diff -Nurd -x'*~' gOpenMol-2.30.orig/data/gopenmol_guirc.tcl gOpenMol-2.30/data/gopenmol_guirc.tcl --- gOpenMol-2.30.orig/data/gopenmol_guirc.tcl 2003-09-19 09:15:17.000000000 -0400 +++ gOpenMol-2.30/data/gopenmol_guirc.tcl 2003-10-15 19:08:53.000000000 -0400 @@ -677,7 +677,7 @@ pack .frame.tools -side left set m .frame.tools.menu menu .frame.tools.menu -$m add cascade -label "DLL/SO plugins" -menu $m.plugins +$m add cascade -label "Plugins" -menu $m.plugins $m add command -label "AutoDock..." -command {lulAutoDock::MainControl} # Plugins menu @@ -15989,11 +15989,8 @@ # a plugin with the same name exist. # Plugin name may start with "lib". # -if {$tcl_platform(platform) == "windows"} { - set files "[glob -nocomplain -tail -directory $gomEnv(GOM_PLUGINS) *.dll]" -} else { - set files "[glob -nocomplain -tail -directory $gomEnv(GOM_PLUGINS) *.so]" -} +set libext "[info sharedlibextension]" +set files "[glob -nocomplain -tail -directory $gomEnv(GOM_PLUGINS) *${libext}]" if {$files == ""} return diff -Nurd -x'*~' gOpenMol-2.30.orig/data/gopenmolrc.tcl gOpenMol-2.30/data/gopenmolrc.tcl --- gOpenMol-2.30.orig/data/gopenmolrc.tcl 2003-09-22 08:47:59.000000000 -0400 +++ gOpenMol-2.30/data/gopenmolrc.tcl 2003-10-15 19:08:53.000000000 -0400 @@ -941,12 +941,15 @@ global tcl_platform global gomEnv + set libext "[info sharedlibextension]" if {$tcl_platform(platform) == "windows"} { - load [file join $gomEnv(GOM_PLUGINS) ${Name}.dll] - } elseif {[file exists [file join $gomEnv(GOM_PLUGINS) lib${Name}.so]]} { - load [file join $gomEnv(GOM_PLUGINS) lib${Name}.so] + load [file join $gomEnv(GOM_PLUGINS) ${Name}${libext}] } else { - load [file join $gomEnv(GOM_PLUGINS) ${Name}.so] + if {[file exists [file join $gomEnv(GOM_PLUGINS) lib${Name}${libext}]]} { + load [file join $gomEnv(GOM_PLUGINS) lib${Name}${libext}] + } else { + load [file join $gomEnv(GOM_PLUGINS) ${Name}${libext}] + } } } diff -Nurd -x'*~' gOpenMol-2.30.orig/src/config.mk.ac gOpenMol-2.30/src/config.mk.ac --- gOpenMol-2.30.orig/src/config.mk.ac 2003-09-17 05:58:43.000000000 -0400 +++ gOpenMol-2.30/src/config.mk.ac 2003-10-15 19:08:53.000000000 -0400 @@ -70,7 +70,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@ # Tools. set_show = set x $(MFLAGS)$${MAKEFLAGS}; \ - case $$2 in *s*) show=':' ;; *) show='echo' ;; esac + show='echo' SHELL = @SHELL@ LN_S = @LN_S@ @SET_MAKE@ @@ -87,7 +87,7 @@ 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) $(GOM_LTLDFLAGS) -rpath __fink_p__/lib/$(gomsubdir)/lib LINKFLAGS_SO = $(LINKFLAGS) -avoid-version LINKFLAGS_A = LTPREINSTALL = : diff -Nurd -x'*~' gOpenMol-2.30.orig/src/configure gOpenMol-2.30/src/configure --- gOpenMol-2.30.orig/src/configure 2003-09-23 04:49:49.000000000 -0400 +++ gOpenMol-2.30/src/configure 2003-10-15 19:08:53.000000000 -0400 @@ -18449,7 +18449,7 @@ echo $ECHO_N "(cached) $ECHO_C" >&6 else gom4_cv_tclsh_LIBRARY="${TCL_LIBRARY-`\ - echo 'puts [info library]' | $TCLSH`}" + echo 'fconfigure stdout -translation lf; puts [info library]' | $TCLSH`}" fi echo "$as_me:$LINENO: result: $gom4_cv_tclsh_LIBRARY" >&5 echo "${ECHO_T}$gom4_cv_tclsh_LIBRARY" >&6 @@ -18794,7 +18794,7 @@ # }}} # Search for Tcl library. -gom_tcl_version=`echo 'puts [info tclversion]' | $TCLSH` +gom_tcl_version=`echo 'fconfigure stdout -translation lf; puts [info tclversion]' | $TCLSH` # Check for the library. gom4_GOM_CHECK_LIB_found=yes for gom4_GOM_CHECK_LIB_header in tcl.h diff -Nurd -x'*~' gOpenMol-2.30.orig/src/general/trajectory.c gOpenMol-2.30/src/general/trajectory.c --- gOpenMol-2.30.orig/src/general/trajectory.c 2003-09-09 08:49:05.000000000 -0400 +++ gOpenMol-2.30/src/general/trajectory.c 2003-10-15 19:08:53.000000000 -0400 @@ -399,7 +399,7 @@ /*************************************************************************/ IMPLEMENT_GET_MODIFIABLE_POINTER( int,FreeAtomListPointer,(int Set), - FreeAtomList.free_atom_list,) + FreeAtomList.free_atom_list,;) /*************************************************************************/ int gomp_SetFreeAtomListPointer(int Set , int NFreat) /*************************************************************************/ @@ -748,7 +748,7 @@ IMPLEMENT_GET_MODIFIABLE_POINTER( float,VelocityXComponentPointer,(void), TrajectoryInfo.retrieve_velocity_ready ? - TrajectoryInfo.Xvelocities : NULL,) + TrajectoryInfo.Xvelocities : NULL,;) /*************************************************************************/ /* gomp_GetVelocityYComponentPointer, */ /* gomp_GetModifiableVelocityYComponentPointer */ @@ -756,7 +756,7 @@ IMPLEMENT_GET_MODIFIABLE_POINTER( float,VelocityYComponentPointer,(void), TrajectoryInfo.retrieve_velocity_ready ? - TrajectoryInfo.Yvelocities : NULL,) + TrajectoryInfo.Yvelocities : NULL,;) /*************************************************************************/ /* gomp_GetVelocityXComponentPointer, */ /* gomp_GetModifiableVelocityXComponentPointer */ @@ -764,7 +764,7 @@ IMPLEMENT_GET_MODIFIABLE_POINTER( float,VelocityZComponentPointer,(void), TrajectoryInfo.retrieve_velocity_ready ? - TrajectoryInfo.Zvelocities : NULL,) + TrajectoryInfo.Zvelocities : NULL,;) /*************************************************************************/ int gomp_GetForceSpace(int Atoms) /*************************************************************************/ @@ -800,21 +800,21 @@ /*************************************************************************/ IMPLEMENT_GET_MODIFIABLE_POINTER( float,ForceXComponentPointer,(void), - TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Xforces : NULL,) + TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Xforces : NULL,;) /*************************************************************************/ /* gomp_GetForceYComponenPointer, */ /* gomp_GetModifiableForceYComponentPointer */ /*************************************************************************/ IMPLEMENT_GET_MODIFIABLE_POINTER( float,ForceYComponentPointer,(void), - TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Yforces : NULL,) + TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Yforces : NULL,;) /*************************************************************************/ /* gomp_GetForceZComponenPointer, */ /* gomp_GetModifiableForceZComponentPointer */ /*************************************************************************/ IMPLEMENT_GET_MODIFIABLE_POINTER( float,ForceZComponentPointer,(void), - TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Zforces : NULL,) + TrajectoryInfo.retrieve_force_ready ? TrajectoryInfo.Zforces : NULL,;) /*************************************************************************/ int gomp_SetVelocityMinMax(float Vmin , float Vmax) /*************************************************************************/ diff -Nurd -x'*~' gOpenMol-2.30.orig/src/include/memalloc.h gOpenMol-2.30/src/include/memalloc.h --- gOpenMol-2.30.orig/src/include/memalloc.h 2003-07-29 05:22:51.000000000 -0400 +++ gOpenMol-2.30/src/include/memalloc.h 2003-10-15 19:08:53.000000000 -0400 @@ -16,6 +16,9 @@ #define INC_GOPENMOL_MEMALLOC #include +#if HAVE_STDLIB_H +#include +#endif extern float *gomp_Fvector(int); extern double *gomp_Dvector(int); diff -Nurd -x'*~' gOpenMol-2.30.orig/src/parser/p_s_atomc.c gOpenMol-2.30/src/parser/p_s_atomc.c --- gOpenMol-2.30.orig/src/parser/p_s_atomc.c 2003-09-22 08:51:01.000000000 -0400 +++ gOpenMol-2.30/src/parser/p_s_atomc.c 2003-10-15 19:08:53.000000000 -0400 @@ -161,9 +161,9 @@ GOM_PARSER_FINAL_FLOAT_CMD("cross",&parseShowAtomCross) static const FloatFunc parseShowAtomCross = { gomp_GetCrossLen }; -/* show atom indentify */ +/* show atom identify */ #define SHOW_ATOM_IDENTIFY \ -GOM_PARSER_FINAL_BOOLEAN_CMD("indentify",&parseShowAtomIdentify) +GOM_PARSER_FINAL_BOOLEAN_CMD("identify",&parseShowAtomIdentify) static const IntFunc parseShowAtomIdentify = { gomp_GetIdentifyAtomActive }; /* show atom selection */ diff -Nurd -x'*~' gOpenMol-2.30.orig/src/plugins/config.mk.ac gOpenMol-2.30/src/plugins/config.mk.ac --- gOpenMol-2.30.orig/src/plugins/config.mk.ac 2003-09-12 05:25:41.000000000 -0400 +++ gOpenMol-2.30/src/plugins/config.mk.ac 2003-10-15 19:08:53.000000000 -0400 @@ -88,7 +88,7 @@ RM_R = ${RM} -r GOM_REMOVE = ${LIBTOOL} --mode=clean ${RM} GOM_COMPILEFLAGS = -GOM_LINKFLAGS = -avoid-version -module -rpath ${gompluginsdir} +GOM_LINKFLAGS = -avoid-version -rpath ${gompluginsdir} # Install library using following commands: # ${GOM_PREINSTALL} ${gompluginsdir} # ${GOM_INSTALL} libexample.${ARSUFFIX} ${gompluginsdir} diff -Nurd -x'*~' gOpenMol-2.30.orig/src/plugins/filters/filters.tcl gOpenMol-2.30/src/plugins/filters/filters.tcl --- gOpenMol-2.30.orig/src/plugins/filters/filters.tcl 2003-09-11 07:11:27.000000000 -0400 +++ gOpenMol-2.30/src/plugins/filters/filters.tcl 2003-10-16 22:34:07.000000000 -0400 @@ -85,7 +85,7 @@ ::lulLoadPlugin "filters" set ::lulFileUtility::coordTypes(chem3d) {{1 0} Chem3D {Chem 3D files} {*}} set ::lulFileUtility::coordTypes(spartan) {{1 0} Spartan {Spartan files} {*}} - unset ::gomPluginsMenuItems(symmetry) + unset ::gomPluginsMenuItems(filters) ::lulMessageDialog {Chem3D/Spartan coordinate input filter is enabled!} ::lulUpdatePluginsMenu } diff -Nurd -x'*~' gOpenMol-2.30.orig/src/plugins/vrml/vrml.tcl gOpenMol-2.30/src/plugins/vrml/vrml.tcl --- gOpenMol-2.30.orig/src/plugins/vrml/vrml.tcl 2003-09-11 07:11:53.000000000 -0400 +++ gOpenMol-2.30/src/plugins/vrml/vrml.tcl 2003-10-19 21:31:56.000000000 -0400 @@ -138,7 +138,7 @@ } if {[show graphics]} { - set ::gomPluginsMenuItems(vrml) "{VRML...} command [namespace current]::makevrml" + set ::gomPluginsMenuItems(vrml) "{VRML...} [namespace current]::makevrml" ::lulUpdatePluginsMenu } diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_rforce.c gOpenMol-2.30/src/readwrite/rw_rforce.c --- gOpenMol-2.30.orig/src/readwrite/rw_rforce.c 2003-07-29 05:23:51.000000000 -0400 +++ gOpenMol-2.30/src/readwrite/rw_rforce.c 2003-10-15 19:08:53.000000000 -0400 @@ -412,7 +412,7 @@ /* gomp_GetVectorListArray */ /*************************************************************************/ IMPLEMENT_GET_MODIFIABLE_POINTER(int,VectorListArray,(void), - atm_vector.sel_list,) + atm_vector.sel_list,;) /*************************************************************************/ int gomp_GetVectorStructureIndex() /*************************************************************************/ diff -Nurd -x'*~' gOpenMol-2.30.orig/src/unix/data/environment.txt gOpenMol-2.30/src/unix/data/environment.txt --- gOpenMol-2.30.orig/src/unix/data/environment.txt 2003-08-05 08:33:27.000000000 -0400 +++ gOpenMol-2.30/src/unix/data/environment.txt 2003-10-15 19:08:53.000000000 -0400 @@ -10,4 +10,4 @@ GOM_PLUGINS {@gomroot@/plugins} GOM_HELP {@gomdataroot@/help} GOM_DEMO {@gomdataroot@/demo} -#GOM_TEMP Default is $TMPDIR or $TMP. +GOM_TEMP /tmp diff -Nurd -x'*~' gOpenMol-2.30.orig/src/unix/make/install.mk gOpenMol-2.30/src/unix/make/install.mk --- gOpenMol-2.30.orig/src/unix/make/install.mk 2003-09-17 05:58:52.000000000 -0400 +++ gOpenMol-2.30/src/unix/make/install.mk 2003-10-15 19:08:53.000000000 -0400 @@ -25,7 +25,7 @@ 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 "$$dir"; \ done @@ -54,7 +54,8 @@ -e 's%@PATH_SEPARATOR@%$(PATH_SEPARATOR)%' \ -e 's%@SHELL@%$(SHELL)%' \ -e 's%@TCL_LIBRARY@%$(TCL_LIBRARY)%' \ - -e 's%@TK_LIBRARY@%$(TK_LIBRARY)%' ) + -e 's%@TK_LIBRARY@%$(TK_LIBRARY)%' \ + -e 's%__fink_d__%%' ) install-local-data: install-local-bin-data \ install-local-include-data \ @@ -64,7 +65,6 @@ # Install to system specific directories: # environment.txt patch # install.tcl patch -# bin/rungOpenMol patch install-local-bin-data: mkinstalldirs-local FORCE @$(set_show); $$show 'Installing $(gomroot)/environment.txt' @$(INSTALL_DATA) \ @@ -72,15 +72,6 @@ '$(gomroot)/environment.txt' @$(patch) <'$(top_srcdir)/unix/data/environment.txt' \ >'$(gomroot)/environment.txt' - @$(set_show); $$show 'Installing $(gomroot)/rungOpenMol' - @$(INSTALL_SCRIPT) \ - '$(top_srcdir)/unix/data/rungOpenMol' \ - '$(gomroot)/bin/rungOpenMol' - @$(patch) <'$(top_srcdir)/unix/data/rungOpenMol' \ - >'$(gomroot)/bin/rungOpenMol' - $(MKDIR_P) '$(bindir)' || test -d '$(bindir)' - $(RM) '$(bindir)/rungOpenMol' - cd '$(bindir)' && $(LN_S) '$(gomroot)/bin/rungOpenMol' . install-install: FORCE $(MKDIR_P) '$(gomroot)' || test -d '$(gomroot)' @@ -101,11 +92,8 @@ # Install to system specific directories: # lib copy from srcdir # Don't install tclX.X and tkX.X directories. +# We get all other libs from other Fink packages install-local-lib-data: mkinstalldirs-local FORCE - @$(MAKE) $(MFLAGS) install-data-dir \ - srcdir='$(rootdir)/lib' \ - dstdir='$(gomroot)/lib' \ - skip='./tcl[0-9]*|./tk[0-9]*' # Install to system specific directories: # src/plugins/nodeps.d copy from srcdir @@ -138,16 +126,17 @@ # Install best of gom-{dynamic,shared,noshared,static} to bin/. # Install libgopenmmol.la if it exists. install-bin: mkinstalldirs-local FORCE - $(LTPREINSTALL) '$(gomroot)/bin' + $(MKDIR_P) '$(bindir)' || test -d '$(bindir)' + $(LTPREINSTALL) '$(bindir)' for file in gom-dynamic gom-shared gom-noshared gom-static; do \ if test -f graphics/$$file; then \ exec $(LTINSTALL) \ - graphics/$$file '$(gomroot)/bin/gopenmol'; \ + graphics/$$file '$(bindir)/gopenmol'; \ fi; \ done; exit 1 test ! -f graphics/libgopenmol.la || \ - $(LTINSTALL) graphics/libgopenmol.la '$(gomroot)/bin' - $(LTPOSTINSTALL) '$(gomroot)/bin' + $(LTINSTALL) graphics/libgopenmol.la '$(gomroot)/lib' + $(LTPOSTINSTALL) '$(gomroot)/lib' # Install plugins. install-plugins: FORCE diff -Nurd -x'*~' gOpenMol-2.30.orig/src/unix/make/utility.mk.ac gOpenMol-2.30/src/unix/make/utility.mk.ac --- gOpenMol-2.30.orig/src/unix/make/utility.mk.ac 2003-09-17 05:58:53.000000000 -0400 +++ gOpenMol-2.30/src/unix/make/utility.mk.ac 2003-10-15 19:08:53.000000000 -0400 @@ -20,7 +20,7 @@ OBJECTS_C = fmalloc.o -BINARIES = $(BINARIES_C) $(BINARIES_CXX) $(BINARIES_F) $(BINARIES_JAR) +BINARIES = $(BINARIES_C) $(BINARIES_CXX) $(BINARIES_F) $(BINARIES_JAR) $(BINARIES_SPECIAL) BINARIES_C = contman$(EXEEXT) \ g94cub2pl$(EXEEXT) \ @@ -47,8 +47,11 @@ xmol2bamber$(EXEEXT) \ xplor2charmm$(EXEEXT) \ gridasc2plt$(EXEEXT) \ - gridbin2plt$(EXEEXT) \ - icon8$(EXEEXT) + gridbin2plt$(EXEEXT) + +BINARIES_SPECIAL = $(BINARIES_icon8) + +BINARIES_icon8 = icon8$(EXEEXT) BINARIES_JAR = xvibs.jar @@ -75,13 +78,16 @@ $(LIBTOOL) --tag=CC --tag=disable-shared --mode=compile $(CC) -c -o $@ $^ $(BINARIES_C): - $(CC) -o $@ $^ $(UTIL_LIBS) + $(CC) -o $@ $^ $(LDFLAGS) $(UTIL_LIBS) $(BINARIES_CXX): - $(CXX) -o $@ $^ $(UTIL_LIBS) + $(CXX) -o $@ $^ $(LDFLAGS) $(UTIL_LIBS) $(BINARIES_F): - $(F77) -o $@ $^ $(UTIL_LIBS) + $(F77) -ffixed-line-length-none -o $@ $^ $(UTIL_LIBS) + +$(BINARIES_icon8): + $(F77) -ffixed-line-length-none -fno-globals -o $@ $^ $(UTIL_LIBS) $(BINARIES_JAR): cp $^ $@ diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/UHBD/gridasc2plt.f gOpenMol-2.30/utility/UHBD/gridasc2plt.f --- gOpenMol-2.30.orig/utility/UHBD/gridasc2plt.f 2003-05-19 13:24:53.000000000 -0400 +++ gOpenMol-2.30/utility/UHBD/gridasc2plt.f 2003-10-15 19:08:53.000000000 -0400 @@ -32,7 +32,7 @@ read (5,991) pltfile 991 format (a80) - open (unit=10,file=uhbdfile,readonly,form='formatted') + open (unit=10,file=uhbdfile,form='formatted') 77 format(a72/2e12.6,5i7/3i7,4e12.6/4e12.6/2e12.6,2i7) 78 format(3i7) diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/UHBD/gridbin2plt.f gOpenMol-2.30/utility/UHBD/gridbin2plt.f --- gOpenMol-2.30.orig/utility/UHBD/gridbin2plt.f 2003-05-19 13:24:54.000000000 -0400 +++ gOpenMol-2.30/utility/UHBD/gridbin2plt.f 2003-10-15 19:08:53.000000000 -0400 @@ -23,7 +23,7 @@ read (5,991) pltfile 991 format (a80) - open (unit=10,file=uhbdfile,readonly,form='unformatted') + open (unit=10,file=uhbdfile,form='unformatted') read (10) title, scale,dum2,grdflg,idum2,km,idum1,kdum1, & im,jm,kdum2, diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/convert.f gOpenMol-2.30/utility/convert.f --- gOpenMol-2.30.orig/utility/convert.f 2003-05-19 13:24:51.000000000 -0400 +++ gOpenMol-2.30/utility/convert.f 2003-10-15 19:08:53.000000000 -0400 @@ -268,7 +268,7 @@ IF(Nrad.gt.0) Then READ(21,200) (Rname(i),Rvalue(I),I=1,NRad) -200 FORMAT(16(A,PF3.0)) +200 FORMAT(16(A,F3.0)) End if * C ATOMS