3|g' **/* 2/dev/null
  perl -pi -e 's|python2 |python2.3 |g' **/* 2/dev/null
@@ -22,7 +22,7 @@
 rm -f **/*.o
 
 InstallScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -efv
 mkdir -p %i/share/pdb2pqr
 cp -R * %i/share/pdb2pqr
 #


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[cvs] dists/10.4/unstable/main/finkinfo/sci pdb2pqr.info,1.6,1.7

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv1822

Modified Files:
pdb2pqr.info 
Log Message:
new version

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- pdb2pqr.info1 Apr 2007 22:37:08 -   1.6
+++ pdb2pqr.info3 Apr 2007 13:54:10 -   1.7
@@ -1,8 +1,8 @@
 Package: pdb2pqr
-Version: 1.1.2
+Version: 1.2.1 
 Revision: 1
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
-Source-MD5: 40386de56577ba6842076483327bc341 
+Source-MD5: 8e38f912c7a63596b2bb5f9632b1b5c2 
 SourceDirectory: %n-%v
 BuildDepends: fort77
 Description: Converts pdb files to pqr


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[cvs] dists/10.4/unstable/main/finkinfo/sci emboss.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv21333

Modified Files:
emboss.info 
Log Message:
fix for missing header file

Index: emboss.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- emboss.info 9 Mar 2007 01:44:28 -   1.8
+++ emboss.info 4 Apr 2007 04:26:25 -   1.9
@@ -1,8 +1,8 @@
 Package: emboss
 Version: 4.1.0
-Revision: 1
-Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14
-BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
+Revision: 2
+Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14, libgcrypt-shlibs
+BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev, 
libgcrypt
 #Replaces: emboss ( 2.7.1-2)
 Source: mirror:custom:EMBOSS-%v.tar.gz
 CustomMirror: 
@@ -16,6 +16,9 @@
   perl -pi -e 's,(pcre\S*\.h),EMBOSS/\1,g' ajax/Makefile.in
   mkdir ajax/EMBOSS
   mv ajax/pcre*.h ajax/EMBOSS
+# Replace crypt.h with gcrypt.h 
+  perl -pi -e 's|crypt.h|gcrypt.h|g'ajax/ajjava.c
+  perl -pi -e 's|crypt.h|gcrypt.h|g'emboss/jembossctl.c
 
 ConfigureParams: 
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home 
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
 --disable-dependency-tracking --libdir=%p/lib/EMBOSS
 Installscript: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci emboss.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv15804

Modified Files:
emboss.info 
Log Message:
remove include crypt.h

Index: emboss.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- emboss.info 4 Apr 2007 04:26:25 -   1.9
+++ emboss.info 4 Apr 2007 08:18:48 -   1.10
@@ -1,8 +1,8 @@
 Package: emboss
 Version: 4.1.0
 Revision: 2
-Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14, libgcrypt-shlibs
-BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev, 
libgcrypt
+Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14
+BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
 #Replaces: emboss ( 2.7.1-2)
 Source: mirror:custom:EMBOSS-%v.tar.gz
 CustomMirror: 
@@ -17,8 +17,8 @@
   mkdir ajax/EMBOSS
   mv ajax/pcre*.h ajax/EMBOSS
 # Replace crypt.h with gcrypt.h 
-  perl -pi -e 's|crypt.h|gcrypt.h|g'ajax/ajjava.c
-  perl -pi -e 's|crypt.h|gcrypt.h|g'emboss/jembossctl.c
+  perl -pi -e 's|\#include \crypt.h\||g'ajax/ajjava.c
+  perl -pi -e 's|\#include \crypt.h\||g'emboss/jembossctl.c
 
 ConfigureParams: 
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home 
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
 --disable-dependency-tracking --libdir=%p/lib/EMBOSS
 Installscript: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci emboss.info,1.11,1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv3227

Modified Files:
emboss.info 
Log Message:
remove include crypt.h and spurious dependencies I put in, with Koen's 
permission

Index: emboss.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- emboss.info 4 Apr 2007 10:34:18 -   1.11
+++ emboss.info 4 Apr 2007 15:17:51 -   1.12
@@ -1,8 +1,8 @@
 Package: emboss
 Version: 4.1.0
-Revision: 2
-Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14, libgcrypt-shlibs
-BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev, 
libgcrypt
+Revision: 3
+Depends: %N-ajax4-shlibs (= %v-%r), %N-nucleus4-shlibs (= %v-%r), 
%N-plplot5-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, 
system-java14
+BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
 #Replaces: emboss ( 2.7.1-2)
 Source: mirror:custom:EMBOSS-%v.tar.gz
 CustomMirror: 
@@ -16,9 +16,9 @@
   perl -pi -e 's,(pcre\S*\.h),EMBOSS/\1,g' ajax/Makefile.in
   mkdir ajax/EMBOSS
   mv ajax/pcre*.h ajax/EMBOSS
-# Replace crypt.h with gcrypt.h 
-  perl -pi -e 's|crypt.h|gcrypt.h|g'ajax/ajjava.c
-  perl -pi -e 's|crypt.h|gcrypt.h|g'emboss/jembossctl.c
+# Replace crypt.h with blank
+  perl -pi -e 's|\#include \crypt.h\||g'ajax/ajjava.c
+  perl -pi -e 's|\#include \crypt.h\||g'emboss/jembossctl.c
 
 ConfigureParams: 
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home 
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
 --disable-dependency-tracking --libdir=%p/lib/EMBOSS
 Installscript: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.30,1.31

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv22175

Modified Files:
coot.info 
Log Message:
new version of coot

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -d -r1.30 -r1.31
--- coot.info   13 Mar 2007 02:58:41 -  1.30
+++ coot.info   7 Apr 2007 15:26:06 -   1.31
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.2.1-pre-5
+Version: 0.3
 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: 7303aff67e72a1f6a69d41bf9362647f 
+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: cbf9e7bc2d145666385651eb6156170b
 SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
@@ -16,7 +16,7 @@
 guile16, guile16-dev, guile16-gtk-dev, gsl, libglade2, gtk-canvas-dev, 
 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, libiconv-dev
+libpng3, gnome-libs-dev, libiconv-dev, gtkglext1-shlibs
 
 #
 Depends: 
@@ -24,7 +24,8 @@
 guile16-gui, guile16-goosh (= 1.3-2), guile16, guile16-net-http, 
 freeglut-shlibs, libart2-shlibs (= 2.3.16-2), coot-shlibs (= %v-%r),
 imlib-shlibs, libjpeg-shlibs, giflib-shlibs, libpng3-shlibs, 
-glib-shlibs, gtk+2-shlibs, gnome-libs-shlibs, povray, raster3d
+glib-shlibs, gtk+2-shlibs, gnome-libs-shlibs, povray, raster3d,
+gtkglext1
 
 #
 BuildDependsOnly: false
@@ -52,6 +53,8 @@
 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
+# Temp fix for an error:
+perl -pi.bak -e 's|1 0.1\)\)\)\)\)\)\)\)|1 0.1)))|g' scheme/fitting.scm
 
 ###
 ConfigureParams:   
@@ -62,7 +65,6 @@
 --with-guile-gtk --with-guile-gtk-prefix=%p  \
 --with-gsl-prefix=%p --with-guile --with-python
 
-# --with-guile-gtk --with-guile-gtk-prefix=%p \
 ###
 CompileScript: 
 #!/bin/zsh -efv
@@ -137,34 +139,34 @@
 lib/libcoot-*.dylib  
 
Shlibs: 
-   %p/lib/libccp4mg-surface.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libccp4mg-utils.0.0.0.dylib  
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-analysis.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-AngleInfo.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-atomutils.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-cabuild.0.0.0.dylib  
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-compat.0.0.0.dylib   
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-coord-extras.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-coord-utils.0.0.0.dylib  1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-coords.0.0.0.dylib   
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-db-main.0.0.0.dylib  
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-geometry.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-high-res.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-ideal.0.0.0.dylib
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-isosurface.0.0.0.dylib   1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-ligand.0.0.0.dylib   
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-map-heavy.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-map-utils.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-mini-mol.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-mmtz-extras.0.0.0.dylib  1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-sequence-view.0.0.0.dylib1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-shelx.0.0.0.dylib
1.0.0 %n (= 0.2-1)
-   %p/lib/libcoot-skeleton.0.0.0.dylib 1.0.0 
%n (= 0.2-1)
-   %p/lib/libcoot-surface.0.0.0.dylib  
1.0.0 %n (= 0.2-1)

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.31,1.32

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv1269

Modified Files:
coot.info 
Log Message:
new version of coot with bug I found fixed upstream

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -d -r1.31 -r1.32
--- coot.info   7 Apr 2007 15:26:06 -   1.31
+++ coot.info   7 Apr 2007 15:56:01 -   1.32
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.3
+Version: 0.3.1
 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-%v.tar.gz
-Source-MD5: cbf9e7bc2d145666385651eb6156170b
+Source-MD5: 72598ba7ad4e094a83a6922efd94b741
 SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
@@ -53,8 +53,8 @@
 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
-# Temp fix for an error:
-perl -pi.bak -e 's|1 0.1\)\)\)\)\)\)\)\)|1 0.1)))|g' scheme/fitting.scm
+# Temp fix for an error (fixed in 0.3.1):
+# perl -pi.bak -e 's|1 0.1\)\)\)\)\)\)\)\)|1 0.1)))|g' scheme/fitting.scm
 
 ###
 ConfigureParams:   


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.32,1.33

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv12671

Modified Files:
coot.info 
Log Message:
tarball on server was changed - new md5sum

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -d -r1.32 -r1.33
--- coot.info   7 Apr 2007 15:56:01 -   1.32
+++ coot.info   8 Apr 2007 17:43:24 -   1.33
@@ -4,7 +4,7 @@
 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: 72598ba7ad4e094a83a6922efd94b741
+Source-MD5: 574d1459ab9f7be3e2d92585444a
 SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv17437

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

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- zsh.info5 Mar 2007 22:53:30 -   1.8
+++ zsh.info16 Apr 2007 17:33:51 -  1.9
@@ -1,6 +1,6 @@
 Package: zsh 
-Version: 4.3.2
-Revision: 1003
+Version: 4.3.3
+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: e13fc4bb338fbb27ef7508a474310c8f 
+Source-MD5: 6cf7061e44d92ff74c59330279f36fe7 
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 69d1ab9d179d7d16eb0251a0a60e0457 
+Source2-MD5: 4bacdd0aa563f733069fd281f11cc436 
 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 
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-multibyte.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv23075

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

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- zsh-multibyte.info  5 Mar 2007 22:53:30 -   1.2
+++ zsh-multibyte.info  16 Apr 2007 20:37:32 -  1.3
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
-Version: 4.3.2
-Revision: 1003
+Version: 4.3.3
+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: e13fc4bb338fbb27ef7508a474310c8f 
-Source2: mirror:custom:zsh-%v-doc.tar.bz2
-Source2-MD5: 69d1ab9d179d7d16eb0251a0a60e0457 
+Source-MD5: 6cf7061e44d92ff74c59330279f36fe7 
+Source2: mirror:custom:/zsh-%v-doc.tar.bz2
+Source2-MD5: 4bacdd0aa563f733069fd281f11cc436
 ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info 
--enable-etcdir=%p/etc/zsh --enable-maildir-support --enable-pcre 
--enable-zsh-secure-free --enable-fndir=%p/share/zsh --enable-function-subdirs 
--with-curses-terminfo --with-tcsetpgrp --enable-multibyte
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-helpfiles.info, 1.5, 1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv7287

Modified Files:
zsh-helpfiles.info 
Log Message:
update version of zsh-helpfiles to correspond to new shell version

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- zsh-helpfiles.info  10 Sep 2006 18:29:17 -  1.5
+++ zsh-helpfiles.info  17 Apr 2007 04:06:22 -  1.6
@@ -1,6 +1,6 @@
 Package: zsh-helpfiles
-Version: 4.3.2
-Revision: 1001
+Version: 4.3.3
+Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
 CustomMirror: 
@@ -26,28 +26,22 @@
 
 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: e13fc4bb338fbb27ef7508a474310c8f 
+Source-MD5: 6cf7061e44d92ff74c59330279f36fe7 
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:
 #!/bin/zsh -efv
+#set -x
 # the perl magic token breaks Util/helpfiles
 perl -pi.bak -e 's|/usr/local/bin/perl -- -\*-perl-\*-|/usr/bin/perl |g' 
Util/helpfiles
 mkdir temp
 cd temp
-command man -M %p/share/man zshall | colcrt - |  ../Util/helpfiles
-# Get rid of the false positives
-mkdir keep
-rm [A-Z][a-z]* # These are all false positives
-rm zsh*  # these are part of the real man pages
-foreach file in $( grep * | awk '{print $1}' | perl -p -e 's|\:||g' 
| sort -u )
- mv $file keep/.
-end
-mv beep cont jobs maps names pods ports rc redo styles tags types urls users   
keep/.
+command man -M %p/share/man zshbuiltins | colcrt - |  ../Util/helpfiles
 
 InstallScript:
 #!/bin/zsh -efv
+#set -x
 mkdir -p %i/share/zsh/zsh_help
-cp temp/keep/* %i/share/zsh/zsh_help/.
+cp temp/* %i/share/zsh/zsh_help/.
 mkdir -p %i/share/zsh/site-functions
 cp ../run-help %i/share/zsh/site-functions/.
 #


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-helpfiles.info, 1.6, 1.7 zsh-multibyte.info, 1.3, 1.4 zsh.info, 1.9, 1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv3368

Modified Files:
zsh-helpfiles.info zsh-multibyte.info zsh.info 
Log Message:
zsh version upgrade

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- zsh-helpfiles.info  17 Apr 2007 04:06:22 -  1.6
+++ zsh-helpfiles.info  19 Apr 2007 14:18:23 -  1.7
@@ -1,5 +1,5 @@
 Package: zsh-helpfiles
-Version: 4.3.3
+Version: 4.3.4
 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://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh/Library/init/zsh/local-functions/run-help
-Source-MD5: 6cf7061e44d92ff74c59330279f36fe7 
+Source-MD5: 8410a30e4f5c6160790bc3afc096424f 
 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 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- zsh.info16 Apr 2007 17:33:51 -  1.9
+++ zsh.info19 Apr 2007 14:18:23 -  1.10
@@ -1,5 +1,5 @@
 Package: zsh 
-Version: 4.3.3
+Version: 4.3.4
 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: 6cf7061e44d92ff74c59330279f36fe7 
+Source-MD5: 8410a30e4f5c6160790bc3afc096424f
 Source2: mirror:custom:%n-%v-doc.tar.bz2
-Source2-MD5: 4bacdd0aa563f733069fd281f11cc436 
+Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
 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 
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- zsh-multibyte.info  16 Apr 2007 20:37:32 -  1.3
+++ zsh-multibyte.info  19 Apr 2007 14:18:23 -  1.4
@@ -1,5 +1,5 @@
 Package: zsh-multibyte
-Version: 4.3.3
+Version: 4.3.4
 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: 6cf7061e44d92ff74c59330279f36fe7 
+Source-MD5: 8410a30e4f5c6160790bc3afc096424f
 Source2: mirror:custom:/zsh-%v-doc.tar.bz2
-Source2-MD5: 4bacdd0aa563f733069fd281f11cc436
+Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
 ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info 
--enable-etcdir=%p/etc/zsh --enable-maildir-support --enable-pcre 
--enable-zsh-secure-free --enable-fndir=%p/share/zsh --enable-function-subdirs 
--with-curses-terminfo --with-tcsetpgrp --enable-multibyte
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv23462

Modified Files:
zsh-templates.info 
Log Message:
zsh shell configuration templates version update

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- zsh-templates.info  17 Feb 2007 00:53:54 -  1.6
+++ zsh-templates.info  27 Apr 2007 04:27:27 -  1.7
@@ -1,21 +1,21 @@
 Package: zsh-templates
-Version: 1.0.3
+Version: 1.0.5
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/%n-%v.tgz
-Source-MD5: f98a76240897e0a316edd2830ed1dfe8 
+Source-MD5: aa5e66f6cc1d2c4466cad36d76175382 
 Depends: macosx, zsh (= 4.2.1-13) | zsh-multibyte 
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]
 Description: Template files for zsh customization 
 PatchScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -efx
 perl -pi.bak -e 's|ALT_SWPREFIX|%p|g' etc/zshenv
 rm -f etc/*.bak
 
 CompileScript:
 
 InstallScript:
-#!/bin/zsh -ef
+#!/bin/zsh -efx
 mkdir -p %i/share/zsh/templates/Library/init/zsh
 mkdir -p %i/share/zsh/templates/Applications 
 #mkdir -p %i/share/zsh/templates/Library/LaunchAgents
@@ -23,7 +23,7 @@
 mkdir -p %i/etc/zsh
 #
 # This isn't needed in the fink version, and interferes:
-rm -f Library/init/zsh/environment.xtal
+# rm -f Library/init/zsh/environment.xtal
 cp -rf Library/init/zsh/* %i/share/zsh/templates/Library/init/zsh/.
 #perl -pi.bak -e 's|/Library/init|%p/share/zsh/templates/Library/init|g' 
Library/LaunchAgents/*
 #rm -f Library/LaunchAgents/*.bak


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv11205

Modified Files:
zsh-templates.info 
Log Message:
revised instructions to make them clearer

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- zsh-templates.info  27 Apr 2007 04:27:27 -  1.7
+++ zsh-templates.info  2 May 2007 04:29:39 -   1.8
@@ -1,6 +1,6 @@
 Package: zsh-templates
 Version: 1.0.5
-Revision: 1
+Revision: 2
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/%n-%v.tgz
 Source-MD5: aa5e66f6cc1d2c4466cad36d76175382 
 Depends: macosx, zsh (= 4.2.1-13) | zsh-multibyte 
@@ -68,65 +68,68 @@
 chmod a+x 
%p/share/zsh/templates/Library/init/zsh/local-functions/darwin/whatsnew
 echo 
 echo 
+
-echo Please issue \fink describe zsh-templates\,
-echo or \man zsh-templates\ for more details.
-echo Please issue 
%p/share/zsh/templates/Library/init/zsh/local-functions/darwin/whatsnew
-echo to find out what is new in this version.
+echo Please issue \fink describe zsh-templates\ for instructions.
 echo 
+
 echo 
 sleep 5
 
 DescDetail:  
-A wiki for zsh-templates has now been created, describing
-what is in the package in detail.  It can be visited at the
-following URL: http://tinyurl.com/y3r4kp 
+===
+These files work out of the box but you must set this up in one of two ways:
 
-These files  work out of the box but the template files
-can be modified as follows. (The /sw/etc/zsh/zshenv and
-/sw/etc/zsh/zshrc should not have to be modified.  If you
-have to modify these, please report this as a bug.)
+Method 1:  
+==
 
-1 Issue sudo mkdir -p /Library/init
+Make %p/bin/zsh your default user shell.  To do so, you must edit the file 
+/etc/shells and add to it the line
 
-2 Issue sudo cp -R /sw/share/zsh/templates/Library/init/zsh /Library/init/.
-Those files will supercede the ones just copied, so edit those to make
-your desired changes, not the ones under /sw.
-Anything that appears in /Users/\$USER/Library/init/zsh 
-will be read IN ADDITION TO the other files.
+ %p/bin/zsh 
 
-3 To change the prompt theme, issue the command switch_prompt
+Then issue the following command:
 
-4 To use with /bin/zsh, copy or link the file
-/sw/share/zsh/templates/etc/zshenv to /etc/zshenv and
-likewise with /sw/share/zsh/templates/etc/zshrc to
-/etc/zshrc.  These two files are both required and have been
-designed in such a way that they should not require editing.
+ chsh -s /sw/bin/zsh
 
-5 The faster-loading open completion function is now enabled
-by default on 10.4, and you should not have to do anything other
-than start a zsh shell. On 10.3 it requires an up-to-date
-locate database to find the various Applications.  
 
-6 You can customize the behavior of X11 by issuing 
-customize_x11 or customize_x11_gui. Several
-somewhat hidden features of X11.app can be enabled or disabled.
+Method 2:  
+==
 
-7 The commands user_setup and host_setup can be invoked
+Make /bin/zsh your default shell. To do this, issue 
+
+ chsh -s /bin/zsh
+
+Then create the following two symbolic links:
+
+ sudo ln -s %p /share/zsh/templates/etc/zshenv /etc/.
+ sudo ln -s %p /share/zsh/templates/etc/zshrc  /etc/.
+
+===
+===
+
+A wiki for zsh-templates has now been created, describing
+what is in the package in detail.  It can be visited at the
+following URL: http://tinyurl.com/y3r4kp
+
+To use vi keybindings instead of emacs, issue the command
+
+ touch ~/.zshvi
+
+To change the prompt theme, issue the command switch_prompt
+
+The commands user_setup and host_setup can be invoked
 to fine-tune username and hostname completions for ssh, scp,
 switch_user, and so on.
 
-8 The command gdirs provides a gui interface to the directory
+You can customize the behavior of X11 by issuing 
+customize_x11 or customize_x11_gui. Several
+somewhat hidden features of X11.app can be enabled or disabled.
+
+The command gdirs provides a gui interface to the directory
 stack.  You can use an applescript-type interface instead of
 a Pashua-type interface by creating a file ~/.zshenv and putting
 into it the following line:
 export GUIDIRS_PASHUA='no'
 
-9 A brief description of the functions and completions
-provided can be had by typing help_template_functions
-optionally with the function name.  Only a subset are
-autoloaded by default.  Load others individually by
-uncommenting autoload -U foo lines or setting the appropriate

[cvs] dists/10.4/unstable/main/finkinfo/shells zsh.info, 1.10, 1.11 zsh-multibyte.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv12959

Modified Files:
zsh.info zsh-multibyte.info 
Log Message:
force use of /usr/bin/awk during compilation to prevent problem with fink gawk

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- zsh.info19 Apr 2007 14:18:23 -  1.10
+++ zsh.info2 May 2007 16:36:00 -   1.11
@@ -1,6 +1,6 @@
 Package: zsh 
 Version: 4.3.4
-Revision: 1
+Revision: 2
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -29,16 +29,20 @@
 Source-MD5: 8410a30e4f5c6160790bc3afc096424f
 Source2: mirror:custom:%n-%v-doc.tar.bz2
 Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
-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 
+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 AWK=/usr/bin/awk 
+
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
 perl -pi.bak -e s;DL_EXT=so;DL_EXT=dylib;g configure
- ./configure %c
+./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
-#cp config.h config.h.bak 
-#grep -v HAVE_POLL config.h.bak  config.h 
+/bin/rm -f *.bak
 make
 
 InstallScript:

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- zsh-multibyte.info  19 Apr 2007 14:18:23 -  1.4
+++ zsh-multibyte.info  2 May 2007 16:36:00 -   1.5
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
 Version: 4.3.4
-Revision: 1
+Revision: 2
 Conflicts: zsh
 Replaces: zsh
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
@@ -29,7 +29,13 @@
 Source-MD5: 8410a30e4f5c6160790bc3afc096424f
 Source2: mirror:custom:/zsh-%v-doc.tar.bz2
 Source2-MD5: 1a4ab09a9d75c5ae8585ad645406f27d
-ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info 
--enable-etcdir=%p/etc/zsh --enable-maildir-support --enable-pcre 
--enable-zsh-secure-free --enable-fndir=%p/share/zsh --enable-function-subdirs 
--with-curses-terminfo --with-tcsetpgrp --enable-multibyte
+ConfigureParams: 
+--mandir=%p/share/man --infodir=%p/share/info \
+--enable-etcdir=%p/etc/zsh --enable-maildir-support \
+--enable-pcre --enable-zsh-secure-free --enable-fndir=%p/share/zsh \ 
+--enable-function-subdirs --with-curses-terminfo --with-tcsetpgrp \
+--enable-multibyte AWK=/usr/bin/awk
+
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
@@ -37,8 +43,7 @@
  ./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
-#cp config.h config.h.bak 
-#grep -v HAVE_POLL config.h.bak  config.h 
+/bin/rm -f *.bak 
 make
 
 InstallScript:


-
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
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[cvs] dists/10.4/unstable/main/finkinfo/languages guile18-gtk.info, NONE, 1.1 guile18-gui.info, NONE, 1.1 guile18-net-http.info, NONE, 1.1 guile18-goosh.info, NONE, 1.1 guile18-www.info, NONE, 1.1 gui

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv19099

Added Files:
guile18-gtk.info guile18-gui.info guile18-net-http.info 
guile18-goosh.info guile18-www.info guile18-goosh.patch 
guile18-net-http.patch 
Log Message:
updated for guile18

--- NEW FILE: guile18-gui.info ---
Package: guile18-gui
Version: 0.2
Revision: 1002
BuildDepends: guile18-dev (= 1.6.7-1010), guile18 (= 1.6.7-1010), 
guile18-libs (= 1.6.7-1010)
Depends: guile18-shlibs (= 1.6.7-1010), guile18-gtk
Source: http://www.ossau.uklinux.net/guile/guile-gui-%v.tar.gz
Source-MD5: 89764951316dc60c21ecdb3a61242bb6 
DocFiles: README AUTHORS NEWS COPYING 
Description: Guile gui scheme code
DescDetail:  
Guile-gui is a collection of Guile Scheme code that aims to implement
a graphical user interface for Guile. 
Please send suggestions, contributions and bug reports to
[EMAIL PROTECTED] 
.
Usuage:   guile-gui 
.
   A GTK window should appear that contains a text area at the top and
   a (small) text entry widget at the bottom.  You should be able to type
   Guile expressions into the entry widget in exactly the same way
   that you would type on the command line.  In particular,
   parenthesis matching and history should both work as normal.  Your
   input is echoed in a distinctive colour and font in the text area,
   and the text area also displays any output that results from the
   evaluation of your input.

CompileScript:
#!/bin/zsh -efv
export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
./configure --prefix=%i  --with-gtk-prefix=%p
export GUILE_LOAD_PATH=%p/share/guile/1.8
make

InstallScript: 
#!/bin/zsh -efv
export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
export GUILE_LOAD_PATH=%p/share/guile/1.8
mkdir -p %i/share/guile/1.8
make install
mv %i/share/guile/gui %i/share/guile/1.8/gui
mv %i/bin/guile-gui %i/bin/guile18-gui

License: GPL
Maintainer:  W. G. Scott [EMAIL PROTECTED]
Homepage: http://www.ossau.uklinux.net/guile/

--- NEW FILE: guile18-goosh.patch ---
--- goosh-1.3/goosh.scm.origSun Jun 27 12:59:32 2004
+++ goosh-1.3/goosh.scm Sun Jun 27 17:49:13 2004
@@ -2,7 +2,7 @@
 ;;; Copyright (C) 1997, 2000, 2001 Free Software Foundation, Inc.
 ;;; version 1.3, 25 June 2001.
 
-(define-module (goosh))
+(define-module (goosh goosh))
 
 (export tail-call-program run run-concurrently run-with-pipe)
 (export-syntax run-concurrently+ run+ tail-call-pipeline+

--- NEW FILE: guile18-goosh.info ---
Package: guile18-goosh
Version: 1.3
Revision: 1005
BuildDepends: guile18-dev, guile18, guile18-libs
Depends: guile18-shlibs 
Source: http://arglist.com/guile/goosh-%v/goosh-%v.tar.gz
Source-MD5: 19a731a16af794c99647cba37ee64495   
DocFiles: README INSTALL NEWS COPYING 
InfoDocs: goosh.info
Description: Guile processs-control lib
DescDetail:  
Goosh is a small process-control library for Guile. It can 
be used to start processes and pipelines of connected processes 
and to communicate with the processes using pipes.

Patch: %n.patch
CompileScript:
#!/bin/zsh -efv
export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
./configure --prefix=%i --infodir=%i/share/info
export GUILE_LOAD_PATH=%p/share/guile/1.8
make

InstallScript: 
#!/bin/zsh -efv
export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
export GUILE_LOAD_PATH=%p/share/guile/1.8
mkdir -p %i/share/guile/1.8/goosh
mkdir -p %i/share/doc/guile18-goosh
make install
mv %i/share/guile/site/goosh.scm %i/share/guile/1.8/goosh/.

License: GPL
Maintainer:  W. G. Scott [EMAIL PROTECTED]
#
SplitOff: 
 Package: %N-doc
 Conflicts: guile16-goosh-doc ,  guile16-goosh (= 1005)
 Replaces: guile16-goosh-doc  ,  guile16-goosh (= 1005)
# DocFile: COPYING
 Files: share/info
 InfoDocs: goosh.info  
 Description: Texinfo documentation files for guile-goosh

   

--- NEW FILE: guile18-net-http.info ---
Package: guile18-net-http
Version: 0.3.1
Revision: 1001
BuildDepends: guile18-dev (= 1.6.7-1010), guile18 (= 1.6.7-1010), 
guile18-libs (= 1.6.7-1010)
Depends: guile18-shlibs  (= 1.6.7-1010)
Source: http://www.ysbl.york.ac.uk/~emsley/software/extras/net-http-%v.tar.gz
Source-MD5: b9428523889522933e4a55c7621ddfdb
SourceDirectory: net-http  
DocFiles: README LICENSE
Description: HTTP library for Guile
DescDetail:  
Guile18-net-http is a fairly straightforward HTTP library for Guile and
GOOPS. It can be used for writing scripts that need to
access web sites, or for writing libraries for protocols based on
HTTP. It models HTTP messages, clients, and servers.

Patch: %n.patch
#ConfigureParams: --infodir=%i/share/info 
CompileScript:
#!/bin/zsh -efv
export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
#./configure %c
./configure --prefix=%i --infodir=%i/share/info
export GUILE_LOAD_PATH=%p/share/guile/1.8
# make

InstallScript: 
#!/bin/zsh -efv
mkdir -p %i/share/guile/1.8
cp -r net  %i/share/guile/1.8/.

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

--- NEW FILE: guile18-gtk.info 

[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-gui.info, 1.2, 1.3 guile16-net-http.info, 1.2, 1.3 guile16-gtk.info, 1.11, 1.12 guile16-goosh.info, 1.3, 1.4 guile16-www.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv19817

Modified Files:
guile16-gui.info guile16-net-http.info guile16-gtk.info 
guile16-goosh.info guile16-www.info 
Log Message:
updated for guile18 compatibility

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- guile16-gtk.info5 Mar 2007 22:53:29 -   1.11
+++ guile16-gtk.info2 May 2007 23:37:06 -   1.12
@@ -1,6 +1,6 @@
 Package: guile16-gtk
 Version: 1.2-0.50
-Revision: 5
+Revision: 7
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
gdk-pixbuf, guile16-libs (= 1.6.7-1010), gtk+, gtk+-shlibs, x11-dev, 
gettext-dev, glib, libiconv-dev
 Depends: guile16-shlibs (= 1.6.7-1010), gtk+-shlibs, gdk-pixbuf-shlibs, 
%n-shlibs (= %v-%r) 
 Source: mirror:gnu:guile-gtk/guile-gtk-0.5.tar.gz
@@ -20,7 +20,7 @@
 sed 's/(ulong)/(unsigned long)/g' guile-gtk.c  tmp.c
 mv tmp.c guile-gtk.c
 perl -pi.bak -e 's|\$rpath/\$soname|%p/lib/\$soname|g' configure
-perl -pi.bak -e 's|exec guile|exec guile-1.6|g' build-guile-gtk-1.2
+perl -pi.bak -e 's|exec guile|exec guile-1.6|g' build-guile-gtk*
 /bin/rm texinfo.tex
 
 NoSetMAKEFLAGS: true
@@ -44,6 +44,8 @@
 perl -pi -e 's|%d||g' %i/share/guile/1.6/gtk-1.2/config.scm
 perl -pi -e 's|%d||g' %i/lib/libguilegtk-1.2.la
 perl -pi -e 's|%d||g' %i/lib/libguilegdkpixbuf-1.2.la
+mv %i/bin/build-guile-gtk %i/bin/build-guile16-gtk
+mv %i/share/guile-gtk %i/share/guile16-gtk
 
 License: GPL
 InfoDocs: %p/share/info/guile-gtk.info
@@ -79,3 +81,12 @@
 
 
 ###
+#
+SplitOff3: 
+ Package: %N-doc
+ Conflicts: guile18-gtk-doc 
+ Replaces: guile18-gtk-doc 
+ Files: share/info
+ InfoDocs: guile-gtk.info  
+ Description: Texinfo documentation files for guile16-gtk
+
\ No newline at end of file

Index: guile16-goosh.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-goosh.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- guile16-goosh.info  12 Mar 2007 05:36:52 -  1.3
+++ guile16-goosh.info  2 May 2007 23:37:06 -   1.4
@@ -1,6 +1,6 @@
 Package: guile16-goosh
 Version: 1.3
-Revision: 1003
+Revision: 1005
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
guile16-libs (= 1.6.7-1010)
 Depends: guile16-shlibs  (= 1.6.7-1010)
 Source: http://arglist.com/guile/goosh-%v/goosh-%v.tar.gz
@@ -15,14 +15,14 @@
 
 Patch: %n.patch
 CompileScript:
-#!/bin/zsh -ef
+#!/bin/zsh -efv
 export PATH=%p/share/guile/1.6/scripts/binoverride:$PATH
 ./configure --prefix=%i --infodir=%i/share/info
 export GUILE_LOAD_PATH=%p/share/guile/1.6
 make
 
 InstallScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -efv
 export PATH=%p/share/guile/1.6/scripts/binoverride:$PATH
 export GUILE_LOAD_PATH=%p/share/guile/1.6
 mkdir -p %i/share/guile/1.6/goosh
@@ -32,4 +32,13 @@
 
 License: GPL
 Maintainer:  W. G. Scott [EMAIL PROTECTED]
-   
+#
+SplitOff: 
+ Package: %N-doc
+ Conflicts: guile18-goosh-doc 
+ Replaces: guile18-goosh-doc 
+# DocFile: COPYING
+ Files: share/info
+ InfoDocs: goosh.info  
+ Description: Texinfo documentation files for guile-goosh
+   

Index: guile16-net-http.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-net-http.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- guile16-net-http.info   24 Jan 2006 16:22:15 -  1.2
+++ guile16-net-http.info   2 May 2007 23:37:06 -   1.3
@@ -17,7 +17,7 @@
 Patch: %n.patch
 #ConfigureParams: --infodir=%i/share/info 
 CompileScript:
-#!/bin/zsh -ef
+#!/bin/zsh -efv
 export PATH=%p/share/guile/1.6/scripts/binoverride:$PATH
 #./configure %c
 ./configure --prefix=%i --infodir=%i/share/info
@@ -25,7 +25,7 @@
 # make
 
 InstallScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -efv
 mkdir -p %i/share/guile/1.6
 cp -r net  %i/share/guile/1.6/.
 

Index: guile16-gui.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gui.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- guile16-gui.info24 Jan 2006 16:22:15 -  1.2
+++ guile16-gui.info2 May 2007 23:37:06 -   1.3
@@ -1,6 +1,6 @@
 Package: guile16-gui
 Version: 0.2
-Revision: 1001
+Revision: 1002
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
guile16-libs (= 1.6.7-1010)
 Depends: guile16-shlibs (= 1.6.7-1010), guile16-gtk
 Source: http://www.ossau.uklinux.net/guile/guile-gui-%v.tar.gz
@@ -25,19 +25,20 @@
evaluation of 

[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-gtk.info, 1.12, 1.13 guile18-gtk.info, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv11884

Modified Files:
guile16-gtk.info guile18-gtk.info 
Log Message:
fix to handle info file previously installed in main package

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -d -r1.12 -r1.13
--- guile16-gtk.info2 May 2007 23:37:06 -   1.12
+++ guile16-gtk.info3 May 2007 00:41:45 -   1.13
@@ -1,6 +1,6 @@
 Package: guile16-gtk
 Version: 1.2-0.50
-Revision: 7
+Revision: 8
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
gdk-pixbuf, guile16-libs (= 1.6.7-1010), gtk+, gtk+-shlibs, x11-dev, 
gettext-dev, glib, libiconv-dev
 Depends: guile16-shlibs (= 1.6.7-1010), gtk+-shlibs, gdk-pixbuf-shlibs, 
%n-shlibs (= %v-%r) 
 Source: mirror:gnu:guile-gtk/guile-gtk-0.5.tar.gz
@@ -56,6 +56,7 @@
 #
 SplitOff: 
 Package: %n-shlibs
+BuildDepends: guile16-gtk-doc
 Files: 
 lib/libguilegdk*.dylib  
 lib/libguilegtk*.dylib 

Index: guile18-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile18-gtk.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- guile18-gtk.info2 May 2007 23:35:48 -   1.1
+++ guile18-gtk.info3 May 2007 00:41:45 -   1.2
@@ -1,6 +1,6 @@
 Package: guile18-gtk
 Version: 2.0
-Revision: 1
+Revision: 2
 BuildDepends: guile18-dev, guile18, gdk-pixbuf, guile18-libs, gtk+2, 
gtk+2-shlibs, x11-dev, gettext-dev, glib, libiconv-dev, libglade2
 Depends: guile18-shlibs, gtk+2-shlibs, gdk-pixbuf-shlibs, libglade2-shlibs, 
%n-shlibs (= %v-%r) 
 Source: mirror:gnu:guile-gtk/guile-gtk-%v.tar.gz
@@ -53,6 +53,7 @@
 #
 SplitOff: 
 Package: %n-shlibs
+BuildDepends: guile18-gtk-doc
 Files: 
 lib/libguilegdk*.dylib  
 lib/libguilegtk*.dylib 


-
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.33,1.34

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv16827

Modified Files:
coot.info 
Log Message:
coot dependency revision

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.33
retrieving revision 1.34
diff -u -d -r1.33 -r1.34
--- coot.info   8 Apr 2007 17:43:24 -   1.33
+++ coot.info   3 May 2007 00:54:41 -   1.34
@@ -1,6 +1,6 @@
 Package:coot
 Version: 0.3.1
-Revision: 1
+Revision: 2
 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
@@ -16,7 +16,7 @@
 guile16, guile16-dev, guile16-gtk-dev, gsl, libglade2, gtk-canvas-dev, 
 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, libiconv-dev, gtkglext1-shlibs
+libpng3, gnome-libs-dev, libiconv-dev, gtkglext1-shlibs, guile16-gtk-doc, 
guile16-www-doc, guile16-goosh-doc 
 
 #
 Depends: 


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[cvs] dists/10.4/unstable/main/finkinfo/languages guile18-gtk.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv3158

Modified Files:
guile18-gtk.info 
Log Message:
fixed up packege with the help of JF Mertens

Index: guile18-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile18-gtk.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- guile18-gtk.info3 May 2007 00:41:45 -   1.2
+++ guile18-gtk.info3 May 2007 23:44:17 -   1.3
@@ -1,8 +1,42 @@
 Package: guile18-gtk
 Version: 2.0
-Revision: 2
-BuildDepends: guile18-dev, guile18, gdk-pixbuf, guile18-libs, gtk+2, 
gtk+2-shlibs, x11-dev, gettext-dev, glib, libiconv-dev, libglade2
-Depends: guile18-shlibs, gtk+2-shlibs, gdk-pixbuf-shlibs, libglade2-shlibs, 
%n-shlibs (= %v-%r) 
+Revision: 3
+BuildDepends: 
+ atk1   ,
+ gdk-pixbuf ,
+ glib2-dev  ,
+ gmp,
+ gtk+2-dev  ,
+ gtkglarea2 ,
+ guile18-dev,
+ guile18-libs   ,
+ libgettext3-dev,
+ libglade2  ,
+ libiconv-dev   ,
+ libtool14  ,
+ libxml2,
+ pango1-xft2-dev,
+ x11-dev
+
+Depends: 
+ gtk+2  ,
+ guile18,
+ %n-shlibs (= %v-%r)   ,
+ atk1-shlibs,
+ gdk-pixbuf-shlibs  ,
+ glib2-shlibs   ,
+ gmp-shlibs ,
+ gtk+2-shlibs   ,
+ gtkglarea2-shlibs  ,
+ guile18-shlibs ,
+ libgettext3-shlibs ,
+ libglade2-shlibs   ,
+ libiconv   ,
+ libtool14-shlibs   ,
+ libxml2-shlibs ,
+ pango1-xft2-shlibs ,
+ x11-shlibs
+
 Source: mirror:gnu:guile-gtk/guile-gtk-%v.tar.gz
 Source-MD5: a450f9f5ffc3c482f8b10590d278776f
 DocFiles: README AUTHORS NEWS COPYING 
@@ -17,32 +51,32 @@
 intrepid Guile hackers around the world.
 
 PatchScript: 
-perl -pi.bak -e 's|\$rpath/\$soname|%p/lib/\$soname|g' configure
-perl -pi.bak -e 's|exec guile|exec guile-1.8|g' build-guile-gtk*
+ perl -pi.bak -e 's|\$rpath/\$soname|%p/lib/\$soname|g' configure
+ perl -pi.bak -e 's|exec guile|exec guile-1.8|g' build-guile-gtk*
 /bin/rm texinfo.tex
 
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
 CompileScript:
 #!/bin/zsh -efv
-export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
-./configure --prefix=%i  --with-gtk-prefix=%p  --infodir=%i/share/info 
--with-gdk-pixbuf=yes --with-glade=yes --with-gtkgl=yes
-export GUILE_LOAD_PATH=%p/share/guile/1.8
-make
+ export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
+ ./configure --prefix=%i  --with-gtk-prefix=%p  --infodir=%i/share/info 
--with-gdk-pixbuf=yes --with-glade=yes --with-gtkgl=yes
+ export GUILE_LOAD_PATH=%p/share/guile/1.8
+ make
 
 InstallScript: 
 #!/bin/zsh -efv
-export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
-export GUILE_LOAD_PATH=%p/share/guile/1.8
-mkdir -p %i/share/guile/1.8
-make install
-mv %i/share/guile/gtk %i/share/guile/1.8/gtk
-mv %i/share/guile/gtk-2.0 %i/share/guile/1.8/gtk-2.0
-perl -pi -e 's|%d||g' %i/share/guile/1.8/gtk/config.scm
-perl -pi -e 's|%d||g' %i/share/guile/1.8/gtk-2.0/config.scm
-perl -pi -e 's|%d||g' %i/lib/*.la
-mv %i/bin/build-guile-gtk %i/bin/build-guile18-gtk
-mv %i/share/guile-gtk %i/share/guile18-gtk
+ export PATH=%p/share/guile/1.8/scripts/binoverride:$PATH
+ export GUILE_LOAD_PATH=%p/share/guile/1.8
+ mkdir -p %i/share/guile/1.8
+ make install
+ mv %i/share/guile/gtk %i/share/guile/1.8/gtk
+ mv %i/share/guile/gtk-2.0 %i/share/guile/1.8/gtk-2.0
+ perl -pi -e 's|%d||g' %i/share/guile/1.8/gtk/config.scm
+ perl -pi -e 's|%d||g' %i/share/guile/1.8/gtk-2.0/config.scm
+ perl -pi -e 's|%d||g' %i/lib/*.la
+ mv %i/bin/build-guile-gtk %i/bin/build-guile18-gtk
+ mv %i/share/guile-gtk %i/share/guile18-gtk
 
 License: GPL
 InfoDocs: %p/share/info/guile-gtk.info
@@ -53,7 +87,22 @@
 #
 SplitOff: 
 Package: %n-shlibs
-BuildDepends: guile18-gtk-doc
+Depends: 
+ atk1-shlibs  ,
+ glib2-shlibs ,
+ gmp-shlibs   ,
+ gtk+2-shlibs ,
+ gtkglarea2-shlibs,
+ guile18-gtk-shlibs   ,
+ guile18-shlibs   ,
+ libgettext3-shlibs   ,
+ libglade2-shlibs ,
+ libiconv ,
+ libtool14-shlibs ,
+ libxml2-shlibs   ,
+ pango1-xft2-shlibs   ,
+ x11-shlibs
+
 Files: 
 lib/libguilegdk*.dylib  
 lib/libguilegtk*.dylib 
@@ -79,6 +128,7 @@
 BuildDependsOnly: True
 Conflicts: guile16-gtk-dev
 Replaces: guile16-gtk-dev
+Depends: %N-shlibs (= %v-%r) 
 Files:
 include/*
 lib/*.a
@@ -93,6 +143,9 @@
  InfoDocs: guile-gtk.info  
  Description: Texinfo documentation files for guile18-gtk
 
-
+DescPackaging: 
+ Advice and help from Jean-Francois Mertens and Paul Emsley is greatfully 
acknowledged.
+ I 

[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-gtk.info, 1.13, 1.14

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv21387

Modified Files:
guile16-gtk.info 
Log Message:
fixed up packege with the help of JF Mertens

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -d -r1.13 -r1.14
--- guile16-gtk.info3 May 2007 00:41:45 -   1.13
+++ guile16-gtk.info4 May 2007 00:32:48 -   1.14
@@ -56,7 +56,14 @@
 #
 SplitOff: 
 Package: %n-shlibs
-BuildDepends: guile16-gtk-doc
+Depends: 
+   gdk-pixbuf-shlibs
+   gettext
+   glib-shlibs
+   gtk+-shlibs
+   guile16-gtk-shlibs
+   libiconv
+
 Files: 
 lib/libguilegdk*.dylib  
 lib/libguilegtk*.dylib 
@@ -76,6 +83,7 @@
 SplitOff2: 
 Package: %n-dev
 BuildDependsOnly: True
+Depends: %n-shlibs (= %v-%r) 
 Files:
 include/*
 lib/*.a


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.34,1.35

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv21775

Modified Files:
coot.info 
Log Message:
added missing dependencies

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -d -r1.34 -r1.35
--- coot.info   3 May 2007 00:54:41 -   1.34
+++ coot.info   4 May 2007 00:33:35 -   1.35
@@ -15,17 +15,17 @@
 ccp4-onlylibs-dev (= 6.0.2-1), glib, gtk+2, freeglut, gtkglarea,
 guile16, guile16-dev, guile16-gtk-dev, gsl, libglade2, gtk-canvas-dev, 
 libart2 (= 2.3.16-2), libart2-shlibs (= 2.3.16-2), 
-guile16-net-http, gtk+2-dev, libgettext3-dev, imlib, libjpeg, giflib,
+guile16-net-http, gtk+-dev, libgettext3-dev, imlib, libjpeg, giflib,
 libpng3, gnome-libs-dev, libiconv-dev, gtkglext1-shlibs, guile16-gtk-doc, 
guile16-www-doc, guile16-goosh-doc 
 
 #
 Depends: 
-guile16-shlibs, gsl-shlibs, libglade2-shlibs, guile16-gtk, guile16-www,
-guile16-gui, guile16-goosh (= 1.3-2), guile16, guile16-net-http, 
+guile16-shlibs, gsl-shlibs, libglade2-shlibs, guile16-gtk,guile16-gtk-shlibs, 
guile16-www,
+guile16-gui, guile16-goosh (= 1.3-2), guile16, guile16-shlibs, 
guile16-net-http, 
 freeglut-shlibs, libart2-shlibs (= 2.3.16-2), coot-shlibs (= %v-%r),
 imlib-shlibs, libjpeg-shlibs, giflib-shlibs, libpng3-shlibs, 
-glib-shlibs, gtk+2-shlibs, gnome-libs-shlibs, povray, raster3d,
-gtkglext1
+glib-shlibs, gtk+-shlibs, gnome-libs-shlibs, povray, raster3d, 
libgettext3-shlibs,
+gtkglext1, giflib-shlibs, libiconv, libtiff-shlibs
 
 #
 BuildDependsOnly: false


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv4050

Modified Files:
coot.info 
Log Message:
removed dependency on non-existent package, keep same revision number

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.35
retrieving revision 1.36
diff -u -d -r1.35 -r1.36
--- coot.info   4 May 2007 00:33:35 -   1.35
+++ coot.info   5 May 2007 02:09:22 -   1.36
@@ -12,21 +12,59 @@
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 ###
 BuildDepends: 
-ccp4-onlylibs-dev (= 6.0.2-1), glib, gtk+2, freeglut, gtkglarea,
-guile16, guile16-dev, guile16-gtk-dev, gsl, libglade2, gtk-canvas-dev, 
-libart2 (= 2.3.16-2), libart2-shlibs (= 2.3.16-2), 
-guile16-net-http, gtk+-dev, libgettext3-dev, imlib, libjpeg, giflib,
-libpng3, gnome-libs-dev, libiconv-dev, gtkglext1-shlibs, guile16-gtk-doc, 
guile16-www-doc, guile16-goosh-doc 
+ ccp4-onlylibs-dev (= 6.0.2-1)  ,
+ glib,
+ gtk+,
+ freeglut,
+ gtkglarea   ,
+ guile16 ,
+ guile16-dev ,
+ guile16-gtk-dev ,
+ gsl ,
+ libglade2   ,
+ gtk-canvas-dev  ,
+ libart2 (= 2.3.16-2)   ,
+ guile16-net-http,
+ libgettext3-dev ,
+ imlib   ,
+ libjpeg ,
+ giflib  ,
+ libpng3 ,
+ gnome-libs-dev  ,
+ libiconv-dev,
+ gtkglext1-shlibs,
+ guile16-gtk-doc ,
+ guile16-www-doc ,
+ guile16-goosh-doc 
 
 #
 Depends: 
-guile16-shlibs, gsl-shlibs, libglade2-shlibs, guile16-gtk,guile16-gtk-shlibs, 
guile16-www,
-guile16-gui, guile16-goosh (= 1.3-2), guile16, guile16-shlibs, 
guile16-net-http, 
-freeglut-shlibs, libart2-shlibs (= 2.3.16-2), coot-shlibs (= %v-%r),
-imlib-shlibs, libjpeg-shlibs, giflib-shlibs, libpng3-shlibs, 
-glib-shlibs, gtk+-shlibs, gnome-libs-shlibs, povray, raster3d, 
libgettext3-shlibs,
-gtkglext1, giflib-shlibs, libiconv, libtiff-shlibs
+ coot-shlibs (= %v-%r),
+ freeglut-shlibs  ,
+ giflib-shlibs,
+ glib-shlibs  ,
+ gnome-libs-shlibs,
+ gsl-shlibs   ,
+ gtk+-shlibs  ,
+ guile16-gtk-shlibs   ,
+ guile16-shlibs   ,
+ imlib-shlibs ,
+ libgettext3-shlibs   ,
+ libiconv ,
+ libjpeg-shlibs   ,
+ libpng3-shlibs   ,
+ libtiff-shlibs   ,
+ guile16-gtk  ,
+ guile16-www  ,
+ guile16-gui  ,
+ guile16-goosh (= 1.3-2) ,
+ guile16  ,
+ guile16-net-http ,
+ povray   ,
+ raster3d ,
+ gtkglext1 
 
+# gtkglext1 required at runtime for stereo functionality
 #
 BuildDependsOnly: false
 NoSetLDFLAGS: true


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[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-gtk.info, 1.14, 1.15

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv6777

Modified Files:
guile16-gtk.info 
Log Message:
put commas between dependencies, no change in revision number

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- guile16-gtk.info4 May 2007 00:32:48 -   1.14
+++ guile16-gtk.info5 May 2007 02:16:12 -   1.15
@@ -1,8 +1,8 @@
 Package: guile16-gtk
 Version: 1.2-0.50
-Revision: 8
-BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
gdk-pixbuf, guile16-libs (= 1.6.7-1010), gtk+, gtk+-shlibs, x11-dev, 
gettext-dev, glib, libiconv-dev
-Depends: guile16-shlibs (= 1.6.7-1010), gtk+-shlibs, gdk-pixbuf-shlibs, 
%n-shlibs (= %v-%r) 
+Revision: 9
+BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
gdk-pixbuf, guile16-libs (= 1.6.7-1010), gtk+, gtk+-shlibs, x11-dev, 
libgettext3-dev, glib, libiconv-dev
+Depends: guile16-shlibs (= 1.6.7-1010), gtk+-shlibs, gdk-pixbuf-shlibs, 
libgettext3-shlibs, %n-shlibs (= %v-%r) 
 Source: mirror:gnu:guile-gtk/guile-gtk-0.5.tar.gz
 Source-MD5: af683e33ef1d575dc501cbcba3acf83e
 DocFiles: README AUTHORS NEWS COPYING 
@@ -57,11 +57,11 @@
 SplitOff: 
 Package: %n-shlibs
 Depends: 
-   gdk-pixbuf-shlibs
-   gettext
-   glib-shlibs
-   gtk+-shlibs
-   guile16-gtk-shlibs
+   gdk-pixbuf-shlibs   ,
+   gettext ,
+   glib-shlibs ,
+   gtk+-shlibs ,
+   guile16-gtk-shlibs  ,
libiconv
 
 Files: 
@@ -93,9 +93,10 @@
 #
 SplitOff3: 
  Package: %N-doc
- Conflicts: guile18-gtk-doc 
- Replaces: guile18-gtk-doc 
+ Conflicts: guile18-gtk-doc, guile16-gtk (= 1.2-0.50-6)
+ Replaces: guile18-gtk-doc , guile16-gtk (= 1.2-0.50-6)
  Files: share/info
  InfoDocs: guile-gtk.info  
  Description: Texinfo documentation files for guile16-gtk
-
\ No newline at end of file
+
+


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[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-gtk.info, 1.15, 1.16

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv18608

Modified Files:
guile16-gtk.info 
Log Message:
fixed one more screwup that prevented compilation

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- guile16-gtk.info5 May 2007 02:16:12 -   1.15
+++ guile16-gtk.info5 May 2007 02:47:27 -   1.16
@@ -83,7 +83,7 @@
 SplitOff2: 
 Package: %n-dev
 BuildDependsOnly: True
-Depends: %n-shlibs (= %v-%r) 
+Depends: guile16-gtk-shlibs (= %v-%r) 
 Files:
 include/*
 lib/*.a


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[cvs] dists/10.4/unstable/main/finkinfo/languages guile16-goosh.info, 1.4, 1.5 guile18-goosh.info, 1.1, 1.2 guile18-www.info, 1.1, 1.2 guile16-www.info, 1.3, 1.4 guile16-gtk.info, 1.16, 1.17 guile18-g

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv19237

Modified Files:
guile16-goosh.info guile18-goosh.info guile18-www.info 
guile16-www.info guile16-gtk.info guile18-gtk.info 
Log Message:
deleted duplicate InfoDocs fields

Index: guile18-goosh.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile18-goosh.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- guile18-goosh.info  2 May 2007 23:35:48 -   1.1
+++ guile18-goosh.info  5 May 2007 04:15:05 -   1.2
@@ -1,12 +1,11 @@
 Package: guile18-goosh
 Version: 1.3
-Revision: 1005
+Revision: 1006
 BuildDepends: guile18-dev, guile18, guile18-libs
 Depends: guile18-shlibs 
 Source: http://arglist.com/guile/goosh-%v/goosh-%v.tar.gz
 Source-MD5: 19a731a16af794c99647cba37ee64495   
 DocFiles: README INSTALL NEWS COPYING 
-InfoDocs: goosh.info
 Description: Guile processs-control lib
 DescDetail:  
 Goosh is a small process-control library for Guile. It can 
@@ -37,7 +36,6 @@
  Package: %N-doc
  Conflicts: guile16-goosh-doc ,  guile16-goosh (= 1005)
  Replaces: guile16-goosh-doc  ,  guile16-goosh (= 1005)
-# DocFile: COPYING
  Files: share/info
  InfoDocs: goosh.info  
  Description: Texinfo documentation files for guile-goosh

Index: guile16-goosh.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-goosh.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- guile16-goosh.info  2 May 2007 23:37:06 -   1.4
+++ guile16-goosh.info  5 May 2007 04:15:05 -   1.5
@@ -1,12 +1,11 @@
 Package: guile16-goosh
 Version: 1.3
-Revision: 1005
+Revision: 1006
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
guile16-libs (= 1.6.7-1010)
 Depends: guile16-shlibs  (= 1.6.7-1010)
 Source: http://arglist.com/guile/goosh-%v/goosh-%v.tar.gz
 Source-MD5: 19a731a16af794c99647cba37ee64495   
 DocFiles: README INSTALL NEWS COPYING 
-InfoDocs: goosh.info
 Description: Guile processs-control lib
 DescDetail:  
 Goosh is a small process-control library for Guile. It can 
@@ -37,7 +36,6 @@
  Package: %N-doc
  Conflicts: guile18-goosh-doc 
  Replaces: guile18-goosh-doc 
-# DocFile: COPYING
  Files: share/info
  InfoDocs: goosh.info  
  Description: Texinfo documentation files for guile-goosh

Index: guile18-www.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile18-www.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- guile18-www.info2 May 2007 23:35:48 -   1.1
+++ guile18-www.info5 May 2007 04:15:05 -   1.2
@@ -36,7 +36,6 @@
  Package: %N-doc
  Conflicts: guile16-www-doc , guile16-www (= 1.1.1-1004)
  Replaces: guile16-www-doc , guile16-www (= 1.1.1-1004)
-# DocFile: COPYING
  Files: share/info
  InfoDocs: guile-www.info  
  Description: Texinfo documentation files for guile-goosh

Index: guile16-www.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-www.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- guile16-www.info2 May 2007 23:37:06 -   1.3
+++ guile16-www.info5 May 2007 04:15:05 -   1.4
@@ -36,7 +36,6 @@
  Package: %N-doc
  Conflicts: guile18-www-doc  
  Replaces: guile18-www-doc  
-# DocFile: COPYING
  Files: share/info
  InfoDocs: guile-www.info  
  Description: Texinfo documentation files for guile-goosh

Index: guile16-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile16-gtk.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- guile16-gtk.info5 May 2007 02:47:27 -   1.16
+++ guile16-gtk.info5 May 2007 04:15:05 -   1.17
@@ -1,6 +1,6 @@
 Package: guile16-gtk
 Version: 1.2-0.50
-Revision: 9
+Revision: 11
 BuildDepends: guile16-dev (= 1.6.7-1010), guile16 (= 1.6.7-1010), 
gdk-pixbuf, guile16-libs (= 1.6.7-1010), gtk+, gtk+-shlibs, x11-dev, 
libgettext3-dev, glib, libiconv-dev
 Depends: guile16-shlibs (= 1.6.7-1010), gtk+-shlibs, gdk-pixbuf-shlibs, 
libgettext3-shlibs, %n-shlibs (= %v-%r) 
 Source: mirror:gnu:guile-gtk/guile-gtk-0.5.tar.gz
@@ -48,7 +48,6 @@
 mv %i/share/guile-gtk %i/share/guile16-gtk
 
 License: GPL
-InfoDocs: %p/share/info/guile-gtk.info
 Maintainer:  W. G. Scott [EMAIL PROTECTED]
 Homepage:  http://www.gnu.org/software/guile-gtk/
 #

Index: guile18-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/languages/guile18-gtk.info,v
retrieving revision 1.3

[cvs] dists/10.4/unstable/main/finkinfo/sci refmac.info, 1.9, 1.10 refmac.patch, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv31913

Modified Files:
refmac.info refmac.patch 
Log Message:
new refmac version

Index: refmac.patch
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.patch,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- refmac.patch29 Jan 2007 04:42:22 -  1.4
+++ refmac.patch11 May 2007 01:41:35 -  1.5
@@ -24,468 +24,4 @@
 +C  ENDIF
IH(5)=IDAY
IH(6)=IMON
-   IH(7)=IYR
-diff -ruN refmac-orig/makefile refmac/makefile
 refmac-orig/makefile   2006-11-23 19:29:38.0 -0800
-+++ refmac/makefile2006-11-23 19:34:38.0 -0800
-@@ -1,305 +1,155 @@
--
--#
--
--i386-linux = linux
--alpha  = alpha
--iris4d = sgin
--sun4   = sun
--
--u = $($(HOSTTYPE))
--
--#
--
--refmac   =   refmac_$(u)_5
--libcheck = libcheck_$(u)_5
--
--tar = $(refmac).tar
--
--#
--
--f_alpha = f77 -O2 -fpe0 -assume dummy_aliases -non_shared -check overflow 
-check bounds
--f_linux = g77 -O1 -fno-second-underscore -fno-globals -fno-automatic 
-unroll-loops -static
--f_sgin = f77 -O1  -n32 -OPT:Olimit=7000 -nocpp  -w -c
--f_sun = /opt/SUNWspro/bin/f77 -xlang=f77 -ftrap=%none -Xlist -xcheck=%all -O3 
-w -KPIC -fpover=yes
--f = $(f_$(u))
--
--#
--
--s_alpha = ALPHA
--s_linux = LINUX
--s_sgin  = SGIn32
--s_sun   = SunOS
--s = $(s_$(u))
--
--l = $(CLIB)/
--
--t = tmp_$(u)/
--
--SUBR =  \
--$(t)refmac_newdic.o \
--$(t)solvent_contr_mask.o\
--$(t)hkon_secder_tch.o   \
--$(t)fast_hessian_tabulation.o   \
--$(t)subvag.o\
--$(t)lsq_symm_atoms.o\
--$(t)oppro_tor1.o\
--$(t)rcard_tor1.o\
--$(t)subcf_scale1.o  \
--$(t)subag_scale_hessian.o   \
--$(t)extra_eigen.o   \
--$(t)rigid_body_newdic.o \
--$(t)aniso_ref_eigen.o   \
--$(t)linalgebra.o\
--$(t)make_CIF.o  \
--$(t)make_subr.o \
--$(t)make_subr_refmac.o  \
--$(t)tls_newdic_non.o\
--$(t)vdw_symmetry.o  \
--$(t)make_lib.o  \
--$(t)make_crd.o  \
--$(t)make_new.o  \
--$(t)make_rst.o  \
--$(t)make_PDB.o  \
--$(t)makecif.o   \
--$(t)make_refmac_dummy.o \
--$(t)ls_scaling_double.o \
--$(t)interpolate_mod.o   \
--$(t)rharvest.o  \
--$(t)newentry_idealise.o \
--$(t)ml_scaling_double.o \
--$(t)ncs_const.o \
--$(t)gaussian_int.o  \
--$(t)subnumrec.o
--
--LIBR =  \
--$(SUBR) \
--$(l)libccp4f.a   \
--$(l)libccp4c.a   \
--$(l)libccif.a
--
--SUBL =  \
--$(t)main_libcheck.o \
--$(t)make_subr_2.o   \
--$(t)make_subr.o \
--$(t)make_lib.o  \
--$(t)libcheck.o  \
--$(t)make_PDB.o  \
--$(t)make_CIF.o  \
--$(t)make_new.o  \
--$(t)make_crd.o  \
--$(t)make_unix_ccp4.o\
--$(t)emin.o  \
--$(t)libcheck_min.o
--
--LIBL =  \
--$(SUBL) \
--$(l)libccp4f.a  \
--$(l)libccp4c.a
--
--#
--
--ed = echo 'g/^CMDW-4.2/s///@[EMAIL PROTECTED]@' | tr @ \012 | ed 
-s
--
--#
--
--all: $(refmac) $(libcheck)
--
--gz:  $(tar).gz
--
--$(tar).gz:   $(refmac) $(libcheck)
--   tar -cvf $(tar) $(refmac) $(libcheck)
--   gzip --best $(tar)
--
--$(refmac):   $(t) $(LIBR)
--   $(f) -o $(refmac) $(LIBR)
--
--$(libcheck): $(t) $(LIBL)
--   $(f) -o $(libcheck) $(LIBL)
--
--$(t):
--   mkdir $(t)
--
--#
--
--clean:
--   /bin/rm -f $(SUBR) $(SUBL) oppro_tor1.f 
rcard_tor1.f
--
--cleanall:
--   /bin/rm -f $(SUBR) $(SUBL) $(refmac) 
$(libcheck) $(tar) $(tar).gz
--
--vars:

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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv13313

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

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- zsh-templates.info  2 May 2007 04:29:39 -   1.8
+++ zsh-templates.info  12 May 2007 17:49:14 -  1.9
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.0.5
-Revision: 2
-Source:  http://xanana.ucsc.edu/~wgscott/mystuff/%n-%v.tgz
-Source-MD5: aa5e66f6cc1d2c4466cad36d76175382 
+Version: 1.1
+Revision: 1
+Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
+Source-MD5: 225be39cceb8e644b974734f27c48b6a 
 Depends: macosx, zsh (= 4.2.1-13) | zsh-multibyte 
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]
@@ -109,25 +109,10 @@
 what is in the package in detail.  It can be visited at the
 following URL: http://tinyurl.com/y3r4kp
 
-To use vi keybindings instead of emacs, issue the command
-
- touch ~/.zshvi
-
-To change the prompt theme, issue the command switch_prompt
-
-The commands user_setup and host_setup can be invoked
-to fine-tune username and hostname completions for ssh, scp,
-switch_user, and so on.
-
-You can customize the behavior of X11 by issuing 
-customize_x11 or customize_x11_gui. Several
-somewhat hidden features of X11.app can be enabled or disabled.
+The command configure_zsh_templates will be issued automatically
+when an interactive shell is started for the first time. A GUI will
+assist the user in fine-tuning the configuration automatically.
 
-The command gdirs provides a gui interface to the directory
-stack.  You can use an applescript-type interface instead of
-a Pashua-type interface by creating a file ~/.zshenv and putting
-into it the following line:
-export GUIDIRS_PASHUA='no'
 
 ===
 


-
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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.9, 1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv22911

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

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/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  12 May 2007 17:49:14 -  1.9
+++ zsh-templates.info  12 May 2007 20:58:49 -  1.10
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.1
+Version: 1.1.1
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: 225be39cceb8e644b974734f27c48b6a 
+Source-MD5: 80cfaef572fa9af6650c7485173e9561 
 Depends: macosx, zsh (= 4.2.1-13) | zsh-multibyte 
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]


-
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[cvs] dists/10.4/unstable/main/finkinfo/sci refmac.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv4941

Modified Files:
refmac.info 
Log Message:
fixed bad md5sum

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- refmac.info 11 May 2007 01:41:35 -  1.10
+++ refmac.info 13 May 2007 01:46:02 -  1.11
@@ -5,7 +5,7 @@
 Source-MD5: 0a5a8a972294801c6bc4b32f365e3aef 
 SourceRename: %n-%v.tar.gz
 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.3_dictionary.tar.gz
-Source2-MD5: 296c773f701c7eda67babdac2875ac4d 
+Source2-MD5: ed1010b9fd7b18e5930402835086fa61
 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


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[cvs] dists/10.4/unstable/main/finkinfo/sci pymol-py.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv6232

Modified Files:
pymol-py.info 
Log Message:
pymol version update

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- pymol-py.info   27 Feb 2007 06:52:27 -  1.9
+++ pymol-py.info   26 May 2007 15:45:49 -  1.10
@@ -1,12 +1,12 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 0.99
-Revision: 1004
+Revision: 1005
 Maintainer: Jack Howarth [EMAIL PROTECTED]
 Type: python (2.3 2.4 2.5)
-Source: mirror:sourceforge:fink/pymol-0_99rev8-src.tgz
-Source-MD5: c8b2cb030dd9aea97c875061fb7ba35a
-SourceDirectory: pymol-%vrev8
+Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-0_99rev10-src.tgz
+Source-MD5: 0aeba9d0c3b372f182bae07a0a161b5a
+SourceDirectory: pymol-%vrev10
 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 (= 4.3.29-1001)|db43 (= 
4.3.29-1001), readline (= 4.3-1028), gdbm3, expat, tcltk-dev, blt, x11-dev
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25
@@ -39,8 +39,8 @@
 DescPackaging: 
 The tarball used for this version was created in accordance to the BSD
 license of pymol using the following instructions...
-   svn export -r 2805 
https://svn.sourceforge.net/svnroot/pymol/branches/b099/pymol pymol-0.99rev8
-   tar --exclude=.svn -zcvf pymol-0_99rev8-src.tgz pymol-0.99rev8
+   svn export -r 2974  
https://svn.sourceforge.net/svnroot/pymol/branches/b099/pymol pymol-0.99rev10
+   tar --exclude=.svn -zcvf pymol-0_99rev10-src.tgz pymol-0.99rev10
 
 DescUsage: Just type 'pymol' at the command prompt inside an X environment.
 License: OSI-Approved


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[cvs] dists/10.4/unstable/main/finkinfo/sci pymol-py.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv7966

Modified Files:
pymol-py.info 
Log Message:
changed Source to fink mirror

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- pymol-py.info   26 May 2007 15:45:49 -  1.10
+++ pymol-py.info   27 May 2007 18:13:37 -  1.11
@@ -4,7 +4,8 @@
 Revision: 1005
 Maintainer: Jack Howarth [EMAIL PROTECTED]
 Type: python (2.3 2.4 2.5)
-Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-0_99rev10-src.tgz
+Source: mirror:sourceforge:fink/pymol-0_99rev10-src.tgz
+# Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-0_99rev10-src.tgz
 Source-MD5: 0aeba9d0c3b372f182bae07a0a161b5a
 SourceDirectory: pymol-%vrev10
 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


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[cvs] dists/10.4/unstable/main/finkinfo/sci apbs-mpi.info,1.6,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv29217

Removed Files:
apbs-mpi.info 
Log Message:
apbs mpi being removed until I can provide a proper package for current version

--- apbs-mpi.info DELETED ---


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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4-onlylibs-dev.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv17362

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
updated package

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/stable/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  22 Nov 2006 17:16:39 -  1.2
+++ ccp4-onlylibs-dev.info  9 Jun 2007 04:06:49 -   1.3
@@ -1,32 +1,29 @@
 Package: ccp4-onlylibs-dev
 # Use version numbering to sync with the current CCP4 release:
-Version: 6.0   
-Revision: 1012
+Version: 6.0.2
+Revision: 2
 GCC: 4.0
+Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz
 #Source: ftp://ftp.ccp4.ac.uk/prerelease/%n.tar.gz
-#Source-MD5: cf085751833aecc7ccef9e67de7e9fcc   
-Source: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-%v.tar.gz
-Source-MD5: d9dd2e786953c812acec42b41a1c08a5   
-SourceRename: %n-%v.tar.gz
+Source-MD5: edb1034b0a2699bcb43abb6463f7b9e9
+#SourceRename: %n-%v.tar.gz
 SourceDirectory: %n
 Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
 Source2-MD5: ea307964e3786bef0868ea560471
-#Source3:  http://chemistry.ucsc.edu/~wgscott/xtal/clipper_%v-src.tgz 
-#Source3-MD5: 1c7a91218a4a27af1c2506f39df4692a
-Depends:  
-# BuildDepends: gcc4 (= 2:4.1.0-1)
-BuildDepends: fort77
+Depends:  gcc42-shlibs
+BuildDepends: gcc42
+# BuildDepends: fort77
 BuildDependsOnly: false
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 ###
-Patch: %n.patch
+#Patch: %n.patch
 PatchScript: 
 #!/bin/zsh -efv
 umask 0022
 # Use my patched configure and ccp4.setup-zsh files
 cp ../ccp4.setup-zsh include/.
-cp ../configure .
+# cp ../configure .
 # setup scripts for tcsh, zsh and bash users
 export TEMPXTAL=$PWD:h
 #
@@ -39,8 +36,18 @@
 # make copy for tcsh users (CCP4 convention is no suffix)
 cp include/ccp4.setup-dist include/ccp4.setup
 #
+# Enable everything.
 # We need the mmdbold clipper libraries built for COOT:
 perl -pi.bak -e 's|enable_mmdbold=no|enable_mmdbold=yes|g' 
lib/clipper/configure*
+perl -pi.bak -e 's|enable_phs=no|enable_phs=yes|g' lib/clipper/configure*
+perl -pi.bak -e 's|enable_mmdb=no|enable_mmdb=yes|g' lib/clipper/configure*
+perl -pi.bak -e 's|enable_minimol=no|enable_minimol=yes|g' 
lib/clipper/configure*
+perl -pi.bak -e 's|enable_cif=no|enable_cif=yes|g' lib/clipper/configure*
+perl -pi.bak -e 's|enable_ccp4=no|enable_ccp4=yes|g' lib/clipper/configure*
+# perl -pi.bak -e 's|enable_cctbx=no|enable_cctbx=yes|g' lib/clipper/configure*
+perl -pi.bak -e 's|enable_cns=no|enable_cns=yes|g' lib/clipper/configure*
+perl -pi.bak -e 's|enable_fortran=no|enable_fortran=yes|g' 
lib/clipper/configure*
+
 # clean up:
 rm -f  include/*.bak lib/clipper/*.bak
 
@@ -53,19 +60,21 @@
 source include/ccp4.setup-zsh
 export DYLD_LIBRARY_PATH=$CLIB
 #
-#FC=gfortran  ./configure --onlylibs Darwin
-FC=fort77  ./configure --onlylibs Darwin
+FC=gfortran  ./configure --onlylibs Darwin
+#FC=fort77  ./configure --onlylibs Darwin
+ln -s $CCP4/lib/src $CCP4/lib/clipper/ccp4
 #
 #  fix some post-configure bugs
 #
-make -i 2../make.log  |tee ../make.log  
-make -i install 2../makeinst.log  |tee ../makeinst.log  
+make  2../make.log  |tee ../make.log  
+make  install 2../makeinst.log  |tee ../makeinst.log  
 #
 echo Ignoring error messages.  They are harmless
 #
 command ls -1 lib/*.a
 sleep 10
 #
+rm $CCP4/lib/clipper/ccp4
 make realclean
 
 ###
@@ -80,7 +89,7 @@
 # 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*
+ perl -pi.bak -e 's|ccp4-6.0|%n-%v|g'include/ccp4.setup*
  rm -f include/*.bak
  perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' bin/clipper-config 
  rm -f bin/clipper-config.bak  

@@ -151,13 +160,12 @@
 error that appears in cpirate and coot fft calculations.
 
 CCP4lib files will be installed under 
-%p/share/xtal/ccp4-onlylibs-dev-6.0. This is essentially
-identical in content to the corresponding files in CCP4 6.0.
-Includes patches from ccp4 through March 22, 2006.
+%p/share/xtal/ccp4-onlylibs-dev-6.0.2. This is slightly newer
+in content relative to the corresponding files in CCP4 6.0.2.
 
 Programs requiring these libraries to build or run need to
 source the appropriate
-%p/share/xtal/ccp4-onlylibs-dev-6.0/include/ccp4.setup
+%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup
 file for the shell, as is done in the coot.info 

[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv17765

Modified Files:
coot.info 
Log Message:
updated version of coot

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- coot.info   28 Dec 2006 09:06:23 -  1.4
+++ coot.info   9 Jun 2007 04:07:46 -   1.5
@@ -1,18 +1,65 @@
 Package:coot
-Version: 0.1.2
-Revision: 1007
+Version: 0.3.1
+Revision: 2
 GCC: 4.0 
 Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source-MD5: 10289f909d6824ef4923a97cfb0e63a4  
+#Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz
+Source-MD5: 574d1459ab9f7be3e2d92585444a
 SourceDirectory: %n-%v
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 ###
-BuildDepends: ccp4-onlylibs-dev (= 6.0-1011), glib, gtk+2, freeglut, 
gtkglarea, guile16, guile16-dev, gsl, libglade2,  gtk-canvas-dev, 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, libiconv-dev
+BuildDepends: 
+ ccp4-onlylibs-dev (= 6.0.2-1)  ,
+ glib,
+ gtk+,
+ freeglut,
+ gtkglarea   ,
+ guile16 ,
+ guile16-dev ,
+ guile16-gtk-dev ,
+ gsl ,
+ libglade2   ,
+ gtk-canvas-dev  ,
+ libart2 (= 2.3.16-2)   ,
+ guile16-net-http,
+ libgettext3-dev ,
+ imlib   ,
+ libjpeg ,
+ giflib  ,
+ libpng3 ,
+ gnome-libs-dev  ,
+ libiconv-dev,
+ gtkglext1-shlibs,
+
 #
-Depends: guile16-shlibs, 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), 
imlib-shlibs, libjpeg-shlibs, giflib-shlibs, libpng3-shlibs, glib-shlibs, 
gtk+2-shlibs, gnome-libs-shlibs
+Depends: 
+ coot-shlibs (= %v-%r),
+ freeglut-shlibs  ,
+ giflib-shlibs,
+ glib-shlibs  ,
+ gnome-libs-shlibs,
+ gsl-shlibs   ,
+ gtk+-shlibs  ,
+ guile16-gtk-shlibs   ,
+ guile16-shlibs   ,
+ imlib-shlibs ,
+ libgettext3-shlibs   ,
+ libiconv ,
+ libjpeg-shlibs   ,
+ libpng3-shlibs   ,
+ libtiff-shlibs   ,
+ guile16-gtk  ,
+ guile16-www  ,
+ guile16-gui  ,
+ guile16-goosh (= 1.3-2) ,
+ guile16  ,
+ guile16-net-http ,
+ gtkglext1 
+
+# gtkglext1 required at runtime for stereo functionality
 #
 BuildDependsOnly: false
 NoSetLDFLAGS: true
@@ -28,20 +75,34 @@
 available from the coot Web site (see below) and is updated regularly.
 
 ###
+# Patch: %n.patch
 PatchScript:  
-#!/bin/zsh -efv
+#!/bin/zsh -exf
 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
-#perl -pi -e 's|no_tips = _coot.no_tips|#no_tips = _coot.no_tips|g' src/coot.py
-#perl -pi -e 's|_coot.set_ncs_homology_leve|_coot.set_ncs_homology_level|g' 
src/coot.py
+#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
+# Temp fix for an error (fixed in 0.3.1):
+# perl -pi.bak -e 's|1 0.1\)\)\)\)\)\)\)\)|1 0.1)))|g' scheme/fitting.scm
 
 ###
-ConfigureParams:  --with-mmdb-prefix=$CCP4  --with-clipper-prefix=$CCP4 
--with-fftw=$CCP4 --with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 

[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info, NONE, 1.1 ccp4.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv14974

Added Files:
ccp4.info ccp4.patch 
Log Message:
ccp4 moved to stable, thanks to gfortran

--- NEW FILE: ccp4.info ---
Package: ccp4
Version: 6.0.2
Revision: 6
GCC: 4
Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
SourceDirectory: ccp4-%v
Source2: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/phaser-1.3.3-cctbx-src.tar.gz
Source2-MD5: edff4d201e7b6d987c05efcf965f6023
Source3: http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
Source3-MD5: 21568dd2475505929573a3fd452c538f
Source4: 
http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/ccp4_i686-apple-darwin8.6.1_libtool.gz
Source4-MD5: e40104835406c75c8aee16471b2dd06e
# The follwing are CCP4-issued version-specific patch files from the website at
# http://www.ccp4.ac.uk/problems.php#ccp4-6.0.2
Source5: ftp://ftp.ccp4.ac.uk/ccp4/%v/patches/topp.f-r1.16.2.5-r1.16.2.6.diff
Source5-MD5: a23e9886620886a694295ac2e671156a
Source6: ftp://ftp.ccp4.ac.uk/ccp4/%v/patches/scala.f-r1.101.2.3-r1.101.2.4.diff
Source6-MD5: 0c78e93e77c892d071ed0732f7a89102
Source7: 
ftp://ftp.ccp4.ac.uk/ccp4/%v/patches/util_windows.tcl-r1.27-r1.27.2.1.diff
Source7-MD5: 52ac21688c047287d4fcbbd1aaaea774
Source8: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/amore.f-r1.115-r1.116.diff
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
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
Source13-MD5: fa9127eaceeb3e20328400a5add6b042
#Source14: 
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various.f-r1.124.2.3-r1.124.2.4.diff
#Source14-MD5: 9fde5290a42032916893cd9d0ffd5b15
#
DescPort: 
CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
Jack Howarth has provided multiple improvements in the patch file to
address several bugs and to permit optimization with gfortran at -O3.

Users typically install all of the ccp4 files into /xtal/ccp4-%v or
into /usr/local/xtal/ccp4-%v.  In the present case, these files are
installed into %p/share/xtal/ccp4-%v.  The library files are installed 
into the directory %p/lib/ccp4-%v and this directory is symbolically 
linked to %p/share/xtal/ccp4-%v/lib which is the canonical location.
Dynamic libraries are provided in the ccp4-shlibs splitoff package, and
static libraries are provided in the ccp4-dev splitoff package. The 
configure files are patched so that the full path to the dynamic 
libraries is hard-coded, per fink policy.  This obviates the need to
set the DYLD_LIBRARY_PATH environment variable, which should remain
unset. The appropriate shell startup files are automatically sourced
when %p/bin/init.(c)sh is invoked upon shell startup; there is no 
need to do so manually. The actual files are located in $CCP4/include.

Although phaser is built, the cctbx files are not installed in $CLIB.
If needed, please install the cctbx fink package.

The ccp4i mail utility by default will only work on machines that run
a mail server.  As a workaround, a public domain perl script called
osx_ccp4_mail is installed that glues the ccp4i mail button to the
Apple OS X Mail.app.

Further adaptations are commented in place in the patch, configure and
install scripts below. Relevant patches specific to this version that
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
end of the PatchScript field.

Depends: 
x11, 
tcltk,
blt,
gcc42-shlibs,
fftw-shlibs, %N-shlibs (= %v-%r)

BuildDepends: 
gcc42, 
f2c, 
fort77, 
tcltk-dev, 
fftw

Replaces: 
mosflm (= 6.2.3-2), 
mosflm-small (= 6.2.3-2), 
refmac (= 5.2), 
ccp4-shlibs (= 6.0.1-), 
ccp4 (= 6.0.1-), 
ccp4-dev (= 6.0.1-), 
bundle-ccp4-intel, 
clipper-bin, 
ccp4-gfortran, 
ccp4-gfortran-dev, 
bundle-ccp4-powerpc

Conflicts: 
ccp4-shlibs (= 6.0.1-) , 
ccp4 (= 6.0.1-), 
ccp4-dev (= 

[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4-g77.info,1.5,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv15981

Removed Files:
ccp4-g77.info 
Log Message:
deleted obsolete package

--- ccp4-g77.info DELETED ---


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv24425

Modified Files:
zsh-templates.info 
Log Message:
bugfix update

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/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  12 May 2007 20:58:49 -  1.10
+++ zsh-templates.info  11 Jun 2007 00:58:15 -  1.11
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.1.1
+Version: 1.1.2
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: 80cfaef572fa9af6650c7485173e9561 
+Source-MD5: 553753f9dd77f6ebd9ff96723c7878d2 
 Depends: macosx, zsh (= 4.2.1-13) | zsh-multibyte 
 License: GPL
 Maintainer: W. G. Scott [EMAIL PROTECTED]


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.patch, 1.2, 1.3 ccp4-onlylibs-dev.info, 1.14, 1.15 ccp4-onlylibs-dev.patch, 1.1, 1.2 coot.info, 1.43, 1.44

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv12559

Modified Files:
ccp4-onlylibs-dev.info ccp4-onlylibs-dev.patch coot.info 
Added Files:
coot.patch 
Log Message:
fixes for 10.5 compatibility while maintaining 10.4 compatibility

Index: ccp4-onlylibs-dev.patch
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- ccp4-onlylibs-dev.patch 23 Mar 2006 06:23:07 -  1.1
+++ ccp4-onlylibs-dev.patch 31 Oct 2007 22:03:21 -  1.2
@@ -1,278 +1,2400 @@
-diff -ruN ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h 
ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h
 ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h   2005-09-08 
13:07:42.0 -0700
-+++ ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h2006-03-22 
21:17:07.0 -0800
-@@ -169,7 +169,7 @@
-   templateclass T Curv_orthT Curv_fracT::curv_orth( const Cell cell ) 
const
-   {
- Mat33T m( cell.matrix_frac() );
--return Curv_fracT( m.transpose() * (*this) * m );
-+return Curv_orthT( m.transpose() * (*this) * m );
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am 
ccp4-onlylibs-dev/lib/src/mmdb/Makefile.am
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am1969-12-31 
16:00:00.0 -0800
[...2604 lines suppressed...]
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp 
ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp2006-08-16 
03:55:23.0 -0700
 ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp 2007-10-21 22:33:35.0 
-0700
+@@ -1,4 +1,4 @@
+-//  $Id$
++//  $Id$
+ //  =
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h 
ccp4-onlylibs-dev/lib/src/mmdb/stream_.h
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h  2006-08-16 
03:55:23.0 -0700
 ccp4-onlylibs-dev/lib/src/mmdb/stream_.h   2007-10-21 22:33:35.0 
-0700
+@@ -1,4 +1,4 @@
+-//  $Id$
++//  $Id$
+ //  =
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related

--- NEW FILE: coot.patch ---
diff -ruN coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc 
coot-0.4-pre-1/coot-utils/coot-fffear.cc
--- coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc   2007-04-16 
15:42:06.0 -0700
+++ coot-0.4-pre-1/coot-utils/coot-fffear.cc2007-10-31 10:28:44.0 
-0700
@@ -160,30 +160,7 @@
   }
 

-  for (unsigned int iop=0; iopops.size(); iop++) {
-
-clipper::Xmapfloat r1;
-r1.init(clipper::Spacegroup::p1(), xmap.cell(), xmap.grid_sampling()); 
// fixed to be consistent with above results init.
-clipper::FFFear_fftfloat search(xmap);
-clipper::NX_operator nxop( xmap, nxmap, ops[iop]);
-search(r1, nxmap, nxmap_mask, nxop); // fill r1 with fffear search 
values at this orientation
-  
-clipper::Xmapfloat::Map_reference_index ix;
-for ( ix = r1.first(); !ix.last(); ix.next() )
-   if ( r1[ix]  results[ix].first) {
-  results[ix].first = r1[ix];
-  results[ix].second = iop;
-   }
-
-icount++;
-//   std::cout  ops.size() - iop   ; 
-std::cout.flush();
-if (icount == 50) {
-   std::cout100*(float(iop)/float(ops.size()))  %;
-   std::cout.flush();
-   icount = 0;
-}
-  }
+  
   std::cout  \n;
}
 }
diff -ruN coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 
coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp
--- coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 2007-07-01 
07:12:02.0 -0700
+++ coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp  2007-10-31 11:08:12.0 
-0700
@@ -193,46 +193,7 @@
   \param resulttrn The best translations.
   \param xmap The map to search.
   \param rtops The oprientations to search. */
-void LLK_map_target::search( clipper::Xmapfloat resultscr, 
clipper::Xmapint resultrot, clipper::Xmapint resulttrn, const 
clipper::Xmapfloat xmap, const std::vectorclipper::RTop_orth rtops ) const
-{
-  // set up results
-  const clipper::Spacegroupspgr = xmap.spacegroup();
-  const clipper::Cell  cell = xmap.cell();
-  const clipper::Grid_sampling grid = xmap.grid_sampling();
-  resultscr.init( spgr, cell, grid );
-  resultrot.init( spgr, cell, grid );
-  resulttrn.init( spgr, cell, grid );
-  resultscr = 1.0e20;
-
-  // now search for ML target in each orientation in turn
-  clipper::Xmapfloat resultp1( clipper::Spacegroup::p1(), cell, grid );
-  clipper::Xmapfloat::Map_reference_index i1(resultp1);
- 

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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv15875

Removed Files:
coot-10.5.info 
Log Message:
now redundant and also it didn't compile

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


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.44,1.45

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv15459

Modified Files:
coot.info 
Log Message:
deleted spurious comma and added the annoying -x back to compilescript

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -d -r1.44 -r1.45
--- coot.info   31 Oct 2007 22:03:21 -  1.44
+++ coot.info   31 Oct 2007 23:32:33 -  1.45
@@ -92,7 +92,7 @@
  libtiff-shlibs   ,
  libtool14-shlibs ,
  librsvg2-gtk ,
- pango1-xft2-shlibs   ,
+ pango1-xft2-shlibs   
 
 #
 # raster3d
@@ -129,7 +129,7 @@
 
 ###
 CompileScript: 
-#!/bin/zsh -ef
+#!/bin/zsh -efx
 
 export 
PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
 export SED=/usr/bin/sed


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[cvs] dists/10.4/unstable/main/finkinfo/sci cctbx.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv17244

Modified Files:
cctbx.info 
Log Message:
version update

Index: cctbx.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/cctbx.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- cctbx.info  22 Nov 2006 17:16:39 -  1.9
+++ cctbx.info  2 Nov 2007 05:17:53 -   1.10
@@ -1,15 +1,14 @@
 Package:cctbx
-Version: 61108
-# 2006_11_08_2311
+Version: 70818
+# 2007_08_18_1856
 Revision: 1001
 GCC: 4.0
 BuildDependsOnly: false
 NoSourceDirectory: true
 NoSetLDFLAGS: true
 NoSetCPPFLAGS: true
-#Source: 
http://cci.lbl.gov/cctbx_build/results/2005_12_29_2029/cctbx_python_242_bundle.tar.gz
-Source: 
http://cci.lbl.gov/cctbx_build/results/2006_11_08_2311/cctbx_python_25_bundle.tar.gz
-Source-MD5: fde01a24360578a44a0b7b14b10cb1d1
+Source: 
http://cci.lbl.gov/cctbx_build/results/2007_08_18_1856/cctbx_bundle.tar.gz
+Source-MD5: 8d1ec7c39128c6b04be6aea5b4cb4555
 SourceRename: %n-%v.tar.gz
 Description: Computational Crystallography Toolbox
 DescDetail: 


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-multibyte.info, 1.5, 1.6 zsh-templates.info, 1.17, 1.18 zsh.info, 1.11, 1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17:/tmp/cvs-serv15802

Modified Files:
zsh-multibyte.info zsh-templates.info zsh.info 
Log Message:
bumped revision to force rebuild after upgrade

Index: zsh-multibyte.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-multibyte.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- zsh-multibyte.info  2 May 2007 16:36:00 -   1.5
+++ zsh-multibyte.info  2 Nov 2007 14:45:59 -   1.6
@@ -1,6 +1,6 @@
 Package: zsh-multibyte
 Version: 4.3.4
-Revision: 2
+Revision: 3
 Conflicts: zsh
 Replaces: zsh
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- zsh.info2 May 2007 16:36:00 -   1.11
+++ zsh.info2 Nov 2007 14:45:59 -   1.12
@@ -1,6 +1,6 @@
 Package: zsh 
 Version: 4.3.4
-Revision: 2
+Revision: 3
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- zsh-templates.info  28 Oct 2007 21:07:22 -  1.17
+++ zsh-templates.info  2 Nov 2007 14:45:59 -   1.18
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.2.3
+Version: 1.2.4
 Revision: 1
 Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: ce193f978a2f2f7f502d9f003fb5c45b
+Source-MD5: 6934b2e9b521224a92334ca45e2f9923
 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 viennarna.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv31598

Modified Files:
viennarna.info 
Log Message:
version upgrade

Index: viennarna.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/viennarna.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- viennarna.info  19 Jul 2007 22:17:23 -  1.3
+++ viennarna.info  3 Nov 2007 04:13:16 -   1.4
@@ -1,13 +1,14 @@
 Package: viennarna
-Version: 1.5beta
-Revision: 15
+Version: 1.6.5
+Revision: 1
 Source: http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-%v.tar.gz   
-Source-MD5: f8737e07fc82ccd130cc30bfd09ccca5 
-SourceDirectory: ViennaRNA-1.5
+Source-MD5: e03a98e6184a4b17eb071f6f67d7d741
+SourceDirectory: ViennaRNA-%v
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
-ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info
-Depends: perl586-core | system-perl586
+InfoDocs: RNAlib.info
+ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info   
--without-forester 
+Depends: perl586-core | system-perl586 | perl588-core | system-perl588
 UpdatePOD: true
 Description: RNA structural prediction
 DescDetail: 


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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4-onlylibs-dev.info, 1.3, 1.4 ccp4-onlylibs-dev.patch, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv6270

Modified Files:
ccp4-onlylibs-dev.info ccp4-onlylibs-dev.patch 
Log Message:
fixed md5sum

Index: ccp4-onlylibs-dev.patch
===
RCS file: 
/cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4-onlylibs-dev.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- ccp4-onlylibs-dev.patch 13 Nov 2006 03:19:48 -  1.1
+++ ccp4-onlylibs-dev.patch 3 Nov 2007 15:23:49 -   1.2
@@ -1,278 +1,2400 @@
-diff -ruN ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h 
ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h
 ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h   2005-09-08 
13:07:42.0 -0700
-+++ ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h2006-03-22 
21:17:07.0 -0800
-@@ -169,7 +169,7 @@
-   templateclass T Curv_orthT Curv_fracT::curv_orth( const Cell cell ) 
const
-   {
- Mat33T m( cell.matrix_frac() );
--return Curv_fracT( m.transpose() * (*this) * m );
-+return Curv_orthT( m.transpose() * (*this) * m );
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am 
ccp4-onlylibs-dev/lib/src/mmdb/Makefile.am
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am1969-12-31 
16:00:00.0 -0800
[...2604 lines suppressed...]
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp 
ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp2006-08-16 
03:55:23.0 -0700
 ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp 2007-10-21 22:33:35.0 
-0700
+@@ -1,4 +1,4 @@
+-//  $Id$
++//  $Id$
+ //  =
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h 
ccp4-onlylibs-dev/lib/src/mmdb/stream_.h
+--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h  2006-08-16 
03:55:23.0 -0700
 ccp4-onlylibs-dev/lib/src/mmdb/stream_.h   2007-10-21 22:33:35.0 
-0700
+@@ -1,4 +1,4 @@
+-//  $Id$
++//  $Id$
+ //  =
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/stable/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  9 Jun 2007 04:06:49 -   1.3
+++ ccp4-onlylibs-dev.info  3 Nov 2007 15:23:49 -   1.4
@@ -1,15 +1,18 @@
 Package: ccp4-onlylibs-dev
 # Use version numbering to sync with the current CCP4 release:
 Version: 6.0.2
-Revision: 2
+Revision: 8
 GCC: 4.0
 Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz
-#Source: ftp://ftp.ccp4.ac.uk/prerelease/%n.tar.gz
-Source-MD5: edb1034b0a2699bcb43abb6463f7b9e9
-#SourceRename: %n-%v.tar.gz
+#Source: ftp://ftp.ccp4.ac.uk/prerelease/ccp4-onlylibs-dev.tar.gz
+# Source-MD5: 67de45f1d718627ab96939f5443937ae
+#Source-MD5: e778478de628c75792d2401248c63350
+Source-MD5: f3d7e391dfc5f03667d8d4504d61f92d
+#
 SourceDirectory: %n
 Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
 Source2-MD5: ea307964e3786bef0868ea560471
+#
 Depends:  gcc42-shlibs
 BuildDepends: gcc42
 # BuildDepends: fort77
@@ -17,7 +20,7 @@
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 ###
-#Patch: %n.patch
+Patch: %n.patch
 PatchScript: 
 #!/bin/zsh -efv
 umask 0022
@@ -50,6 +53,7 @@
 
 # clean up:
 rm -f  include/*.bak lib/clipper/*.bak
+   
 
 ###
 CompileScript: 
@@ -60,7 +64,7 @@
 source include/ccp4.setup-zsh
 export DYLD_LIBRARY_PATH=$CLIB
 #
-FC=gfortran  ./configure --onlylibs Darwin
+FC=gfortran  ./configure --with-ssm --with-mmdb --onlylibs Darwin
 #FC=fort77  ./configure --onlylibs Darwin
 ln -s $CCP4/lib/src $CCP4/lib/clipper/ccp4
 #
@@ -74,7 +78,7 @@
 command ls -1 lib/*.a
 sleep 10
 #
-rm $CCP4/lib/clipper/ccp4
+# rm $CCP4/lib/clipper/ccp4
 make realclean
 
 ###
@@ -96,6 +100,11 @@
  perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la
  rm -f lib/*.la.bak
 #
+# Temp fix for coot (needed in 10.4 but not 10.5)
+if [[ $(sw_vers -productVersion)  10.5 ]]; then
+cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig
+perl -pi -e 's|ivector   FF1,FF2;||g' include/ssm/ssm_superpose.h
+fi
 # Now install:
  mkdir -p %i/bin
  mkdir -p %i/share/xtal/%n-%v


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4-onlylibs-dev.info, 1.15, 1.16

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17:/tmp/cvs-serv5477

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
fixed md5sum

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- ccp4-onlylibs-dev.info  31 Oct 2007 22:03:21 -  1.15
+++ ccp4-onlylibs-dev.info  3 Nov 2007 15:21:51 -   1.16
@@ -3,10 +3,11 @@
 Version: 6.0.2
 Revision: 8
 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
+Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz
+#Source: ftp://ftp.ccp4.ac.uk/prerelease/ccp4-onlylibs-dev.tar.gz
 # Source-MD5: 67de45f1d718627ab96939f5443937ae
-Source-MD5: e778478de628c75792d2401248c63350
+#Source-MD5: e778478de628c75792d2401248c63350
+Source-MD5: f3d7e391dfc5f03667d8d4504d61f92d
 #
 SourceDirectory: %n
 Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz


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[cvs] dists/10.4/unstable/main/finkinfo/sci molmol-10.5.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv26912

Added Files:
molmol-10.5.patch 
Log Message:
10.5-specific patch for molmol

--- NEW FILE: molmol-10.5.patch ---
diff -urN molmol_orig/makedef molmol/makedef
--- molmol_orig/makedef 1969-12-31 16:00:00.0 -0800
+++ molmol/makedef  2005-05-28 09:44:47.0 -0700
@@ -0,0 +1,60 @@
+ TIFFDIR = @PREFIX@/lib
+ MESADIR = $(TOP)/widgets-sgi
+ JPEGDIR = @PREFIX@/lib
+
+ PNGDIR = @PREFIX@/lib
+ ZLIBDIR = /usr/lib
+
+# If you configured any of the above three image formats, uncomment
+# the following four lines, and delete the non-relevant parts if
+# necessary, i. e. if you did not configure all three formats.
+#
+ IMGDEF  = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT
+ IMGINCL = -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR)
+ IMGLIB  = $(TIFFDIR)/libtiff.3.dylib $(JPEGDIR)/libjpeg.dylib \
+   $(PNGDIR)/libpng.dylib $(ZLIBDIR)/libz.dylib
+
+# Some systems do not have the float versions of various math functions,
+# uncomment the following lines if this is the case
+
+  MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log \
+ -Dsinf=sin -Dcosf=cos  \
+ -Dfabsf=fabs  -DMAXINT=INT_MAX
+
+# -Dceilf=ceil
+
+CPP = /usr/bin/cpp
+
+MCPPFLAGS =  -DMAXINT=INT_MAX -I/usr/X11R6/include [EMAIL PROTECTED]@/include 
-bind_at_load 
+
+CC = /usr/bin/gcc
+
+MCFLAGS = -O -bind_at_load 
+
+RANLIB = /usr/bin/ranlib
+
+WAIT = /bin/sleep 2
+
+SHELL = /bin/sh
+
+SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm
+
+SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB 
-DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
+
+PUDEVDIR = motif tty
+
+PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY
+
+IODEVDIR = motx11 motogl ttyno
+
+IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_MOTIF_OGL -DIO_DEV_TTY_NO
+
+
+MOTIFDEF = -DFUNCPROTO
+
+SYSLIB = -L/usr/lib [EMAIL PROTECTED]@/lib -L/usr/X11R6/lib  \
+ -lX11 -lXm -lGLU -lGL 
/System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib 
$(MESADIR)/libGLw.a \
+ -lXmu -lXt -lXp -lXpm -lX11 -lXext -lSM -lICE -lm -lc -lmx
+
+TOOLSDIR = $(TOP)/tools
+SGDIR= $(TOP)/sg
diff -urN molmol_orig/molmol molmol/molmol
--- molmol_orig/molmol  2003-01-20 17:44:58.0 -0800
+++ molmol/molmol   2005-05-28 09:44:48.0 -0700
@@ -1,9 +1,9 @@
-#!/bin/ksh
+#!/bin/zsh
 #
 # startup script for MOLMOL
 #
 
-MOLMOLHOME=/opt/group/MOLMOL
[EMAIL PROTECTED]@/share/molmol;MOLMOLDEV=Motif/OpenGL
 export MOLMOLHOME
 export MOLMOLDEV
 
@@ -11,55 +11,8 @@
 osrel=`uname -r`
 osmaj=`echo $osrel | awk -F. '{print $1}'`
 osmin=`echo $osrel | awk -F. '{print $2}'`
-localdev=
-glxdev=
-
-if [ $ostype = IRIX -o $ostype = IRIX64 ]; then
-  if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
-arch=sgi6
-localdev=Motif/OpenGL
-glxdev=Motif/OpenGL
-  elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
-arch=sgi5
-localdev=Motif/OpenGL
-glxdev=Motif/OpenGL
-  else
-arch=sgi4
-localdev=Motif/GL
-  fi
-  MONITOR=72HZ; export MONITOR
-elif [ $ostype = AIX ]; then
-  arch=aix
-  localdev=Motif/OpenGL
-elif [ $ostype = HP-UX ]; then
-  arch=hp
-  localdev=Motif/OpenGL
-  glxdev=Motif/OpenGL
-elif [ $ostype = OSF1 ]; then
-  arch=dec
-  localdev=Motif/OpenGL
-elif [ $ostype = Linux ]; then
-  arch=lnx
-  localdev=Motif/OpenGL
-elif [ $ostype = SunOS ]; then
-  if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
-arch=sol
-localdev=Motif/OpenGL
-  else
-arch=sun
-  fi
-else
-  arch=unknown
-fi
-
-if [ $ostype = SunOS ]; then
-  xdpy=/usr/openwin/bin/xdpyinfo
-elif [ $ostype = HP-UX ]; then
-  xdpy=/usr/contrib/bin/X11/xdpyinfo
-else
-  xdpy=/usr/bin/X11/xdpyinfo
-fi
-
+localdev=Motif/OpenGL
+glxdev=Motif/OpenGL
 printUsage () {
   echo Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files
   echo 
@@ -209,7 +162,7 @@
 fi
 
 if [ $input = - -o -n $nograph ]; then
-  $MOLMOLHOME/molmol.$arch $xopt
+echo LineBond solid 1| $startmacro ; 
@PREFIX@/share/molmol/src/main/molmol $xopt
 else
-  $MOLMOLHOME/molmol.$arch $xopt  /dev/null
+echo LineBond solid 1| $startmacro ; 
@PREFIX@/share/molmol/src/main/molmol $xopt  /dev/null 
 fi
diff -urN molmol_orig/molmol.orig molmol/molmol.orig
--- molmol_orig/molmol.orig 1969-12-31 16:00:00.0 -0800
+++ molmol/molmol.orig  2005-05-28 09:44:48.0 -0700
@@ -0,0 +1,215 @@
+#!/bin/ksh
+#
+# startup script for MOLMOL
+#
+
+MOLMOLHOME=/opt/group/MOLMOL
+export MOLMOLHOME
+export MOLMOLDEV
+
+ostype=`uname`
+osrel=`uname -r`
+osmaj=`echo $osrel | awk -F. '{print $1}'`
+osmin=`echo $osrel | awk -F. '{print $2}'`
+localdev=
+glxdev=
+
+if [ $ostype = IRIX -o $ostype = IRIX64 ]; then
+  if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
+arch=sgi6
+localdev=Motif/OpenGL
+glxdev=Motif/OpenGL
+  elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj 

[cvs] dists/10.4/unstable/main/finkinfo/sci molmol.info,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-serv28258

Modified Files:
molmol.info 
Log Message:
molmol update for 10.5 compatibility

Index: molmol.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- molmol.info 27 Nov 2006 17:13:19 -  1.6
+++ molmol.info 10 Nov 2007 17:05:29 -  1.7
@@ -1,6 +1,6 @@
 Package: molmol
 Version: 2k.2.0
-Revision: 1034
+Revision: 1035
 CustomMirror: 
  eur-CH: ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/
  nam-US:http://freedom7.swmed.edu/pub/software/MOLMOL/
@@ -10,13 +10,30 @@
 SourceDirectory: ../%f
 Source2: mirror:custom:unix-gzip/%n-%v-doc.tar.gz
 Source2-MD5: 517545b60b0179ab691a679ed29903a7
+# Source3: mirror:custom:unix-gzip/widgets-sgi.tar.gz
+Source3: http://xanana.ucsc.edu/xtal/widgets-sgi.tar.gz
+Source3-MD5: 83509f5ee7ecd9287a3334cfd8585d08
 Depends: x11, freeglut-shlibs, openmotif3-shlibs, libtiff-shlibs, 
libjpeg-shlibs, libpng3-shlibs
 BuildDepends: freeglut, openmotif3-shlibs, openmotif3, libtiff, libjpeg, 
libpng3, x11-dev
 PatchScript: 
+#!/bin/zsh -evf
 chmod -R +w *
-sed 's|@PREFIX@|%p|g' %a/%n.patch | patch -p1
+if [[ $(sw_vers -productVersion)  10.5 ]]; then
+sed 's|@PREFIX@|%p|g' %a/%n.patch | patch -p1
+else
+sed 's|@PREFIX@|%p|g' %a/%n-10.5.patch | patch -p1
+fi
 
 CompileScript:  
+#!/bin/sh -ev
+cd widgets-sgi
+cc -bind_at_load -I/usr/X11R6/include -I/%p/include -O3 -c GLwDrawA.c
+cc -bind_at_load -I/usr/X11R6/include -I/%p/include -O3 -c GLwMDrawA.c
+ar rv libGLw.a GLwDrawA.o GLwMDrawA.o
+ranlib libGLw.a
+mkdir GL
+mv *.h GL
+cd ..
 make
 
 InstallScript: 
@@ -32,6 +49,11 @@
 
 Homepage: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
 Description:  Molecular graphics display program
+DescPackaging: 
+Build molmol against a local copy of the original widgets-sgi
+sources for libGLw.a until Apple updates Leopard with a libGLw
+which is actually built with Motif support again.
+
 DescDetail: 
 MOLMOL is a molecular graphics program for displaying, analyzing, 
 and manipulating the three-dimensional structure of biological 


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[cvs] dists/10.4/unstable/main/finkinfo/sci molmol-10.5.patch, 1.1, NONE

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16060

Removed Files:
molmol-10.5.patch 
Log Message:
removed in favor of a better fix

--- molmol-10.5.patch DELETED ---


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[cvs] dists/10.4/unstable/main/finkinfo/sci molmol.info, 1.7, 1.8 molmol.patch, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16111

Modified Files:
molmol.info molmol.patch 
Log Message:
revision for molmol so it builds identically on 10.4 and 10.5 and as an extra 
bonus fixes a 4 year old bug that caused the Xserver to crash when plotting a 
jpg

Index: molmol.patch
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/molmol.patch,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- molmol.patch1 Feb 2007 18:03:24 -   1.4
+++ molmol.patch10 Nov 2007 19:10:58 -  1.5
@@ -3,7 +3,7 @@
 +++ molmol/makedef 2005-05-28 09:44:47.0 -0700
 @@ -0,0 +1,60 @@
 + TIFFDIR = @PREFIX@/lib
-+
++ MESADIR = $(TOP)/widgets-sgi
 + JPEGDIR = @PREFIX@/lib
 +
 + PNGDIR = @PREFIX@/lib
@@ -29,7 +29,7 @@
 +
 +CPP = /usr/bin/cpp
 +
-+MCPPFLAGS =  -DMAXINT=INT_MAX -I/usr/X11R6/include [EMAIL PROTECTED]@/include 
-bind_at_load 
++MCPPFLAGS =  -DMAXINT=INT_MAX -I/usr/X11R6/include [EMAIL PROTECTED]@/include 
-bind_at_load -I$(TOP)
 +
 +CC = /usr/bin/gcc
 +
@@ -57,8 +57,8 @@
 +MOTIFDEF = -DFUNCPROTO
 +
 +SYSLIB = -L/usr/lib [EMAIL PROTECTED]@/lib -L/usr/X11R6/lib  \
-+ -lX11 -lXm -lXmu -lXt -lXp -lXpm -lX11 -lXext \
-+ -lSM -lICE -lm -lc -lGLU -lGL -lGLw -lmx
++ -lX11 -lXm -lGLU -lGL 
/System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib 
$(MESADIR)/libGLw.a \
++ -lXmu -lXt -lXp -lXpm -lX11 -lXext -lSM -lICE -lm -lc -lmx
 +
 +TOOLSDIR = $(TOP)/tools
 +SGDIR= $(TOP)/sg
@@ -73,7 +73,7 @@
  #
  
 -MOLMOLHOME=/opt/group/MOLMOL
[EMAIL PROTECTED]@/share/molmol
[EMAIL PROTECTED]@/share/molmol;MOLMOLDEV=Motif/OpenGL
  export MOLMOLHOME
  export MOLMOLDEV
  
@@ -565,3 +565,14 @@
 @@ -0,0 +1,2 @@
 +#include math.h
 +#include limits.h
+--- molmol-2k.2.0-1035/src/motogl/MotOGL.c.sav 2007-11-10 12:41:40.0 
-0500
 molmol-2k.2.0-1035/src/motogl/MotOGL.c 2007-11-10 12:43:37.0 
-0500
+@@ -31,7 +31,7 @@
+ #include Xm/XmStrDefs.h
+ 
+ #define BOOL MOTIF_BOOL  /* hack to avoid naming conflict */
+-#include GL/GLwMDrawA.h
++#include widgets-sgi/GL/GLwMDrawA.h
+ #undef BOOL
+ 
+ #include sg.h

Index: molmol.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- molmol.info 10 Nov 2007 17:05:29 -  1.7
+++ molmol.info 10 Nov 2007 19:10:57 -  1.8
@@ -1,6 +1,6 @@
 Package: molmol
 Version: 2k.2.0
-Revision: 1035
+Revision: 1036
 CustomMirror: 
  eur-CH: ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/
  nam-US:http://freedom7.swmed.edu/pub/software/MOLMOL/
@@ -10,19 +10,13 @@
 SourceDirectory: ../%f
 Source2: mirror:custom:unix-gzip/%n-%v-doc.tar.gz
 Source2-MD5: 517545b60b0179ab691a679ed29903a7
-# Source3: mirror:custom:unix-gzip/widgets-sgi.tar.gz
-Source3: http://xanana.ucsc.edu/xtal/widgets-sgi.tar.gz
+Source3: mirror:custom:unix-gzip/widgets-sgi.tar.gz
 Source3-MD5: 83509f5ee7ecd9287a3334cfd8585d08
 Depends: x11, freeglut-shlibs, openmotif3-shlibs, libtiff-shlibs, 
libjpeg-shlibs, libpng3-shlibs
 BuildDepends: freeglut, openmotif3-shlibs, openmotif3, libtiff, libjpeg, 
libpng3, x11-dev
 PatchScript: 
-#!/bin/zsh -evf
 chmod -R +w *
-if [[ $(sw_vers -productVersion)  10.5 ]]; then
-sed 's|@PREFIX@|%p|g' %a/%n.patch | patch -p1
-else
-sed 's|@PREFIX@|%p|g' %a/%n-10.5.patch | patch -p1
-fi
+sed 's|@PREFIX@|%p|g' %a/%n.patch | patch -p1
 
 CompileScript:  
 #!/bin/sh -ev


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[cvs] dists/10.4/stable/main/finkinfo/sci molmol.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv5751

Modified Files:
molmol.info 
Log Message:
fixed wrong tarball source

Index: molmol.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- molmol.info 10 Nov 2007 19:13:54 -  1.7
+++ molmol.info 10 Nov 2007 22:48:24 -  1.8
@@ -10,7 +10,7 @@
 SourceDirectory: ../%f
 Source2: mirror:custom:unix-gzip/%n-%v-doc.tar.gz
 Source2-MD5: 517545b60b0179ab691a679ed29903a7
-Source3: mirror:custom:unix-gzip/widgets-sgi.tar.gz
+Source3: http://xanana.ucsc.edu/xtal/widgets-sgi.tar.gz
 Source3-MD5: 83509f5ee7ecd9287a3334cfd8585d08
 Depends: x11, freeglut-shlibs, openmotif3-shlibs, libtiff-shlibs, 
libjpeg-shlibs, libpng3-shlibs
 BuildDepends: freeglut, openmotif3-shlibs, openmotif3, libtiff, libjpeg, 
libpng3, x11-dev


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[cvs] dists/10.4/unstable/main/finkinfo/sci pdb2pqr.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv13930

Modified Files:
pdb2pqr.info 
Log Message:
update for 10.5 compatibility

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- pdb2pqr.info3 Apr 2007 13:54:10 -   1.7
+++ pdb2pqr.info11 Nov 2007 14:35:04 -  1.8
@@ -1,6 +1,6 @@
 Package: pdb2pqr
 Version: 1.2.1 
-Revision: 1
+Revision: 2
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 8e38f912c7a63596b2bb5f9632b1b5c2 
 SourceDirectory: %n-%v
@@ -9,20 +9,21 @@
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 SetLDFLAGS: -F/System/Library/Frameworks/Python.framework
-ConfigureParams: py_path=/usr/bin/python2.3
+ConfigureParams: py_path=/usr/bin/python
 CompileScript: 
 #!/bin/zsh -efv 
  PATH=/usr/bin:$PATH
- perl -pi -e 's|python2.2|python2.3|g' **/* 2/dev/null
- perl -pi -e 's|python2 |python2.3 |g' **/* 2/dev/null
+ 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|/usr/bin/python2.3|/usr/bin/python|g **/*.py 2/dev/null
 #  
-FC=fort77 py_path=/usr/bin/python2.3 
LDFLAGS=-F/System/Library/Frameworks/Python.framework  ./configure  
--with-f77=fort77
+FC=fort77 py_path=/usr/bin/python 
LDFLAGS=-F/System/Library/Frameworks/Python.framework  ./configure  
--with-f77=fort77
 make
 rm -f **/*.o
 
 InstallScript: 
 #!/bin/zsh -efv
+rm -Rf **/.svn  # fink validate complains if this junk is left behind.
 mkdir -p %i/share/pdb2pqr
 cp -R * %i/share/pdb2pqr
 #


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[cvs] dists/10.4/unstable/main/finkinfo/sci apbs.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv14468

Modified Files:
apbs.info 
Log Message:
update for 10.5 compatibility and version update

Index: apbs.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- apbs.info   7 Feb 2007 05:07:54 -   1.9
+++ apbs.info   11 Nov 2007 14:36:34 -  1.10
@@ -1,21 +1,21 @@
 Package: apbs
-Version: 0.5.0
-Revision: 3 
-Source: mirror:sourceforge:%n/%n-%v-source-2.tar.gz
+Version: 0.5.1
+Revision: 1
+Source: mirror:sourceforge:%n/%n-%v-source.tar.gz
 #SourceRename: %n-%v.tar.gz
-Source-MD5: 80b201d182536cb5f914a23fca4a4732
+Source-MD5: e0619222398c499de8f4457c455bdaf4
 #SourceDirectory: %n-%v
 Depends: readline-shlibs (= 4.3-1028), gnuplot (= 4.0.0-1002), pdb2pqr, 
gcc42-shlibs
 BuildDepends: gcc42
 Conflicts: apbs-mpi, maloc, maloc-mpi-lammpi,  maloc-mpi-openmpi
 Replaces:  apbs-mpi, maloc, maloc-mpi-lammpi,  maloc-mpi-openmpi
-ConfigureParams: py_path=/usr/bin/python2.3
+ConfigureParams: py_path=/usr/bin/python
 Description: Adaptive Poisson-Boltzmann Solver
 CompileScript: 
 #!/bin/zsh -efv
 PATH=/usr/bin:$PATH
 
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
-py_path=/usr/bin/python2.3 F77=gfortran ./configure %c \
+py_path=/usr/bin/python F77=gfortran ./configure %c \
 --enable-python  \
 --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib -Wl,-undefined 
-Wl,dynamic_lookup 
 perl -pi -e 's|cp -Rf tools \${prefix}||g' Makefile
@@ -31,8 +31,8 @@
 # rm -Rf **/.svn  # fink validate complains if this junk is left behind.
 mkdir -p %i/share/%n
 mkdir -p %i/lib
-perl -pi -e 's|/usr/bin/env python|/usr/bin/python2.3|g' examples/**/*.py
-perl -pi -e 's|/usr/bin/env python|/usr/bin/python2.3|g' tools/**/*.py
+perl -pi -e 's|/usr/bin/env python|/usr/bin/python|g' examples/**/*.py
+perl -pi -e 's|/usr/bin/env python|/usr/bin/python|g' tools/**/*.py
 mv examples %i/share/%n
 mv tools %i/share/%n
 mv doc %i/share/%n


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[cvs] dists/10.4/unstable/main/finkinfo/sci apbs-mpi.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv15246

Added Files:
apbs-mpi.info 
Log Message:
update for 10.5 compatibility and version update

--- NEW FILE: apbs-mpi.info ---
Info2: 
Package: apbs-mpi-%type_pkg[handler]
Version: 0.5.1
Revision: 1000
Type: handler (lammpi openmpi)
Conflicts: apbs, apbs-mpi-lammpi, apbs-mpi-openmpi
Replaces: apbs, apbs-mpi-lammpi, apbs-mpi-openmpi
Source: http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-%v-source.tar.gz
Source-MD5: e0619222398c499de8f4457c455bdaf4
SourceDirectory: apbs-%v-source
Depends: (%type_pkg[handler] = lammpi) lammpi (= 7.1.2-1000), 
(%type_pkg[handler] = openmpi) openmpi, readline-shlibs (= 4.3-1028), gnuplot 
(= 4.0.0-1002)
BuildDepends: gcc42, (%type_pkg[handler] = lammpi) lammpi-dev (= 7.1.2-1000), 
(%type_pkg[handler] = openmpi) openmpi-dev
Description: Adaptive Poisson-Boltzmann Solver
CompileScript: 
#!/bin/zsh -efv
PATH=/usr/bin:$PATH
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
 py_path=/usr/bin/python
F77=gfortran ./configure %c  --enable-mpi --disable-blas  
--with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib -Wl,-undefined 
-Wl,dynamic_lookup --with-mpi --with-mpilib=%p/lib/%type_raw[handler] 
--with-mpiinc=%p/include/%type_raw[handler]
perl -pi -e 's|cp -Rf tools \${prefix}||g' Makefile
perl -pi -e 's|cp -Rf examples \${prefix}||g' Makefile
perl -pi -e 's|cp -Rf doc \${prefix}||g' Makefile
perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g'  
contrib/blas/Makefile
make

InstallScript: 
#!/bin/zsh -efv
make install DESTDIR=%d
rm -Rf **/CVS # fink validate complains if this junk is left behind.
# rm -Rf **/.svn  # fink validate complains if this junk is left behind.
mkdir -p %i/share/%n
mkdir -p %i/lib
perl -pi -e 's|/usr/bin/env python|/usr/bin/python|g' examples/**/*.py
perl -pi -e 's|/usr/bin/env python|/usr/bin/python|g' tools/**/*.py
mv examples %i/share/%n
mv tools %i/share/%n
mv doc %i/share/%n
rm -Rf %i/src
rm -f **/*.o

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


SplitOff: 
Package: %N-dev
BuildDependsOnly: true
Description: apbs headers, static libraries and libtool files
Files:
include/apbs
lib/libapbs.a
lib/libapbsmainroutines.a
lib/libapbs.la
lib/libapbsmainroutines.la



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. The Fink 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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[cvs] dists/10.4/unstable/main/finkinfo/sci fftw.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv10961

Modified Files:
fftw.info 
Log Message:
Had to comment out Info field to prevent install failure

Index: fftw.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/fftw.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- fftw.info   11 Nov 2007 22:24:19 -  1.7
+++ fftw.info   12 Nov 2007 00:13:14 -  1.8
@@ -79,7 +79,7 @@
 
 DocFiles: README COPYING INSTALL COPYRIGHT NEWS README.hacks AUTHORS
 Description: Discrete Fourier Transform Library
-InfoDocs: fftw.info fftw.info-1 fftw.info-2 fftw.info-3 fftw.info-4 fftw.info-5
+#InfoDocs: fftw.info fftw.info-1 fftw.info-2 fftw.info-3 fftw.info-4 
fftw.info-5
 DescDetail: 
  Performs the DFT in one or more dimensions, of both real and complex data, 
  for arbitrary input size. 


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[cvs] dists/10.4/unstable/main/finkinfo/sci eden.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv13707

Modified Files:
eden.info 
Log Message:
revision for 10.5

Index: eden.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/eden.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- eden.info   14 Oct 2007 00:01:09 -  1.4
+++ eden.info   12 Nov 2007 00:20:17 -  1.5
@@ -1,7 +1,7 @@
 Package: eden
 Version: 5.3
 Revision: 6
-Distribution: 10.4
+#Distribution: 10.4
 Source: http://www.edencrystallography.org/%n_V%v.tar.gz
 SourceRename: %n-%v.tar.gz
 Source-MD5: 17f4908db1944d788bac44e59c8a5cb5 


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[cvs] dists/10.4/unstable/main/finkinfo/utils a2ps.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/utils
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv4853

Modified Files:
a2ps.info 
Log Message:
Added ac_cv_exeext='' to ConfigureParams as suggested by Martin Costabel

Index: a2ps.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/utils/a2ps.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- a2ps.info   6 Jun 2007 03:32:24 -   1.7
+++ a2ps.info   12 Nov 2007 14:45:13 -  1.8
@@ -1,6 +1,6 @@
 Package: a2ps
 Version: 4.13
-Revision: 2
+Revision: 3
 Source: ftp://ftp.enst.fr/pub/unix/%n/%n-%v.tar.gz
 Source-MD5: c4361045913b27dbb6b6315874f6b196
 UpdateConfigGuessInDirs: auxdir
@@ -8,7 +8,7 @@
 Depends: libpaper1-shlibs, psutils, ghostscript
 BuildDepends: libgettext3-dev, gettext-bin, gettext-tools, libpaper1-dev
 PatchScript: perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
-ConfigureParams: --mandir='${prefix}/share/man' 
--infodir='${prefix}/share/info'
+ConfigureParams: --mandir='${prefix}/share/man' 
--infodir='${prefix}/share/info' ac_cv_exeext=''
 ConfFiles: 
 %p/etc/a2ps.cfg
 %p/etc/a2ps-site.cfg


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.45,1.46

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv5416

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

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -d -r1.45 -r1.46
--- coot.info   31 Oct 2007 23:32:33 -  1.45
+++ coot.info   20 Nov 2007 15:23:26 -  1.46
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-1-revision-449
-Revision: 4
+Version: 0.4-pre-1-revision-470
+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: da881ab7c09592fe4b766d4cac419d8c
+Source-MD5: 3f10ffc44da11e31dc3aa7f41e67a75f
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-1
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
@@ -27,6 +27,9 @@
  echo include \/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\~/.gtkrc-2.0
 or simply create a file called ~/.gtkrc-2.0 and put this line in it:
  include \/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\
+.
+Install fink's povray and raster3d to use the F8 key for producing ray-traced
+images.
 
 ###
 Recommends:  povray, ccp4, raster3d  


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[cvs] dists/10.4/unstable/main/finkinfo/shells zsh-templates.info, 1.18, 1.19

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv30172

Modified Files:
zsh-templates.info 
Log Message:
new url and version update

Index: zsh-templates.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/shells/zsh-templates.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- zsh-templates.info  2 Nov 2007 14:45:59 -   1.18
+++ zsh-templates.info  22 Nov 2007 20:24:25 -  1.19
@@ -1,8 +1,8 @@
 Package: zsh-templates
-Version: 1.2.4
+Version: 1.2.5
 Revision: 1
-Source:  http://xanana.ucsc.edu/~wgscott/mystuff/zsh/%n-%v.tgz
-Source-MD5: 6934b2e9b521224a92334ca45e2f9923
+Source:  http://zsh-templates-osx.googlecode.com/files/%n-%v.tgz
+Source-MD5: fcaf764e301bf7ebbb7393aa79c41090  
 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,1.46,1.47

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv7880

Modified Files:
coot.info 
Log Message:
coot version update and bug fixes

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -d -r1.46 -r1.47
--- coot.info   20 Nov 2007 15:23:26 -  1.46
+++ coot.info   23 Nov 2007 06:37:53 -  1.47
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-1-revision-470
+Version: 0.4-pre-1-revision-480
 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: 3f10ffc44da11e31dc3aa7f41e67a75f
+Source-MD5: 3a4105584b2db8fd5629f26928a5d0e0
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-1
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/x11 rxvt.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/x11
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv23158

Modified Files:
rxvt.info 
Log Message:
Jack Howarth fixed rxvt to compile on 10.5

Index: rxvt.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/x11/rxvt.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- rxvt.info   13 Jan 2007 19:58:16 -  1.3
+++ rxvt.info   24 Nov 2007 02:35:21 -  1.4
@@ -1,17 +1,17 @@
 Package: rxvt
-Version: 2.7.8
-Revision: 2
+Version: 2.7.10
+Revision: 1
 Conflicts: rxvt-ml
 Replaces: rxvt-ml
 Source: mirror:custom:%n-%v.tar.gz
-Source-MD5: e91b733b4f480f218db4b3b331ea42f6
+Source-MD5: 302c5c455e64047b02d1ef19ff749141
 BuildDepends: x11-dev
 Depends: x11
 CustomMirror: 
  Primary: ftp://ftp.rxvt.org/pub/rxvt/
  Secondary: ftp://ftp.rxvt.org/pub/rxvt/old
 
-ConfigureParams: --enable-everything --mandir='${prefix}/share/man' 
+ConfigureParams: --enable-everything --mandir='${prefix}/share/man' 
--disable-utmp
 Description: VT102 emulator for X11
 DescDetail: 
 rxvt is intended as an xterm replacement for users who  do  


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[cvs] dists/10.4/unstable/main/finkinfo/sci rnamotif.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-serv26883

Modified Files:
rnamotif.info 
Log Message:
version upgrade and fix for 10.5

Index: rnamotif.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/rnamotif.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- rnamotif.info   20 Jan 2006 20:30:40 -  1.1
+++ rnamotif.info   26 Nov 2007 21:56:09 -  1.2
@@ -1,10 +1,12 @@
 Package: rnamotif
-Version: 3.0.0
-Revision: 10
-Source: ftp://ftp.scripps.edu/case/macke/rnamotif-%v.tar.gz 
+Version: 3.0.4
+Revision: 1
+Source: http://www.scripps.edu/case/%n-%v.tar.gz
 SourceDirectory: %n-%v
-Source-MD5: ac54b92c7f47dfbc955b636c2d6d450f
+Source-MD5: 76b603bec11554c81a4cc3cd81f1b9cd
 CompileScript:  
+perl -pi -e 's|/usr/local|%p|g' config.h
+perl -pi -e 's|#include malloc.h||g' src/*.c
 make
 rm -f src/*.o
 


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[cvs] dists/10.4/unstable/crypto/finkinfo firefox.info,1.11,1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/crypto/finkinfo
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv25564

Modified Files:
firefox.info 
Log Message:
no workie on 10.5/ppc:( change made by Hanspeter Niederstrasser

Index: firefox.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/crypto/finkinfo/firefox.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- firefox.info19 Jul 2007 20:42:58 -  1.11
+++ firefox.info27 Nov 2007 15:48:47 -  1.12
@@ -2,6 +2,7 @@
 Version: 1.0.8
 Revision: 1005
 Architecture: powerpc
+Distribution: 10.4
 Description: Lightweight browser from mozilla.org
 License: OSI-Approved
 Maintainer: Hanspeter Niederstrasser [EMAIL PROTECTED]
@@ -45,10 +46,10 @@
 PatchScript: 
   /usr/bin/sed 's|@PREFIX@|%p|g' %a/%n.patch | /usr/bin/patch -p1
   /usr/bin/perl -pi -e 's,[EMAIL PROTECTED],%p/lib/%n,g' `/usr/bin/grep -lr 
@executable_path .`
-perl -pi.bak -e 's,-no-cpp-precomp,,' configure
+  /usr/bin/perl -pi -e 's,-no-cpp-precomp,,' configure
 
-GCC: 4.0
 ConfigureParams: --disable-dependency-tracking
+GCC: 4.0
 CompileScript: 
 ./configure %c
 /usr/bin/make -w


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.25,1.26

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv6516

Modified Files:
ccp4.info 
Log Message:
ccp4 fixed for 10.5 but unchanged for 10.4, keep revision number as 7

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -d -r1.25 -r1.26
--- ccp4.info   14 Oct 2007 00:01:09 -  1.25
+++ ccp4.info   28 Nov 2007 00:27:55 -  1.26
@@ -1,7 +1,6 @@
 Package: ccp4
 Version: 6.0.2
 Revision: 7
-Distribution: 10.4
 GCC: 4
 Source: ftp://ftp.ccp4.ac.uk/ccp4/%v/source/ccp4-%v-core-src.tar.gz
 Source-MD5: a47ae8b8e6fa76eef7f17baa85e8dc16
@@ -183,16 +182,27 @@
  export rpath=%p/lib/ccp4-%v
  export RPATH=%p/lib/ccp4-%v
 
-   # The cctbx sub-package requires us to use the system's own Python
- export 
PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:$PATH
- export 
PYTHONHOME=/System/Library/Frameworks/Python.framework/Versions/Current
- export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3
+if [[ $(sw_vers -productVersion)  10.5 ]]; then
+#   # The cctbx sub-package requires us to use the system's own Python
+ export 
PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:$PATH
+ export 
PYTHONHOME=/System/Library/Frameworks/Python.framework/Versions/Current
+ export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3
+fi
 
# gfortran is actually used by default, but to ensure the right thing 
happens, specify it.
+
+# 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
+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
+fi
 
#  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/gcc4.2/bin/||g' lib/clipper/**/Makefile*
@@ -204,7 +214,13 @@
  fi
 
  ( cd x-windows/XCCPJIFFY; perl -pi.bak -e 's|-lgfortran|-lgfortran 
-L%p/lib/gcc4.2/lib |g' *akefile* ) || exit 1
-
+if [[ $(sw_vers -productVersion)  10.5 ]]; then
+ :
+else
+ perl -pi.bak -e 's|-lcrt1.10.5.o||g' **/*akefile
+ perl -pi.bak -e 's|-lcrt1.o||g' **/*akefile
+fi
+   
#
  make
  make install
@@ -435,6 +451,14 @@
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0.2
This revision includes all available CCP4 patches as of June 28, 2007. 
and new bash and zsh command completions specific to ccp4. 
+
+On 10.5, phaser and cctbx fail to compile. Current workaround is to
+install the fink cctbx package, and to obtain phaser from here
+http://www-structmed.cimr.cam.ac.uk/phaser/download.html
+or obtain phenix, which includes phenix.phaser, from here
+http://www.phenix-online.org/
+Both are restricted downloads that require registration.
+This will be corrected upstream for the CCP4 6.1 release.
 
 DocFiles: 
README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps 


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.47,1.48

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv21923

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 1.47
retrieving revision 1.48
diff -u -d -r1.47 -r1.48
--- coot.info   23 Nov 2007 06:37:53 -  1.47
+++ coot.info   28 Nov 2007 02:17:33 -  1.48
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-1-revision-480
+Version: 0.4-pre-1-revision-496
 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: 3a4105584b2db8fd5629f26928a5d0e0
+Source-MD5: b53355064c1f7ad5d7d81b7a9fc3ae0a
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-1
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.48,1.49

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv10703

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 1.48
retrieving revision 1.49
diff -u -d -r1.48 -r1.49
--- coot.info   28 Nov 2007 02:17:33 -  1.48
+++ coot.info   6 Dec 2007 19:56:39 -   1.49
@@ -1,12 +1,12 @@
 Package:coot
-Version: 0.4-pre-1-revision-496
+Version: 0.4-pre-2-revision-521
 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: b53355064c1f7ad5d7d81b7a9fc3ae0a
+Source-MD5: 1cb2e09f1a7e0b6fe41bea3af180a7e0 
 #SourceDirectory: %n-%v
-SourceDirectory: %n-0.4-pre-1
+SourceDirectory: %n-0.4-pre-2
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
 Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
 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 molmol.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv25084

Modified Files:
molmol.info 
Log Message:
changed maintainer to Jack Howarth

Index: molmol.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- molmol.info 10 Nov 2007 22:48:50 -  1.9
+++ molmol.info 8 Dec 2007 17:06:32 -   1.10
@@ -60,6 +60,7 @@
 molmol files and documentation located in /sw/share/molmol.
 
 License: Restrictive
-Maintainer: W. G. Scott [EMAIL PROTECTED]  
+# Maintainer: W. G. Scott [EMAIL PROTECTED]  
+Maintainer: Jack Howarth [EMAIL PROTECTED]
 
 


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[cvs] dists/10.4/stable/main/finkinfo/sci molmol.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv24695

Modified Files:
molmol.info 
Log Message:
changed maintainer to Jack Howarth

Index: molmol.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/molmol.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- molmol.info 10 Nov 2007 22:48:24 -  1.8
+++ molmol.info 8 Dec 2007 17:05:59 -   1.9
@@ -60,6 +60,8 @@
 molmol files and documentation located in /sw/share/molmol.
 
 License: Restrictive
-Maintainer: W. G. Scott [EMAIL PROTECTED]  
+# Maintainer: W. G. Scott [EMAIL PROTECTED]  
+Maintainer: Jack Howarth [EMAIL PROTECTED]
+
 
 


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[cvs] dists/10.4/unstable/main/finkinfo/sci cctbx.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv4197

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

Index: cctbx.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/cctbx.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- cctbx.info  2 Nov 2007 05:17:53 -   1.10
+++ cctbx.info  12 Dec 2007 00:15:42 -  1.11
@@ -1,14 +1,14 @@
 Package:cctbx
-Version: 70818
-# 2007_08_18_1856
-Revision: 1001
+Version: 71118
+# 2007_11_18_2203
+Revision: 1
 GCC: 4.0
 BuildDependsOnly: false
 NoSourceDirectory: true
 NoSetLDFLAGS: true
 NoSetCPPFLAGS: true
-Source: 
http://cci.lbl.gov/cctbx_build/results/2007_08_18_1856/cctbx_bundle.tar.gz
-Source-MD5: 8d1ec7c39128c6b04be6aea5b4cb4555
+Source: 
http://cci.lbl.gov/cctbx_build/results/2007_11_18_2203/cctbx_bundle.tar.gz
+Source-MD5: d6d4ce016a438c502436e8b8699fc163
 SourceRename: %n-%v.tar.gz
 Description: Computational Crystallography Toolbox
 DescDetail: 


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[cvs] dists/10.4/unstable/main/finkinfo/gnome gtk-canvas.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/gnome
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv10400

Modified Files:
gtk-canvas.info 
Log Message:
added missing dependency

Index: gtk-canvas.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/gnome/gtk-canvas.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- gtk-canvas.info 18 Jul 2007 02:13:28 -  1.7
+++ gtk-canvas.info 12 Dec 2007 00:31:49 -  1.8
@@ -1,8 +1,8 @@
 Package: gtk-canvas
 Version: 0.1.1
 Revision: 26
-BuildDepends: gtk+, glib, libiconv-dev, gettext-dev, x11-dev, imlib, 
gnome-libs-dev, libart2 (= 2.3.16-2)
-Depends: gnome-libs-shlibs, gtk+-shlibs, imlib-shlibs, glib-shlibs, 
gtk+-shlibs, libiconv, gettext
+BuildDepends: pwlib1, pwlib1-shlibs, gtk+, glib, libiconv-dev, gettext-dev, 
x11-dev, imlib, gnome-libs-dev, libart2 (= 2.3.16-2)
+Depends: pwlib1-shlibs, gnome-libs-shlibs, gtk+-shlibs, imlib-shlibs, 
glib-shlibs, gtk+-shlibs, libiconv, gettext
 # The Depends files are only required for the test program AFAIK.
 BuildDependsOnly: true
 Source: http://www.atai.org/%n/%n-%v.tar.gz


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[cvs] dists/10.4/stable/main/finkinfo/gnome gtk-canvas.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/gnome
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv10794

Modified Files:
gtk-canvas.info 
Log Message:
added missing dependency

Index: gtk-canvas.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/gnome/gtk-canvas.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- gtk-canvas.info 25 Jul 2007 04:07:27 -  1.4
+++ gtk-canvas.info 12 Dec 2007 00:32:34 -  1.5
@@ -1,8 +1,8 @@
 Package: gtk-canvas
 Version: 0.1.1
 Revision: 26
-BuildDepends: gtk+, glib, libiconv-dev, gettext-dev, x11-dev, imlib, 
gnome-libs-dev, libart2 (= 2.3.16-2)
-Depends: gnome-libs-shlibs, gtk+-shlibs, imlib-shlibs, glib-shlibs, 
gtk+-shlibs, libiconv, gettext
+BuildDepends: pwlib1, pwlib1-shlibs, gtk+, glib, libiconv-dev, gettext-dev, 
x11-dev, imlib, gnome-libs-dev, libart2 (= 2.3.16-2)
+Depends: pwlib1-shlibs, gnome-libs-shlibs, gtk+-shlibs, imlib-shlibs, 
glib-shlibs, gtk+-shlibs, libiconv, gettext
 # The Depends files are only required for the test program AFAIK.
 BuildDependsOnly: true
 Source: http://www.atai.org/%n/%n-%v.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci pointless.patch, NONE, 1.1 pointless.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16040

Modified Files:
pointless.info 
Added Files:
pointless.patch 
Log Message:
another pointless update, now with a pointless patch

--- 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}
 

Index: pointless.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pointless.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- pointless.info  14 Oct 2007 00:01:09 -  1.7
+++ pointless.info  12 Dec 2007 02:07:44 -  1.8
@@ -1,26 +1,23 @@
 Package: pointless
-Version: 1.1.5
+Version: 1.2.10
 Revision: 1
-Distribution: 10.4
-Source: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n-%v-src.tar.gz
-Source-MD5: baa2c6b75119707f25cea1ced17f5b97
+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: f2a318a6ba5914dab202780825c5d423
+Source2-MD5: 9e26dd2b8892e400f82f7b14c4e5c285
 Source3: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/%n-ccp4i-0.0.8.tar.gz
 Source3-MD5: e4d9a43059ad3981ea7eda165c5ba5aa
-Source4: ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/source/phaser-1.3.3-cctbx-src.tar.gz
-Source4-MD5: edff4d201e7b6d987c05efcf965f6023
 NoSourceDirectory: yes
-Depends: ccp4 (= 6.0.2) | ccp4-g77 (= 6.0.2) , fftw-shlibs
-BuildDepends: ccp4-dev (= 6.0.2) | ccp4-g77-dev (= 6.0.2), fftw
+Depends: ccp4 (= 6.0.2), fftw-shlibs
+BuildDepends: fftw, ccp4-onlylibs-dev (= 6.0.2-8) , cctbx (= 71118-1 )
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 PatchScript: 
-#!/bin/bash -efv
-mv pointless pointless-ccp4i
+ 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
+#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


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.49,1.50

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv18965

Modified Files:
coot.info 
Log Message:
coot update and bug fixes

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.49
retrieving revision 1.50
diff -u -d -r1.49 -r1.50
--- coot.info   6 Dec 2007 19:56:39 -   1.49
+++ coot.info   12 Dec 2007 15:49:53 -  1.50
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-2-revision-521
+Version: 0.4-pre-2-revision-567
 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: 1cb2e09f1a7e0b6fe41bea3af180a7e0 
+Source-MD5: 29ac89fb215ede40348e59cdcba29089
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-2
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci phaser.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv17226

Added Files:
phaser.info 
Log Message:
new version of ccp4-associated program phaser now available as its own package

--- NEW FILE: phaser.info ---
Package: phaser
Version: 2.1.1
Revision: 1
Source: ftp://ftp.ccp4.ac.uk/ccp4/current/prerelease/%n-%v-cctbx-src.tar.gz
Source-MD5: 28891623d3e0bca66794323113d14bf5
NoSourceDirectory: yes
Depends: ccp4 (= 6.0.2) 
BuildDepends: ccp4 (= 6.0.2)   
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
CompileScript:  
#!/bin/bash -efv
 CCP4=
 export CCP4=$PWD/ccp4-6.0.2
 cd $CCP4/src/phaser
 pwd
 export CCP4_BIN=$CCP4/bin
 export CCP4_LIB=$CCP4/lib
 binary_inst=no
 bindir=${bindir:-$CCP4_BIN}
 libdir=${libdir:-$CCP4_LIB}
 incdir=${incdir:-$CCP4/include}
 # Get Phaser environment variables, so we know where executable is.
 PHASER_MTYPE=`bin/machine_type`
 PHASER_VERSION=`grep PHASER_VERSION conf/version | awk '{print $3}'`
 ./install --prefix=$CCP4/src/phaser --force-compile --static_libraries  
--component=mmtbx --component=phaser
 echo  
 echo  Building static phaser executable
 echo  

InstallScript: 
#!/bin/bash -efv
 mkdir -p %i/bin
 cp ccp4-6.0.2/src/%n/%n-%v/build/mac-osx/exe/phaser  %i/bin

Description: CCP4 automated molecular replacement program
DescDetail: 
Updated version of phaser for ccp4. This installs just the executable
to replace the older version in ccp4 (which does not compile on 10.5).
If you use this software please cite:
Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, 
P.D. Adams, M.D. Winn, L.C. Storoni  R.J. Read
J. Appl. Cryst. (2007). 40, 658-674

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


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.26,1.27

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv17619

Modified Files:
ccp4.info 
Log Message:
added more descriptive information to ccp4 package to inform user of associated 
packages

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -d -r1.26 -r1.27
--- ccp4.info   28 Nov 2007 00:27:55 -  1.26
+++ ccp4.info   13 Dec 2007 02:32:43 -  1.27
@@ -451,14 +451,23 @@
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0.2
This revision includes all available CCP4 patches as of June 28, 2007. 
and new bash and zsh command completions specific to ccp4. 
-
-On 10.5, phaser and cctbx fail to compile. Current workaround is to
-install the fink cctbx package, and to obtain phaser from here
-http://www-structmed.cimr.cam.ac.uk/phaser/download.html
-or obtain phenix, which includes phenix.phaser, from here
-http://www.phenix-online.org/
-Both are restricted downloads that require registration.
-This will be corrected upstream for the CCP4 6.1 release.
+   
+   A new version of phaser (2.1.1) is available separately in fink as
+   a package called, imaginatively, phaser. 
+   
+   A new version of cctbx is available in fink from the cctbx package.
+   
+   A new version of pointless is available as a separate fink package
+   of that name.
+   
+   The ccp4-associated chooch package is available separately via fink.
+   
+   The latest version of mosflm is available in two forms from fink; the
+   standard large form, and a special small display useful for 13 inch
+   laptop displays.
+   
+   The ccp4-associated molecular graphics display program coot is also
+   available as a fink package.
 
 DocFiles: 
README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps 


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

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28797

Added Files:
cctbx-10.4.info cctbx-10.5.info 
Log Message:
OSX-version-specific packages for cctbx -- debians were incompatible

--- NEW FILE: cctbx-10.4.info ---
Package: cctbx-10.4
Version: 71118
# 2007_11_18_2203
Revision: 2
Distribution: 10.4
Conflicts: cctbx (= 71118-1), cctbx-10.5
Replaces: cctbx (= 71118-1), cctbx-10.5
GCC: 4.0
BuildDependsOnly: false
NoSourceDirectory: true
NoSetLDFLAGS: true
NoSetCPPFLAGS: true
Source: 
http://cci.lbl.gov/cctbx_build/results/2007_11_18_2203/cctbx_bundle.tar.gz
Source-MD5: d6d4ce016a438c502436e8b8699fc163
SourceRename: cctbx-%v.tar.gz
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/sh -efv
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=$( sysctl hw.logicalcpu | awk '{print $NF}' )
# On a machine with multiple CPUs enter:

libtbx.scons -j $num_cpu .

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

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/cctbx/cctbx_build
/System/Library/Frameworks/Python.framework/Versions/Current/bin/python \

[cvs] dists/10.4/unstable/main/finkinfo/sci cctbx.info,1.11,1.12

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv29192

Modified Files:
cctbx.info 
Log Message:
cctbx version-independent placeholder for compatibility

Index: cctbx.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/cctbx.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- cctbx.info  12 Dec 2007 00:15:42 -  1.11
+++ cctbx.info  13 Dec 2007 05:47:34 -  1.12
@@ -1,106 +1,21 @@
 Package:cctbx
 Version: 71118
 # 2007_11_18_2203
-Revision: 1
+Revision: 2
+Depends: cctbx-10.5 | cctbx-10.4
 GCC: 4.0
 BuildDependsOnly: false
 NoSourceDirectory: true
+Type: NoSource
 NoSetLDFLAGS: true
 NoSetCPPFLAGS: true
-Source: 
http://cci.lbl.gov/cctbx_build/results/2007_11_18_2203/cctbx_bundle.tar.gz
-Source-MD5: d6d4ce016a438c502436e8b8699fc163
-SourceRename: %n-%v.tar.gz
-Description: Computational Crystallography Toolbox
+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/sh -efv
-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=$( sysctl hw.logicalcpu | awk '{print $NF}' )
-# On a machine with multiple CPUs enter:
-
-libtbx.scons -j $num_cpu .
-
-InstallScript: 
-perl -pi -e 's|prepend|append|g' %n_build/setpaths.csh
-perl -pi -e 's|prepend|append|g' %n_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  

[cvs] dists/10.4/unstable/main/finkinfo/sci mosflm-small.info, 1.16, 1.17 mosflm.info, 1.15, 1.16

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv2460

Modified Files:
mosflm-small.info mosflm.info 
Log Message:
mosflm works on 10.5

Index: mosflm-small.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm-small.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- mosflm-small.info   14 Oct 2007 00:01:09 -  1.16
+++ mosflm-small.info   13 Dec 2007 06:01:17 -  1.17
@@ -1,7 +1,6 @@
 Package: mosflm-small
 Version: 7.0.1
 Revision: 2
-Distribution: 10.4
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
 SourceDirectory: mosflm701
 Source-MD5: 9cca259141a3dabaacbe29a90af96e49 

Index: mosflm.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mosflm.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- mosflm.info 14 Oct 2007 00:01:09 -  1.15
+++ mosflm.info 13 Dec 2007 06:01:17 -  1.16
@@ -1,7 +1,6 @@
 Package: mosflm
 Version: 7.0.1
 Revision: 2
-Distribution: 10.4
 Source: 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/build-it-yourself/mosflm701.tgz
 SourceDirectory: mosflm701
 Source-MD5: 9cca259141a3dabaacbe29a90af96e49 


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[cvs] dists/10.4/unstable/main/finkinfo/sci pointless.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv15631

Modified Files:
pointless.info 
Log Message:
minor change to dependecy specification that does not change package

Index: pointless.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/pointless.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- pointless.info  12 Dec 2007 02:07:44 -  1.8
+++ pointless.info  21 Dec 2007 00:52:32 -  1.9
@@ -9,7 +9,7 @@
 Source3-MD5: e4d9a43059ad3981ea7eda165c5ba5aa
 NoSourceDirectory: yes
 Depends: ccp4 (= 6.0.2), fftw-shlibs
-BuildDepends: fftw, ccp4-onlylibs-dev (= 6.0.2-8) , cctbx (= 71118-1 )
+BuildDepends: fftw, ccp4-onlylibs-dev (= 6.0.2-8) , cctbx-10.4 | cctbx-10.5
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
 PatchScript: 


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.50,1.51

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16064

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 1.50
retrieving revision 1.51
diff -u -d -r1.50 -r1.51
--- coot.info   12 Dec 2007 15:49:53 -  1.50
+++ coot.info   21 Dec 2007 00:53:20 -  1.51
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-2-revision-567
+Version: 0.4-pre-2-revision-601
 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: 29ac89fb215ede40348e59cdcba29089
+Source-MD5: f0f63c4b198301f75fe5ff5887f64a1e
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-2
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz


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[cvs] dists/10.4/unstable/main/finkinfo/sci phaser.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-serv8564

Modified Files:
phaser.info 
Log Message:
alternate url

Index: phaser.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/phaser.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- phaser.info 13 Dec 2007 02:31:44 -  1.1
+++ phaser.info 21 Dec 2007 20:33:19 -  1.2
@@ -1,7 +1,8 @@
 Package: phaser
 Version: 2.1.1
 Revision: 1
-Source: ftp://ftp.ccp4.ac.uk/ccp4/current/prerelease/%n-%v-cctbx-src.tar.gz
+Source: http://xanana.ucsc.edu/xtal/%n-%v-cctbx-src.tar.gz
+#Source: ftp://ftp.ccp4.ac.uk/ccp4/current/prerelease/%n-%v-cctbx-src.tar.gz
 Source-MD5: 28891623d3e0bca66794323113d14bf5
 NoSourceDirectory: yes
 Depends: ccp4 (= 6.0.2) 


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[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4-onlylibs-dev.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-serv28242

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
unified fix for 10.4/10.5 for coot compatibility

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- ccp4-onlylibs-dev.info  3 Nov 2007 15:21:51 -   1.16
+++ ccp4-onlylibs-dev.info  22 Dec 2007 01:20:39 -  1.17
@@ -1,7 +1,7 @@
 Package: ccp4-onlylibs-dev
 # Use version numbering to sync with the current CCP4 release:
 Version: 6.0.2
-Revision: 8
+Revision: 9
 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
@@ -100,11 +100,9 @@
  perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la
  rm -f lib/*.la.bak
 #
-# Temp fix for coot (needed in 10.4 but not 10.5)
-if [[ $(sw_vers -productVersion)  10.5 ]]; then
 cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig
 perl -pi -e 's|ivector   FF1,FF2;||g' include/ssm/ssm_superpose.h
-fi
+#  
 # Now install:
  mkdir -p %i/bin
  mkdir -p %i/share/xtal/%n-%v


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[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.51,1.52

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28660

Modified Files:
coot.info 
Log Message:
new version pygtk+2 scripting window now works

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.51
retrieving revision 1.52
diff -u -d -r1.51 -r1.52
--- coot.info   21 Dec 2007 00:53:20 -  1.51
+++ coot.info   22 Dec 2007 01:21:26 -  1.52
@@ -1,14 +1,14 @@
 Package:coot
-Version: 0.4-pre-2-revision-601
+Version: 0.4-pre-2-revision-611
 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: f0f63c4b198301f75fe5ff5887f64a1e
+Source-MD5: aa41d33a8f29ef6f9e0fa5c0ccc0dc96
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-2
-Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
-Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
+Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz
+Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 #
@@ -28,13 +28,13 @@
 or simply create a file called ~/.gtkrc-2.0 and put this line in it:
  include \/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\
 .
-Install fink's povray and raster3d to use the F8 key for producing ray-traced
-images.
+Install povray and raster3d fink packages to use the F8 key for producing 
+ray-traced images.
 
 ###
-Recommends:  povray, ccp4, raster3d  
+Recommends:  povray, ccp4, raster3d
 BuildDepends: 
- ccp4-onlylibs-dev   (= 6.0.2-8),
+ ccp4-onlylibs-dev   (= 6.0.2-9),
  atk1   ,
  freeglut,
  giflib  ,
@@ -60,6 +60,8 @@
  librsvg2-gtk,
  libtool14  ,
  pango1-xft2-dev,
+ pygtk2-py25-dev ,
+ python25,
  swig
 
 # Note: gtkglext1 IS required at runtime for stereo functionality
@@ -95,10 +97,11 @@
  libtiff-shlibs   ,
  libtool14-shlibs ,
  librsvg2-gtk ,
- pango1-xft2-shlibs   
+ pango1-xft2-shlibs   ,
+ pygtk2-py25  ,
+ python25 ,   
 
 #
-# raster3d
 ###
 BuildDependsOnly: false
 NoSetLDFLAGS: true
@@ -133,33 +136,18 @@
 ###
 CompileScript: 
 #!/bin/zsh -efx
-
-export 
PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
+export PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
 export SED=/usr/bin/sed
-# Use the system-supplied python, which differs for 10.4 vs. 10.5
-if [[ -d  
/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5 
]];then
-alias 
python=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5
-export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5
-FLIBS=-L/System/Library/Frameworks/Python.framework/Versions/Current/lib 
-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 
-I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.5
 \
-LDFLAGS=-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib -L/usr/lib 
-lSystemStubs -flat_namespace 
-L/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5/config
 -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
-CXX=/usr/bin/g++ \
-CC=/usr/bin/gcc \
-
py_path=/System/Library/Frameworks/Python.framework/Versions/Current/bin/python2.5
 \
-./configure %c
-else
-   alias 
python=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3
-   export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3
-   
FLIBS=-L/System/Library/Frameworks/Python.framework/Versions/Current/lib 
-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 
-I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.3
 \
-   LDFLAGS=-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib 
-L/usr/lib -lSystemStubs 

[cvs] dists/10.4/unstable/main/finkinfo/sci coot.info,1.52,1.53

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16509

Modified Files:
coot.info 
Log Message:
coot update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v
retrieving revision 1.52
retrieving revision 1.53
diff -u -d -r1.52 -r1.53
--- coot.info   22 Dec 2007 01:21:26 -  1.52
+++ coot.info   25 Dec 2007 02:21:28 -  1.53
@@ -1,10 +1,10 @@
 Package:coot
-Version: 0.4-pre-2-revision-611
+Version: 0.4-pre-2-revision-612
 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: aa41d33a8f29ef6f9e0fa5c0ccc0dc96
+Source-MD5: 75a9a5d0138c8b0ce97234cf5cd058d2
 #SourceDirectory: %n-%v
 SourceDirectory: %n-0.4-pre-2
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz


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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4-onlylibs-dev.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv12095

Modified Files:
ccp4-onlylibs-dev.info 
Log Message:
revision update for coot

Index: ccp4-onlylibs-dev.info
===
RCS file: 
/cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- ccp4-onlylibs-dev.info  3 Nov 2007 15:23:49 -   1.4
+++ ccp4-onlylibs-dev.info  29 Dec 2007 19:55:45 -  1.5
@@ -1,7 +1,7 @@
 Package: ccp4-onlylibs-dev
 # Use version numbering to sync with the current CCP4 release:
 Version: 6.0.2
-Revision: 8
+Revision: 9
 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
@@ -100,11 +100,9 @@
  perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la
  rm -f lib/*.la.bak
 #
-# Temp fix for coot (needed in 10.4 but not 10.5)
-if [[ $(sw_vers -productVersion)  10.5 ]]; then
 cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig
 perl -pi -e 's|ivector   FF1,FF2;||g' include/ssm/ssm_superpose.h
-fi
+#  
 # Now install:
  mkdir -p %i/bin
  mkdir -p %i/share/xtal/%n-%v


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[cvs] dists/10.4/stable/main/finkinfo/sci coot.patch, NONE, 1.1 coot.info, 1.9, 1.10

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv12910

Modified Files:
coot.info 
Added Files:
coot.patch 
Log Message:
a reasonably stable coot for sci-stable

--- NEW FILE: coot.patch ---
diff -ruN coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc 
coot-0.4-pre-1/coot-utils/coot-fffear.cc
--- coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc   2007-04-16 
15:42:06.0 -0700
+++ coot-0.4-pre-1/coot-utils/coot-fffear.cc2007-10-31 10:28:44.0 
-0700
@@ -160,30 +160,7 @@
   }
 

-  for (unsigned int iop=0; iopops.size(); iop++) {
-
-clipper::Xmapfloat r1;
-r1.init(clipper::Spacegroup::p1(), xmap.cell(), xmap.grid_sampling()); 
// fixed to be consistent with above results init.
-clipper::FFFear_fftfloat search(xmap);
-clipper::NX_operator nxop( xmap, nxmap, ops[iop]);
-search(r1, nxmap, nxmap_mask, nxop); // fill r1 with fffear search 
values at this orientation
-  
-clipper::Xmapfloat::Map_reference_index ix;
-for ( ix = r1.first(); !ix.last(); ix.next() )
-   if ( r1[ix]  results[ix].first) {
-  results[ix].first = r1[ix];
-  results[ix].second = iop;
-   }
-
-icount++;
-//   std::cout  ops.size() - iop   ; 
-std::cout.flush();
-if (icount == 50) {
-   std::cout100*(float(iop)/float(ops.size()))  %;
-   std::cout.flush();
-   icount = 0;
-}
-  }
+  
   std::cout  \n;
}
 }
diff -ruN coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 
coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp
--- coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 2007-07-01 
07:12:02.0 -0700
+++ coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp  2007-10-31 11:08:12.0 
-0700
@@ -193,46 +193,7 @@
   \param resulttrn The best translations.
   \param xmap The map to search.
   \param rtops The oprientations to search. */
-void LLK_map_target::search( clipper::Xmapfloat resultscr, 
clipper::Xmapint resultrot, clipper::Xmapint resulttrn, const 
clipper::Xmapfloat xmap, const std::vectorclipper::RTop_orth rtops ) const
-{
-  // set up results
-  const clipper::Spacegroupspgr = xmap.spacegroup();
-  const clipper::Cell  cell = xmap.cell();
-  const clipper::Grid_sampling grid = xmap.grid_sampling();
-  resultscr.init( spgr, cell, grid );
-  resultrot.init( spgr, cell, grid );
-  resulttrn.init( spgr, cell, grid );
-  resultscr = 1.0e20;
-
-  // now search for ML target in each orientation in turn
-  clipper::Xmapfloat resultp1( clipper::Spacegroup::p1(), cell, grid );
-  clipper::Xmapfloat::Map_reference_index i1(resultp1);
-  clipper::Xmapfloat::Map_reference_coord ix(resultscr);
-
-  // set up z scoring
-  clipper::FFFear_fftfloat srch( xmap );
-  clipper::NX_operator nxop( xmap, target, rtops[0] );
-  srch( resultp1, target, weight, nxop );
-  clipper::Map_stats zstats( resultp1 );
-
-  // loop over orientations
-  for ( int op = 0; op  rtops.size(); op++ ) {
-// do the fffear search
-clipper::NX_operator nxop( xmap, target, rtops[op].inverse() );
-srch( resultp1, target, weight, nxop );
-
-// store best scores
-for ( i1 = resultp1.first(); !i1.last(); i1.next() ) {
-  ix.set_coord( i1.coord() );
-  float score = ( resultp1[i1] - zstats.mean() ) / zstats.std_dev();
-  if ( score  resultscr[ix] ) {
-   resultscr[ix] = score;
-   resultrot[ix] = op;
-   resulttrn[ix] = grid.index( i1.coord() );
-  }
-}
-  }
-}
+ 
 
 
 clipper::String LLK_map_target::format() const

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- coot.info   12 Sep 2007 18:53:40 -  1.9
+++ coot.info   29 Dec 2007 19:57:20 -  1.10
@@ -1,14 +1,14 @@
 Package:coot
-Version: 0.4-pre-1-revision-375
+Version: 0.4.0-pre-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-%v.tar.gz
-Source-MD5: a43cc7d3f4e32b85d55d5748359c18aa
+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/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
-Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
+Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz
+Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: c09bb6b5524901cb0fde14589546224e 
 #
@@ -27,16 +27,19 @@
  echo include \/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\~/.gtkrc-2.0
 or simply create a 

[cvs] dists/10.4/stable/main/finkinfo/sci cctbx-10.5.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-serv24833

Added Files:
cctbx-10.5.info 
Log Message:
cctbx for 10.5 stable/sci

--- NEW FILE: cctbx-10.5.info ---
Package: cctbx-10.5
Version: 71118
# 2007_11_18_2203
Revision: 2
Distribution: 10.5
Conflicts: cctbx (= 71118-1), cctbx-10.4
Replaces: cctbx (= 71118-1),  cctbx-10.4
GCC: 4.0
BuildDependsOnly: false
NoSourceDirectory: true
NoSetLDFLAGS: true
NoSetCPPFLAGS: true
Source: 
http://cci.lbl.gov/cctbx_build/results/2007_11_18_2203/cctbx_bundle.tar.gz
Source-MD5: d6d4ce016a438c502436e8b8699fc163
SourceRename: cctbx-%v.tar.gz
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/sh -efv
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=$( sysctl hw.logicalcpu | awk '{print $NF}' )
# On a machine with multiple CPUs enter:

libtbx.scons -j $num_cpu .

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

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/cctbx/cctbx_build
/System/Library/Frameworks/Python.framework/Versions/Current/bin/python \
../cctbx_sources/libtbx/configure.py mmtbx
#

License: OSI-Approved
Maintainer: W. G. Scott 

[cvs] dists/10.4/unstable/main/finkinfo/sci ccp4.info,1.27,1.28

[William Scott]

Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv13478

Modified Files:
ccp4.info 
Log Message:
updated DescDetail but otherwise unchanged so keep rev number

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -d -r1.27 -r1.28
--- ccp4.info   13 Dec 2007 02:32:43 -  1.27
+++ ccp4.info   30 Dec 2007 04:13:12 -  1.28
@@ -428,26 +428,22 @@
 

 Description:  Macromolecular crystallography package
 DescDetail: 
-   These are the ccp4 programs compiled with gfortran instead of g77.
-
-   The (currently default) g77 version does not work on intel.  The hope
-   is that this will. (With gfortran-4.2, everything compiles.) Thanks 
-   to Jack Howarth for many helpful improvements.
-
-   CCP4 macromolecular crystallography suite has approximately
-   200 programs and utilities. This version included Clipper
-   libraries, and ccif and phaser. If you need cctbx, please
-   install the cctbx fink package separately.
+   The CCP4 macromolecular crystallography suite has approximately
+   200 programs and utilities. This version includes the Clipper
+   libraries. Current phaser and cctbx programs are available as 
+   separate fink packages.
 
Type ccp4help for a summary listing of all ccp4 programs.
Type ccp4help foo for a detailed description of program foo.
 
-   Invoke optional ccp4i gui for the first run using: sudo ccp4i
-   Thereafter, invoke without sudo.
+   Invoke optional ccp4i gui for the first run using sudo ccp4i
+   on 10.4, or sudo -s followed by ccp4i on 10.5 to permit
+   global configuration. Thereafter, you can invoke ccp4i without sudo.
 
-   This version compiles with the Apple Lapack/Blas framework
+   This version compiles with the Apple Lapack/Blas framework.
License agreement is part of configure file -- print out form and mail 
in,
additional comments at http://xanana.ucsc.edu/xtal/ccp4.html
+   
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0.2
This revision includes all available CCP4 patches as of June 28, 2007. 
and new bash and zsh command completions specific to ccp4. 
@@ -468,6 +464,8 @@

The ccp4-associated molecular graphics display program coot is also
available as a fink package.
+   
+   Thanks to Jack Howarth for many helpful improvements.
 
 DocFiles: 
README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps 


-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
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[cvs] dists/10.4/stable/main/finkinfo/sci fftw.info, 1.4, 1.5 fftw.patch, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv15117

Modified Files:
fftw.info fftw.patch 
Log Message:
fftw with gfortran suitable for 10.5, promoted from unstable with permission 
from M. Costabel

Index: fftw.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/fftw.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- fftw.info   14 Oct 2007 00:00:07 -  1.4
+++ fftw.info   30 Dec 2007 04:17:57 -  1.5
@@ -1,14 +1,14 @@
 Info2: 
 Package: fftw%type_pkg[-mpi]
-Type: -mpi (.)
+Type: -mpi (boolean)
 Version: 2.1.5
-Revision: 1009
-Distribution: 10.4
+Revision: 1012
+#Distribution: 10.4
 Maintainer: Jeffrey Whitaker [EMAIL PROTECTED]
 Source:  ftp://ftp.fftw.org/pub/%n/old/fftw-%v.tar.gz
 Source-MD5: 8d16a84f3ca02a785ef9eb36249ba433
-BuildDepends:  g95 (= 0.50-20060413), (%type_raw[-mpi] = -mpi) lammpi-dev (= 
7.0.6-1011)
-Depends: %N-shlibs (= %v-%r), (%type_raw[-mpi] = -mpi) lammpi (= 7.0.6-1011)
+BuildDepends: gcc42 (= 4.2.2-1000), (%type_raw[-mpi] = -mpi) lammpi-dev (= 
7.0.6-1011)
+Depends: %N-shlibs (= %v-%r), gcc42-shlibs (= 4.2.2-1000), (%type_raw[-mpi] = 
-mpi) lammpi (= 7.0.6-1011)
 BuildDependsOnly: True
 Patch: fftw.patch
 Conflicts: fftw-absoft, fftw, fftw-mpi
@@ -21,39 +21,43 @@
 InstallScript: 
  #!/bin/bash -ev
  if [ %type_raw[-mpi] == -mpi ]; then
- if [ %m = i386 ]; then 
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --without-gcc-arch 
--enable-mpi
+ if [ %m = i386 ]; then
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--without-gcc-arch --enable-mpi
  else
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --enable-mpi
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--enable-mpi
  fi
  else
  if [ %m = i386 ]; then 
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --without-gcc-arch 
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--without-gcc-arch 
  else
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c 
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
  fi
  fi
  make install DESTDIR=%d
  make clean
  if [ %type_raw[-mpi] == -mpi ]; then
  if [ %m = i386 ]; then 
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --without-gcc-arch 
--enable-mpi --enable-float
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--without-gcc-arch --enable-mpi --enable-float
  else
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --enable-float 
--enable-altivec --enable-mpi
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--enable-float --enable-altivec --enable-mpi
  fi
  else
  if [ %m = i386 ]; then 
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --without-gcc-arch 
--enable-float
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--without-gcc-arch --enable-float
  else
- FC=%p/bin/g95 FLIBS=-L%p/lib -lg95 ./configure %c --enable-float 
--enable-altivec 
+ F77=%p/bin/gfortran FLIBS=-L%p/lib/gcc4.2/lib -lgfortran ./configure %c 
--enable-float --enable-altivec 
  fi
  fi
  make
+ cd doc
+ rm -f fftw.info fftw.info-1 fftw.info-2 fftw.info-3 fftw.info-4 fftw.info-5
+ make info
+ cd ..
  make install DESTDIR=%d
- (cd %i/lib; ln -s %p/lib/libdfftw.2.0.7.dylib libfftw.dylib)
- (cd %i/lib; ln -s %p/lib/libdrfftw.2.0.7.dylib librfftw.dylib)
- (cd %i/include; ln -s %p/include/dfftw.h fftw.h)
- (cd %i/include; ln -s %p/include/drfftw.h rfftw.h)
+ (cd %i/lib; ln -s %p/lib/libdfftw.2.0.7.dylib libfftw.dylib) || exit 1
+ (cd %i/lib; ln -s %p/lib/libdrfftw.2.0.7.dylib librfftw.dylib) || exit 1
+ (cd %i/include; ln -s %p/include/dfftw.h fftw.h) || exit 1
+ (cd %i/include; ln -s %p/include/drfftw.h rfftw.h) || exit 1
 
 SplitOff: 
   Package: %N-shlibs
@@ -79,6 +83,7 @@
 
 DocFiles: README COPYING INSTALL COPYRIGHT NEWS README.hacks AUTHORS
 Description: Discrete Fourier Transform Library
+InfoDocs: fftw.info
 DescDetail: 
  Performs the DFT in one or more dimensions, of both real and complex data, 
  for arbitrary input size. 

Index: fftw.patch
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/fftw.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- fftw.patch  20 Jan 2006 20:12:58 -  1.1
+++ fftw.patch  30 Dec 2007 04:17:57 -  1.2
@@ -1,5 +1,6 @@
 fftw-2.1.13/configure.orig Mon Jan 27 16:24:14 2003
-+++ fftw-2.1.13/configure  Mon Jan 27 16:24:25 2003
+diff -ruN --exclude '*~' fftw-2.1.5/configure fftw-2.1.5.patched/configure
+--- fftw-2.1.5/configure   2003-03-24 02:09:56.0 -0500
 fftw-2.1.5.patched/configure   2007-11-12 12:14:33.0 

[cvs] dists/10.4/stable/main/finkinfo/sci phaser.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-serv17561

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

--- NEW FILE: phaser.info ---
Package: phaser
Version: 2.1.1
Revision: 1
Source: http://xanana.ucsc.edu/xtal/%n-%v-cctbx-src.tar.gz
#Source: ftp://ftp.ccp4.ac.uk/ccp4/current/prerelease/%n-%v-cctbx-src.tar.gz
Source-MD5: 28891623d3e0bca66794323113d14bf5
NoSourceDirectory: yes
Depends: ccp4 (= 6.0.2) 
BuildDepends: ccp4 (= 6.0.2)   
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
CompileScript:  
#!/bin/bash -efv
 CCP4=
 export CCP4=$PWD/ccp4-6.0.2
 cd $CCP4/src/phaser
 pwd
 export CCP4_BIN=$CCP4/bin
 export CCP4_LIB=$CCP4/lib
 binary_inst=no
 bindir=${bindir:-$CCP4_BIN}
 libdir=${libdir:-$CCP4_LIB}
 incdir=${incdir:-$CCP4/include}
 # Get Phaser environment variables, so we know where executable is.
 PHASER_MTYPE=`bin/machine_type`
 PHASER_VERSION=`grep PHASER_VERSION conf/version | awk '{print $3}'`
 ./install --prefix=$CCP4/src/phaser --force-compile --static_libraries  
--component=mmtbx --component=phaser
 echo  
 echo  Building static phaser executable
 echo  

InstallScript: 
#!/bin/bash -efv
 mkdir -p %i/bin
 cp ccp4-6.0.2/src/%n/%n-%v/build/mac-osx/exe/phaser  %i/bin

Description: CCP4 automated molecular replacement program
DescDetail: 
Updated version of phaser for ccp4. This installs just the executable
to replace the older version in ccp4 (which does not compile on 10.5).
If you use this software please cite:
Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, 
P.D. Adams, M.D. Winn, L.C. Storoni  R.J. Read
J. Appl. Cryst. (2007). 40, 658-674

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


-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
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