svn commit: r366620 - in head/science/vmd: . files

John Marino marino at FreeBSD.org
Sat Aug 30 14:17:54 UTC 2014 

Author: marino
Date: Sat Aug 30 14:17:53 2014
New Revision: 366620
URL: http://svnweb.freebsd.org/changeset/ports/366620
QAT: https://qat.redports.org/buildarchive/r366620/

Log:
  Stage science/vmd
  
  I clobbered the Makefile diff (sorry danfe@).  The entire makefile was
  tabbed over 3 times.  There was also no respect for 80 columns so a good
  part of the clobber came from line wrapping.  I also made $TAR use
  real switches (e.g. -xzf) rather than undocumented by supported (zxf)
  
  This is another manual package / obtain restricted data files/ only port
  so I can't test much of it.
  
  PR:		193090
  Submitted by:	turutani (Kyoto)

Modified:
  head/science/vmd/Makefile
  head/science/vmd/files/patch-configure

Modified: head/science/vmd/Makefile
==============================================================================
--- head/science/vmd/Makefile	Sat Aug 30 13:47:57 2014	(r366619)
+++ head/science/vmd/Makefile	Sat Aug 30 14:17:53 2014	(r366620)
@@ -1,46 +1,40 @@
 # Created by: Stephen Montgomery-Smith <stephen at math.missouri.edu>
 # $FreeBSD$
 
-PORTNAME=		vmd
-DISTVERSION=		1.9.1
-PORTREVISION=		1
-CATEGORIES=		science graphics python tcl tk
-MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b2/:tachyon \
-			http://www.photonlimited.com/~johns/tachyon/files/0.99b2/:tachyon \
-			http://www.ks.uiuc.edu/Research/vmd/extsrcs/:stride
-DISTFILES=		${VMD_DIST} \
-			${TACHYON_DIST}:tachyon \
-			${STRIDE_DIST}:stride
+PORTNAME=	vmd
+DISTVERSION=	1.9.1
+PORTREVISION=	2
+CATEGORIES=	science graphics python tcl tk
+MASTER_SITES=	http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b2/:tachyon \
+		http://www.photonlimited.com/~johns/tachyon/files/0.99b2/:tachyon \
+		http://www.ks.uiuc.edu/Research/vmd/extsrcs/:stride
+DISTFILES=	${VMD_DIST} \
+		${TACHYON_DIST}:tachyon \
+		${STRIDE_DIST}:stride
 
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	Molecular visualization program
 
-BUILD_DEPENDS=		makedepend:${PORTSDIR}/devel/makedepend \
-			${PYNUMERIC}
-LIB_DEPENDS=		libtcl85.so:${PORTSDIR}/lang/tcl85 \
-			libtk85.so:${PORTSDIR}/x11-toolkits/tk85 \
-			libfltk.so:${PORTSDIR}/x11-toolkits/fltk \
-			libnetcdf.so:${PORTSDIR}/science/netcdf
-RUN_DEPENDS=		${PYNUMERIC}
-
-USES=			gmake perl5
-USE_PERL5=		build
-USE_GL=			glu
-USE_PYTHON=		yes
-
-ONLY_FOR_ARCHS=		i386 amd64
-
-RESTRICTED=		License has restrictions
-
-VMD_DIST=		${PORTNAME}-${DISTVERSION}.src.tar.gz
-TACHYON_DIST=		tachyon-0.99b2.tar.gz
-# I get stride.tar.gz from ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/
-# but the www.ks.uiuc.edu site (that gives Stride_src.tar.Z) is closer
-# to vmd upstream (and google actually knows about it).
-#STRIDE_DIST=		stride.tar.gz
-STRIDE_DIST=		Stride_src.tar.Z
+BUILD_DEPENDS=	makedepend:${PORTSDIR}/devel/makedepend \
+		${PYNUMERIC}
+LIB_DEPENDS=	libtcl85.so:${PORTSDIR}/lang/tcl85 \
+		libtk85.so:${PORTSDIR}/x11-toolkits/tk85 \
+		libfltk.so:${PORTSDIR}/x11-toolkits/fltk \
+		libnetcdf.so:${PORTSDIR}/science/netcdf
+RUN_DEPENDS=	${PYNUMERIC}
+
+USES=		gmake perl5 python
+USE_PERL5=	build
+USE_GL=		glu
+
+ONLY_FOR_ARCHS=	i386 amd64
+
+RESTRICTED=	License has restrictions
+
+VMD_DIST=	${PORTNAME}-${DISTVERSION}.src.tar.gz
+TACHYON_DIST=	tachyon-0.99b2.tar.gz
+STRIDE_DIST=	Stride_src.tar.Z
 
-NO_STAGE=	yes
 .include <bsd.port.pre.mk>
 
 .if ${ARCH} == "amd64"
@@ -55,15 +49,19 @@ PLIST_SUB+=		VMD_ARCH=${VMD_ARCH}
 
 # Check for VMD sources
 .if !exists(${DISTDIR}/${VMD_DIST})
-IGNORE=	Because of licensing restrictions, you must fetch the source distribution manually.  Please access http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD with a web browser.  You will be required to log in and register, but you can create an account on this page.  After registration and accepting the University of Illinois agreement, download the source file, ${VMD_DIST}.  Please place this file in ${DISTDIR}, and re-run make
+IGNORE=	license restrictions require manual fetching of the distribution\
+	source.  Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\
+	with a browser.  You will be required to register, log in,  and accept\
+	the University of Illinois agreement before you can download the\
+	${VMD_DIST} source file.  Place this file in ${DISTDIR} and try again.
 .endif
 
 do-extract:
 	${MKDIR} ${WRKDIR}
-	${TAR} xfz ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
-	${TAR} xfz ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf
-	${TAR} xfz ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib
-	${TAR} xfz ${DISTDIR}/${STRIDE_DIST} -C ${WRKSRC}/lib/stride
+	${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
+	${TAR} -xzf ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf
+	${TAR} -xzf ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib
+	${TAR} -xzf ${DISTDIR}/${STRIDE_DIST} -C ${WRKSRC}/lib/stride
 
 post-patch:
 	${REINPLACE_CMD} "s/-lpthread/${PTHREAD_LIBS}/" ${WRKSRC}/configure
@@ -78,15 +76,42 @@ post-patch:
 		-e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure
 
 do-build:
-	${SETENV} ${MAKE_ENV} ${MAKE_CMD} bsd -C ${WRKSRC}/lib/tachyon/unix && ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon ${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH}
-	${SETENV} ${MAKE_ENV} TCLLIB=-L${PREFIX}/lib/tcl8.5 TCLINC=-I${PREFIX}/include/tcl8.5 PLUGINDIR=${WRKSRC}/plugins ${MAKE_CMD} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins
-	${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.5 TK_INCLUDE_DIR=${PREFIX}/include/tk8.5 ${MAKE_CMD} ${VMD_TARGET} -C ${WRKSRC}
+	${SETENV} ${MAKE_ENV} ${MAKE_CMD} bsd -C ${WRKSRC}/lib/tachyon/unix \
+		&& ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon \
+			${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} TCLLIB=-L${PREFIX}/lib/tcl8.5 \
+		TCLINC=-I${PREFIX}/include/tcl8.5 PLUGINDIR=${WRKSRC}/plugins \
+		${MAKE_CMD} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins
+	${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.5 \
+		TK_INCLUDE_DIR=${PREFIX}/include/tk8.5 ${MAKE_CMD} \
+		${VMD_TARGET} -C ${WRKSRC}
 	${SETENV} ${MAKE_ENV} ${MAKE_CMD} all -C ${WRKSRC}/src
-	${SETENV} ${MAKE_ENV} ${MAKE_CMD} depend -C ${WRKSRC}/lib/surf && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} surf -C ${WRKSRC}/lib/surf && ${MV} ${WRKSRC}/lib/surf/surf ${WRKSRC}/lib/surf/surf_${VMD_ARCH}
-	${SETENV} ${MAKE_ENV} ${MAKE_CMD} -C ${WRKSRC}/lib/stride && ${MV} ${WRKSRC}/lib/stride/stride ${WRKSRC}/lib/stride/stride_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} ${MAKE_CMD} depend -C ${WRKSRC}/lib/surf \
+		&& ${SETENV} ${MAKE_ENV} ${MAKE_CMD} surf -C \
+			${WRKSRC}/lib/surf \
+		&& ${MV} ${WRKSRC}/lib/surf/surf \
+			${WRKSRC}/lib/surf/surf_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} ${MAKE_CMD} -C ${WRKSRC}/lib/stride \
+		&& ${MV} ${WRKSRC}/lib/stride/stride \
+			${WRKSRC}/lib/stride/stride_${VMD_ARCH}
 
 do-install:
-	${SETENV} ${MAKE_ENV} ${MAKE_CMD} -C ${WRKSRC}/src install
-	@${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${PREFIX}/lib/vmd
+	${SETENV} ${MAKE_ENV} DESTDIR=${STAGEDIR} \
+	    ${MAKE_CMD} -C ${WRKSRC}/src install
+	${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/*${VMD_ARCH} \
+	    ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/molfile/*.so
+.for f in tcl/autopsf1.3/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
+	  tcl/mutator1.4/libalchemify.so tcl/pmepot1.0/libpmepot.so \
+	  tcl/psfgen1.6/libpsfgen.so tcl/rnaview1.1/rnaview \
+	  tcl/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \
+	  tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \
+	  tcl/clustalw1.1/clustalw tcl/libbiokit1.1/tcl_libbiokit.so \
+	  tcl/libbiokit1.1/q tcl/libbiokit1.1/seqqr \
+	  tcl/libbiokit1.1/structqr tcl/libbiokit1.1/qpair \
+	  tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \
+	  tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \
+	  bin/catdcd4.0/catdcd bin/cionize1.0/cionize
+	${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f}
+.endfor
 
 .include <bsd.port.post.mk>

Modified: head/science/vmd/files/patch-configure
==============================================================================
--- head/science/vmd/files/patch-configure	Sat Aug 30 13:47:57 2014	(r366619)
+++ head/science/vmd/files/patch-configure	Sat Aug 30 14:17:53 2014	(r366620)
@@ -1,5 +1,5 @@
---- configure.orig	2009-08-01 03:19:34.000000000 -0400
-+++ configure	2010-01-08 22:01:38.000000000 -0500
+--- configure.orig	2012-02-02 16:53:54.000000000 +0900
++++ configure	2014-08-28 16:42:38.000000000 +0900
 @@ -13,10 +13,10 @@
  $install_name = "vmd";
  
@@ -37,3 +37,72 @@
  
  NVCC        = $arch_nvcc
  NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+@@ -2997,38 +2997,38 @@
+ 	\$(COMPILERC) \$(RCFLAGS)
+ 
+ install:
+-	if [ ! -d "$install_library_dir" ]; then \\
+-		\$(MAKEDIR) "$install_library_dir" ; \\
++	if [ ! -d "\${DESTDIR}$install_library_dir" ]; then \\
++		\$(MAKEDIR) "\${DESTDIR}$install_library_dir" ; \\
+ 	fi ; \\
+-	if [ ! -d "$install_bin_dir" ]; then \\
+-		\$(MAKEDIR) "$install_bin_dir" ; \\
++	if [ ! -d "\${DESTDIR}$install_bin_dir" ]; then \\
++		\$(MAKEDIR) "\${DESTDIR}$install_bin_dir" ; \\
+ 	fi ; \\
+-	if [ ! -d "$install_library_dir"/doc ]; then \\
+-		\$(MAKEDIR) "$install_library_dir"/doc; \\
++	if [ ! -d "\${DESTDIR}$install_library_dir"/doc ]; then \\
++		\$(MAKEDIR) "\${DESTDIR}$install_library_dir"/doc; \\
+ 	fi
+-	-\$(COPY) ../Announcement  "$install_library_dir"
+-	-\$(COPY) ../README        "$install_library_dir"
+-	-\$(COPY) ../LICENSE       "$install_library_dir"
+-	-\$(COPY) $vmd_doc_dir/ug.pdf        "$install_library_dir"/doc
+-	if [ -f $install_library_dir/$config_progname ]; then \\
+-           \$(MOVE) "$install_library_dir/$config_progname" "$install_library_dir/OLD_$config_progname" ; \$(DELETE) "$install_library_dir/OLD_$config_progname" ; fi
+-	-\$(COPY) ../$config_arch/$config_progname "$install_library_dir"
++	-\$(COPY) ../Announcement  "\${DESTDIR}$install_library_dir"
++	-\$(COPY) ../README        "\${DESTDIR}$install_library_dir"
++	-\$(COPY) ../LICENSE       "\${DESTDIR}$install_library_dir"
++	-\$(COPY) $vmd_doc_dir/ug.pdf        "\${DESTDIR}$install_library_dir"/doc
++	if [ -f \${DESTDIR}$install_library_dir/$config_progname ]; then \\
++           \$(MOVE) "\${DESTDIR}$install_library_dir/$config_progname" "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; \$(DELETE) "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; fi
++	-\$(COPY) ../$config_arch/$config_progname "\${DESTDIR}$install_library_dir"
+ 	if [ -d "../lib/redistrib/lib_$config_arch" ]; then \\
+ 		\$(CD) ../lib/redistrib/lib_$config_arch; \$(TAR) -cf - ./* | \\
+-		(cd "$install_library_dir" ; \$(TAR) -xf -) \\
++		(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -) \\
+ 	fi ;
+-	-\$(COPY) @vmd_other_exe "$install_library_dir"
++	-\$(COPY) @vmd_other_exe "\${DESTDIR}$install_library_dir"
+ 	-\$(CD) ..; \$(TAR) -cf - scripts | \\
+-	(cd "$install_library_dir" ; \$(TAR) -xf -)
++	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
+ 	-\$(CD) $vmd_library_dir; \$(TAR) -cf - scripts | \\
+-	(cd "$install_library_dir" ; \$(TAR) -xf -)
++	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
+ 	-\$(CD) ..; \$(TAR) -cf - python | \\
+-	(cd "$install_library_dir"/scripts ; \$(TAR) -xf -)
++	(cd "\${DESTDIR}$install_library_dir"/scripts ; \$(TAR) -xf -)
+ 	-\$(CD) ..; \$(TAR) -cf - plugins | \\
+-	(cd "$install_library_dir" ; \$(TAR) -xf -)
++	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
+ 	-\$(CD) ..; \$(TAR) -cf - shaders | \\
+-	(cd "$install_library_dir" ; \$(TAR) -xf -)
+-	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
++	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
++	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "\${DESTDIR}$install_library_dir"
+ 	\$(CD) $vmd_bin_dir ; \\
+ 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
+ 	if [ ! -x "/bin/csh" ]; then \\
+@@ -3044,7 +3044,7 @@
+ 		cat $vmd_bin_csh >> run_vmd_tmp ; \\
+ 	fi ; \\
+ 	chmod +x run_vmd_tmp ; \\
+-	\$(COPY) run_vmd_tmp "$install_bin_dir"/$install_name ; \\
++	\$(COPY) run_vmd_tmp "\${DESTDIR}$install_bin_dir"/$install_name ; \\
+ 	\$(DELETE) run_vmd_tmp
+ 	\$(ECHO) Make sure "$install_bin_dir"/$install_name is in your path.
+ 	\$(ECHO) "VMD installation complete.  Enjoy!"

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