Update of /cvsroot/fink/experimental/dmacks/finkinfo
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv20685

Added Files:
        gopenmol.info gopenmol.patch 
Log Message:
trying to get new version built
disable shared due to (possibly hackable) problem during nmedit, but
now missing makefile targets for plugins


--- NEW FILE: gopenmol.info ---
Package: gopenmol
Version: 3.00
Revision: 1
GCC: 3.3
Description: Molecular visualization and analysis program
DescDetail: <<
With gOpenMol small molecules, and to lesser extent protein
structures, as well as the chemical properties, total electron
densities and molecule orbitals of small molecules can be visualized
and analyzed. Data from a variety of computational chemistry programs
such as TurboMole, Gaussian, Gamess, etc., can be analyzed if the
output files from these programs have been converted into the
.plt-file format understood by gOpenMol. Moreover, dynamics done with,
e.g., InsightII can be visualized and a short mpeg animation of the
dynamics files generated.

Copyright info (from the website):
  The program is distributed free of charge for academic installations
  and academic use.
  If you have used gOpenMol for your publication, please use the
  following references:
    * Laaksonen, L. (1992) A graphics program for the analysis and
      display of molecular dynamics trajectories. J. Mol. Graph. 10:
      33-34.
    * Bergman, D.L., Laaksonen, L., and Laaksonen, A. (1997)
      Visualization of solvation structures in liquid mixtures.
      J. Mol. Graph. Model. 15: 301-306.
<<
DescPort: <<
Require modern tcltk to avoid bug in line-endings emitted from older tclsh

Standard darwin malloc.h fix

OTOH, GOM_PARSER_RETRIEVE_SELECTIONLIST is only a mild warning? But it
does cause a cpp-precomp segfault (not necessarily cause/effect). Apple
engineers say just -no-cpp-precomp and get on with our life; so be it.

#I don't understand why when set_show in config.mk causes ": command
#not found" when show=':', but making it always 'echo' seems to allow
#the install.mk install-data-dir target to proceed.

The build/install process doesn't understand how to install in a temp
packaging location for later installation somewhere else, so need to
fix the pathnames in some runtime scripts.

Package installs lots of docs in its private hierarchies, so move to
or make links from the standard share/doc/%n location.

Patch install.mk to not install libs that we already have from other
Fink packages. Set our Depends for each of those packages >= version
that comes in Source tarball.

#Put libgopenmol.* in lib instead of private bin. Still in its private
#space since I don't know version info (so leave -avoid-version) so
#cannot do -shlibs.

#Patch plugins/config.mk.ac to link plugins as shared libraries
#(.dylib) instead of bundles (.so), obeying dyld error message given
#when using default options. Patch data/{gopenmol_guirc,gopenmolrc}.tcl
#to use the platform-correct lib extension.

Some plugins fail to load because "couldn't find procedure Thing_Init"
(during a tcl "load" call for libthing.dylib). These functions all
exist in the associated source files and it's not consistent which
ones fail. It seems to depend on order loaded, so there may be
something weird going on with memory or symbol namespaces.

#I can't find a make target to use the src/plugins/*/*.tcl instead of
#(or to first copy these into) data/autotcl/plugins/*.tcl so will
#manually copy these during PatchScript (so do all patching to src/ not
#data/).

Disabled icon8 because there are too many compiling problems
(non-portable code and old coding standards).

No default $TMP or $TMPDIR, so set GOM_TEMP in environment.txt

The rungOpenMol script just sets vars and calls the actual gopenmol,
so put the vars in a profile.d and patch install.mk to not bother with
the wrapper. Move the actual binary into %p/bin.

Utility programs are in %p/lib/gOpenMol-%v/bin so you have to either
add that to yout PATH or call the programs using the full pathname.
This is so we don't conflict with (for example) imagemagick's convert
program. This will eventually be handled automatically via a splitoff
for placing these programs in PATH and/or using alternatives.

Make sure local -I flags go ahead of global ones.
See https://postit.csc.fi/sympa/arc/gopenmol/2007-01/msg00000.html

Implements a non-standard dependency-tracking configure flag. How odd.

Make sure plugins build aborts if any plugins/* build fails.
See https://postit.csc.fi/sympa/arc/gopenmol/2007-01/msg00001.html

Fix prototypes in p_showc.c
See https://postit.csc.fi/sympa/arc/gopenmol/2006-12/msg00002.html
    https://postit.csc.fi/sympa/arc/gopenmol/2006-12/msg00003.html

nmedit failure if building shared, so disable shared for now,
  https://postit.csc.fi/sympa/arc/gopenmol/2007-01/msg00002.html
which disables plugins. #define ENABLE_EXTENSIONS so that API macros
are defined,
  https://postit.csc.fi/sympa/arc/gopenmol/2007-01/msg00012.html
and can compile.
<<
DescPackaging: <<
Headers/libs/etc are all %v-dependent and in versioned path. Would
have to recompile modules for new %v and place in new %v location? So
scrapping %N-dev for now.
<<
DescUsage: <<
  May not run correctly over remote X11
<<
Homepage: http://www.csc.fi/gopenmol/
License: Restrictive
Maintainer: Daniel Macks <[EMAIL PROTECTED]>

BuildDepends: tcltk-dev (>= 8.4.13-1), tclxml-dev, tclexpat-dev, freeglut, 
libjpeg, python24, g77, x11-dev
Depends: tcltk (>= 8.4.13-1), tcltk-shlibs (>= 8.4.13-1), tcllib (>= 1.4-1), 
bwidget (>= 1.6.0), tclxml (>= 2.6-1), tclexpat (>= 2.6-1), freeglut-shlibs, 
libjpeg-shlibs, python24-shlibs, x11

Conflicts: %N-dev (<< %v-%r)
Replaces: %N-dev (<< %v-%r)

Source: http://www.csc.fi/english/pages/g0penMol/Downloads/%n-%v-linux.tar.gz
Source-MD5: 4e12ee6680c093a3bf056dde1d28fea2
SourceDirectory: gOpenMol-%v
Patch: %n.patch
PatchScript: <<
  perl -pi -e 's/<malloc.h>/<stdlib.h>/' `find . -name \*.\[hc\]`
  perl -pi -e 's#__fink_d__#%d#g;s#__fink_p__#%p#g' src/config.mk.ac 
src/unix/make/install.mk
# cp -f 
src/plugins/{ball/ball.tcl,fchk203/fchk.tcl,filters/filters.tcl,sararea/surfarea.tcl,sym602/symmetry.tcl,vrml/vrml.tcl}
  data/autotcl/plugins
<<
SetCPPFLAGS: -no-cpp-precomp
ConfigureParams: --with-x --disable-shared --disable-deps
CompileScript: <<
#!/bin/sh -ev
  cd src
  TCLSH=%p/bin/tclsh PYTHON=%p/bin/python2.4 ./configure %c
  perl -pi -e 's/.*def.*\s(ENABLE_EXTENSIONS).*/#define \1/' config.h
  make all
<<
InstallScript: <<
  cd src; make prefix=%i install
#  mkdir -p -m 0755 %i/share/doc/%n
#  ln -s ../../gOpenMol-%v/help %i/share/doc/%n/html
#  mv %i/share/gOpenMol-%v/docs/* %i/share/doc/%n
#  rmdir %i/share/gOpenMol-%v/docs
#  mv %i/share/gOpenMol-%v/utility %i/share/doc/%n
#  rm %i/share/gOpenMol-%v/README-GLUT-win32.txt
#  mv %i/share/gOpenMol-%v/{COPYRIGHT,README.txt} %i/share/doc/%n
<<
RuntimeVars: <<
  GOM_ROOT: %p/lib/gOpenMol-%v
<<

--- NEW FILE: gopenmol.patch ---
diff -Nurd -x'*~' gOpenMol-3.00.orig/environment.txt 
gOpenMol-3.00/environment.txt
--- gOpenMol-3.00.orig/environment.txt  2005-08-29 10:04:23.000000000 -0400
+++ gOpenMol-3.00/environment.txt       2007-01-26 03:48:18.000000000 -0500
@@ -16,4 +16,4 @@
 # GOM_HOME    ""
 ### On Windows, the default value is system temp directory.
 ### On UNIX, the default is $TMPDIR, $TMP or /tmp.
-# GOM_TEMP    temp
+GOM_TEMP    /tmp
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/config.mk.ac 
gOpenMol-3.00/src/config.mk.ac
--- gOpenMol-3.00.orig/src/config.mk.ac 2004-09-23 17:24:29.000000000 -0400
+++ gOpenMol-3.00/src/config.mk.ac      2007-01-26 03:48:18.000000000 -0500
@@ -64,7 +64,7 @@
 CCTAGS           = @CCTAGS@
 CCDEPMODE        = @CCDEPMODE@
 CCDEPCOMP        = @CCDEPCOMP@
-GOM_CPPFLAGS     = @CPPFLAGS@ -I$(incdir) -Iinclude -I.
+GOM_CPPFLAGS     = -I$(incdir) -Iinclude -I. @CPPFLAGS@
 GOM_CFLAGS       = @ALL_CFLAGS@
 GOM_FFLAGS       = @ALL_FFLAGS@
 GOM_LDFLAGS      = @ALL_LDFLAGS@
@@ -100,7 +100,7 @@
 LINK             = $(LIBTOOL) --mode=link $(CC) $(GOM_CFLAGS) -o
 LINK_SO          = $(LINK)
 LINK_A           = $(LINK)
-LINKFLAGS        = $(GOM_LDFLAGS) $(GOM_LIBS) $(GOM_LTLDFLAGS) -rpath 
$(gomlibdir)
+LINKFLAGS        = $(GOM_LDFLAGS) $(GOM_LIBS) $(GOM_LTLDFLAGS) -rpath 
__fink_p__/lib/$(gomlibdir)/lib
 LINKFLAGS_SO     = $(LINKFLAGS) -avoid-version
 LINKFLAGS_A      =
 LTPREINSTALL     = :
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/parser/p_showc.c 
gOpenMol-3.00/src/parser/p_showc.c
--- gOpenMol-3.00.orig/src/parser/p_showc.c     2005-08-29 10:05:21.000000000 
-0400
+++ gOpenMol-3.00/src/parser/p_showc.c  2007-01-26 03:48:18.000000000 -0500
@@ -42,21 +42,21 @@
 
 #define ALIAS GOM_PARSER_CMD_ALIAS
 
-int gomp_ParserReturnFloatValueFromFunc(GOM_PARSER_ARGLIST,ptrdiff_t Offset)
+int gomp_ParserReturnFloatValueFromFunc(GOM_PARSER_ARGLIST,intptr_t Offset)
 {
     FloatFunc *floatf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_RETURN_DOUBLE(floatf->Func());
     GOM_PARSER_SUCCEEDED;
 }
 
-int gomp_ParserReturnIntValueFromFunc(GOM_PARSER_ARGLIST,ptrdiff_t Offset)
+int gomp_ParserReturnIntValueFromFunc(GOM_PARSER_ARGLIST,intptr_t Offset)
 {
     IntFunc *intf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_RETURN_INT(intf->Func());
     GOM_PARSER_SUCCEEDED;
 }
 
-int gomp_ParserReturnBooleanValueFromFunc(GOM_PARSER_ARGLIST,ptrdiff_t Offset)
+int gomp_ParserReturnBooleanValueFromFunc(GOM_PARSER_ARGLIST,intptr_t Offset)
 {
     IntFunc *intf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_RETURN_BOOLEAN(intf->Func());
@@ -64,7 +64,7 @@
 }
 
 int gomp_ParserReturnBooleanEnumValueFromFunc(GOM_PARSER_ARGLIST,
-                                              ptrdiff_t Offset)
+                                              intptr_t Offset)
 {
     BooleanEnumFunc *booleanf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_RETURN_STRING(
@@ -74,14 +74,14 @@
     GOM_PARSER_SUCCEEDED;
 }
 
-int gomp_ParserReturnStringValueFromFunc(GOM_PARSER_ARGLIST,ptrdiff_t Offset)
+int gomp_ParserReturnStringValueFromFunc(GOM_PARSER_ARGLIST,intptr_t Offset)
 {
     StringFunc *stringf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_RETURN_STRING(stringf->Func());
     GOM_PARSER_SUCCEEDED;
 }
 
-int gomp_ParserVerifyFuncResult(GOM_PARSER_ARGLIST,ptrdiff_t Offset)
+int gomp_ParserVerifyFuncResult(GOM_PARSER_ARGLIST,intptr_t Offset)
 {
     IntFunc *intf = GOM_PARSER_GET_POINTER_VALUE(Offset);
     GOM_PARSER_VERIFY( intf->Func() == 0 );
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/plugins/Makefile 
gOpenMol-3.00/src/plugins/Makefile
--- gOpenMol-3.00.orig/src/plugins/Makefile     2005-08-29 10:05:21.000000000 
-0400
+++ gOpenMol-3.00/src/plugins/Makefile  2007-01-26 03:48:18.000000000 -0500
@@ -22,7 +22,7 @@
 build compile clean clean-libs clean-objs: FORCE
        [EMAIL PROTECTED] dir in *; do \
            if test -f "$$dir/Makefile"; then \
-               ( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) ;\
+               ( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) || exit 1;\
            fi ;\
        done
 
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/plugins/config.mk.ac 
gOpenMol-3.00/src/plugins/config.mk.ac
--- gOpenMol-3.00.orig/src/plugins/config.mk.ac 2004-09-23 17:24:54.000000000 
-0400
+++ gOpenMol-3.00/src/plugins/config.mk.ac      2007-01-26 03:48:18.000000000 
-0500
@@ -59,7 +59,7 @@
 COMMON_LTLDFLAGS = @COMMON_LTLDFLAGS@
 # Values used by gOpenMol.
 # Not quite... Don't show private gOpenMol headers to plugins.
-GOM_CPPFLAGS     = @CPPFLAGS@ -I${gomincdir} -I${gombltdir}/include/gomlib
+GOM_CPPFLAGS     = -I${gomincdir} -I${gombltdir}/include/gomlib @CPPFLAGS@
 GOM_CFLAGS       = @CFLAGS@
 GOM_FFLAGS       = @FFLAGS@
 GOM_LDFLAGS      = @LDFLAGS@
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/unix/make/install.mk 
gOpenMol-3.00/src/unix/make/install.mk
--- gOpenMol-3.00.orig/src/unix/make/install.mk 2005-08-29 10:05:31.000000000 
-0400
+++ gOpenMol-3.00/src/unix/make/install.mk      2007-01-26 03:48:18.000000000 
-0500
@@ -26,6 +26,7 @@
        -e 's%^TCL_LIBRARY=.*%TCL_LIBRARY='"'"'$(TCL_LIBRARY)'"'%" \
        -e 's%^TK_LIBRARY=.*%TK_LIBRARY='"'"'$(TK_LIBRARY)'"'%" \
        -e 's%^GOM_ROOT=.*%GOM_ROOT='"'"'$(gomroot)'"'%" \
+       -e 's%__fink_d__%%" \
        -e '[EMAIL PROTECTED]@%$(PATH_SEPARATOR)%' \
        -e "[EMAIL PROTECTED]@%$${shlibpath_var}%g" )
 
@@ -36,7 +37,7 @@
 mkinstalldirs-local: FORCE
        $(MKDIR_P) '$(gomroot)' || test -d '$(gomroot)'
        @$(set_show); set -e; \
-       for dir in bin src/plugins src/unix; do \
+       for dir in bin lib src/plugins src/unix; do \
            dir='$(gomroot)'/$$dir; \
            $$show $(MKDIR_P) "$$dir"; \
            $(MKDIR_P) "$$dir" || test -d "$$dir"; \
@@ -62,7 +63,7 @@
        for file in gom-dynamic gom-shared gom-noshared gom-static; do \
            if test -f graphics/$$file; then \
                exec $(LTINSTALL) \
-                   graphics/$$file '$(gomroot)/bin/gopenmol'; \
+                   graphics/$$file '$(bindir)/gopenmol'; \
            fi; \
        done; exit 1
 
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/unix/make/utility.mk.ac 
gOpenMol-3.00/src/unix/make/utility.mk.ac
--- gOpenMol-3.00.orig/src/unix/make/utility.mk.ac      2005-08-29 
10:05:31.000000000 -0400
+++ gOpenMol-3.00/src/unix/make/utility.mk.ac   2007-01-26 03:48:18.000000000 
-0500
@@ -47,8 +47,7 @@
                xmol2bamber$(EXEEXT) \
                xplor2charmm$(EXEEXT) \
                gridasc2plt$(EXEEXT) \
-               gridbin2plt$(EXEEXT) \
-               icon8$(EXEEXT)
+               gridbin2plt$(EXEEXT)
 
 BINARIES_JAR = xvibs.jar
 


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