Date: Sat, 30 Aug 2014 14:17:53 +0000 (UTC) From: John Marino <marino@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r366620 - in head/science/vmd: . files Message-ID: <201408301417.s7UEHrOq056825@svn.freebsd.org>
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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@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 \ + ${STRIDE_DIST}:stride MAINTAINER= ports@FreeBSD.org COMMENT= Molecular visualization program -BUILD_DEPENDS= makedepend:${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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