gopenmol stable port information

Package: gopenmol
Version: 3.00
Revision: 1007

# reported incompatible with tcltk8.5, which is what x86_64 has
Architecture: powerpc, i386

GCC: 4.0
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

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 private lib/ instead of private bin/

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 variables (many of which are not
needed for fink's installation and/or are not appropriate for OS X)
and calls the actual "gopenmol" program, so put the key variable in a
profile.d and patch install.mk to omit the wrapper. Symlink "gopenmol"
from %p/bin.

Data files get installed in %p/share but program looks in %p/lib
(==$GOM_ROOT), so symlink them to the GOM_ROOT location.

Utility programs are in %p/lib/gOpenMol-%v/bin so you have to either
add that to your 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 (misformatted symbol that doesn't
exist anyway),
https://postit.csc.fi/sympa/arc/gopenmol/2007-01/msg00002.html
Hack gomapi.exp to remove bogus symbol.

Library interface is not guaranteed to be stable (compatibility 0.0.0
and placed in %v-specific path), so no hope for true Shlibs policy.
Could off-load libs/headers into into %N%v-{shlibs,dev} if others need
a stable way to link it.
<<
DescPackaging: <<
Starting in gopenmol-3.00-1, headers are in %p/lib/gOpenMol-%v/include
not %p/include, and %N-dev is re-absorbed into %N.
<<
DescUsage: <<
The main program is called "gopenmol" and is in the default fink
command PATH. Utility programs are in %p/lib/gOpenMol-%v/bin so you
have to either add that to your PATH or call the programs using the
full pathname.

May not run correctly over remote X11
<<
Homepage: http://www.csc.fi/gopenmol/
License: Restrictive
Maintainer: Daniel Macks

BuildDepends: tcltk-dev (>= 8.4.13-1), tclxml-dev, tclexpat-dev, freeglut, libjpeg8, python27, gcc46, x11-dev, fink (>= 0.28-1), fink-package-precedence
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, libjpeg8-shlibs, python27-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
PatchFile: %n.patch
PatchFile-MD5: 879e641de06379067608fffb1009f293
PatchScript: <<
%{default_script}
perl -pi -e 's///' `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
<<
ConfigureParams: --with-x --enable-shared --disable-deps --disable-static --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --enable-dependency-tracking
CompileScript: <<
#!/bin/sh -ev
cd src
F77=gfortran FFLAGS=-O3 GL_LIBS='-lGL /System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib -Wl,/System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib' TCLSH=%p/bin/tclsh PYTHON=%p/bin/python2.7 ./configure %c
# perl -pi -e 's/.*def.*\s(ENABLE_EXTENSIONS).*/#define \1/' config.h
make all
fink-package-precedence --depfile-ext='\.d' .
<<
InstallScript: <<
cd src; make prefix=%i install

mkdir -p -m 0755 %i/bin
ln -s %p/lib/gOpenMol-%v/bin/gopenmol %i/bin

mkdir -p -m 0755 %i/share/doc/%n
ln -s %p/share/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

mv %i/include %i/lib/gOpenMol-%v

ln -s %p/share/gOpenMol-%v/{data,demo,help} %i/lib/gOpenMol-%v

rm -r %i/lib/gOpenMol-%v/include
<<
Shlibs: <<
!%p/lib/gOpenMol-3.00/lib/libgopenmol.dylib
!%p/lib/gOpenMol-3.00/plugins/libball.dylib
!%p/lib/gOpenMol-3.00/plugins/libfchk.dylib
!%p/lib/gOpenMol-3.00/plugins/libfilters.dylib
!%p/lib/gOpenMol-3.00/plugins/libsurfarea.dylib
!%p/lib/gOpenMol-3.00/plugins/libsymmetry.dylib
!%p/lib/gOpenMol-3.00/plugins/libvrml.dylib
<<
RuntimeVars: <<
GOM_ROOT: %p/lib/gOpenMol-%v
<<

gopenmol stable port .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 2007-02-01 01:29:25.000000000 -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 2007-02-01 01:30:10.000000000 -0500
@@ -18,7 +18,7 @@
gomdataroot = $(datadir)/$(gomsubdir)
gombindir = $(gomroot)/bin
gomincdir = $(includedir)/$(gomsubdir)
-gomlibdir = $(gomroot)/bin
+gomlibdir = $(gomroot)/lib
# Tcl/Tk entries.
TCL_LIBRARY = @TCL_LIBRARY@
TK_LIBRARY = @TK_LIBRARY@
@@ -64,7 +64,7 @@
CCTAGS = @CCTAGS@
CCDEPMODE = @CCDEPMODE@
CCDEPCOMP = @CCDEPCOMP@
-GOM_CPPFLAGS = @CPPFLAGS@ -I$(incdir) -Iinclude -I.
+GOM_CPPFLAGS = -I$(incdir) -Iinclude -I. @CPPFLAGS@
GOM_CFLAGS = @ALL_CFLAGS@
GOM_FFLAGS = @ALL_FFLAGS@
GOM_LDFLAGS = @ALL_LDFLAGS@
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 2007-02-01 01:29:25.000000000 -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 2007-02-01 01:29:25.000000000 -0500
@@ -22,7 +22,7 @@
build compile clean clean-libs clean-objs: FORCE
-@for 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 2007-02-01 01:30:34.000000000 -0500
@@ -11,7 +11,7 @@
gombindir = ${gomroot}/bin
gomincdir = ${gomsrcdir}/include/gomlib
#INS gomincdir = ${includedir}/${gomsubdir}
-gomlibdir = ${gomroot}/bin
+gomlibdir = ${gomroot}/lib
gomsrcdir = @abs_top_srcdir@
gombltdir = @abs_top_builddir@
#INS gomsrcdir = ${gomroot}/src
@@ -59,7 +59,7 @@
COMMON_LTLDFLAGS = @COMMON_LTLDFLAGS@
# Values used by gOpenMol.
# Not quite... Don't show private gOpenMol headers to plugins.
-GOM_CPPFLAGS = @CPPFLAGS@ -I${gomincdir} -I${gombltdir}/include/gomlib
+GOM_CPPFLAGS = -I${gomincdir} -I${gombltdir}/include/gomlib @CPPFLAGS@
GOM_CFLAGS = @CFLAGS@
GOM_FFLAGS = @FFLAGS@
GOM_LDFLAGS = @LDFLAGS@
diff -Nurd -x'*~' gOpenMol-3.00.orig/src/unix/make/gomapi.mk gOpenMol-3.00/src/unix/make/gomapi.mk
--- gOpenMol-3.00.orig/src/unix/make/gomapi.mk 2005-08-29 10:05:30.000000000 -0400
+++ gOpenMol-3.00/src/unix/make/gomapi.mk 2007-02-01 01:29:25.000000000 -0500
@@ -47,6 +47,7 @@
# (see case statement above).
graphics/gomapi.exp: include/gomext/*.h
{ cat include/gomext/*.h | sed 's/^.*gom_/gom_/'; echo gom_main; } >$@
+ perl -ni.bak -e 'print unless /dummy_func/' $@

clean: clean-gomapi clean-stamps FORCE

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 2007-02-01 02:24:45.000000000 -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='"'"'$(gomroot)'"'%" \
+ -e 's%__fink_d__%%' \
-e 's%@PATH_SEPARATOR@%$(PATH_SEPARATOR)%' \
-e "s%@SHLIBPATHVAR@%$${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"; \
@@ -85,7 +86,6 @@

install-local-local: install-local-generated \
install-local-environment \
- install-local-rungopenmol \
install-local-data \
FORCE ;

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 2007-02-01 01:29:25.000000000 -0500
@@ -47,8 +47,7 @@
xmol2bamber$(EXEEXT) \
xplor2charmm$(EXEEXT) \
gridasc2plt$(EXEEXT) \
- gridbin2plt$(EXEEXT) \
- icon8$(EXEEXT)
+ gridbin2plt$(EXEEXT)

BINARIES_JAR = xvibs.jar

gopenmol _unstable_ port .patch