Date: Wed, 16 Nov 2016 14:52:53 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r426241 - in head: . biology biology/njplot biology/njplot/files Message-ID: <201611161452.uAGEqrRx091129@repo.freebsd.org>
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Author: jrm Date: Wed Nov 16 14:52:53 2016 New Revision: 426241 URL: https://svnweb.freebsd.org/changeset/ports/426241 Log: biology/njplot: Revive and update to version 2.4 Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8518 Added: head/biology/njplot/ - copied from r400159, head/biology/njplot/ Modified: head/MOVED head/biology/Makefile head/biology/njplot/Makefile head/biology/njplot/distinfo head/biology/njplot/files/patch-makefile Modified: head/MOVED ============================================================================== --- head/MOVED Wed Nov 16 13:23:57 2016 (r426240) +++ head/MOVED Wed Nov 16 14:52:53 2016 (r426241) @@ -7966,7 +7966,6 @@ cad/slffea||2015-11-28|Has expired: Brok audio/cripple||2015-11-28|Has expired: Broken for more than 6 months cad/geda-gattrib||2015-11-28|Has expired: Broken for more than 6 months cad/findhier||2015-11-28|Has expired: Broken for more than 6 months -biology/njplot||2015-11-28|Has expired: Broken for more than 6 months audio/wmmp||2015-11-28|Has expired: Broken for more than 6 months x11/avant-window-navigator||2015-11-28|Has expired: Broken for more than 6 months cad/geda-netlist||2015-11-28|Has expired: Broken for more than 6 months Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Nov 16 13:23:57 2016 (r426240) +++ head/biology/Makefile Wed Nov 16 14:52:53 2016 (r426241) @@ -55,6 +55,7 @@ SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit + SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Das Modified: head/biology/njplot/Makefile ============================================================================== --- head/biology/njplot/Makefile Sun Oct 25 19:23:40 2015 (r400159) +++ head/biology/njplot/Makefile Wed Nov 16 14:52:53 2016 (r426241) @@ -2,52 +2,38 @@ # $FreeBSD$ PORTNAME= njplot -PORTVERSION= 2.1 -PORTREVISION= 3 +PORTVERSION= 2.4 CATEGORIES= biology -MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/ +MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/ \ + ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/ -MAINTAINER= mzaki@m.u-tokyo.ac.jp -COMMENT= Phylogenetic tree drawing program capable of interactive manipulation +MAINTAINER= jrm@FreeBSD.org +COMMENT= Phylogenetic tree drawing program -BROKEN= Unfetchable +LICENSE= NONE -OPTIONS_DEFINE= DOCS X11 -OPTIONS_DEFAULT= DOCS X11 +BUILD_DEPENDS= blastall:biology/ncbi-toolkit -.include <bsd.port.options.mk> +MAKEFILE= makefile -.if ${PORT_OPTIONS:MX11} -BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit -USE_XORG= x11 xt xmu xp USES= motif -.endif +USE_XORG= x11 xmu xp xt -MAKEFILE= makefile +BINARIES= newicktops newicktotxt njplot unrooted +PLIST_FILES= ${BINARIES:S|^|bin/|} man/man1/njplot.1.gz \ + man/man1/unrooted.1.gz ${DATADIR}/njplot.help +PORTDOCS= njplot.html njplot.gif -BINARIES= newicktops newicktotxt -.if ${PORT_OPTIONS:MX11} -BINARIES+= njplot unrooted -.endif -.for file in ${BINARIES} -PLIST_FILES+= bin/${file} -.endfor - -PORTDOCS= njplot.help njplot.html njplot.gif - -MAN_1= njplot.1 unrooted.1 -PLIST_FILES+= man/man1/njplot.1.gz \ - man/man1/unrooted.1.gz - -.if !${PORT_OPTIONS:MX11} -post-patch: - ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile -.endif +OPTIONS_DEFINE= DOCS do-install: ${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_MAN} ${MAN_1:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/man/man1 - ${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MANPREFIX}/man/man1 + @${MKDIR} ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/njplot.help ${STAGEDIR}${DATADIR} + +do-install-DOCS-on: + @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include <bsd.port.mk> Modified: head/biology/njplot/distinfo ============================================================================== --- head/biology/njplot/distinfo Sun Oct 25 19:23:40 2015 (r400159) +++ head/biology/njplot/distinfo Wed Nov 16 14:52:53 2016 (r426241) @@ -1,2 +1,3 @@ -SHA256 (njplot-2.1.tar.gz) = dd8a54c3903cd104d8322257a87b5fbf3afb7776a96fcf9bee504ae1ad54c0c1 -SIZE (njplot-2.1.tar.gz) = 85735 +TIMESTAMP = 1479168824 +SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3 +SIZE (njplot-2.4.tar.gz) = 83239 Modified: head/biology/njplot/files/patch-makefile ============================================================================== --- head/biology/njplot/files/patch-makefile Sun Oct 25 19:23:40 2015 (r400159) +++ head/biology/njplot/files/patch-makefile Wed Nov 16 14:52:53 2016 (r426241) @@ -1,69 +1,49 @@ ---- makefile.orig Thu Oct 11 01:54:00 2007 -+++ makefile Mon Dec 3 22:08:28 2007 +--- makefile.orig 2012-01-04 08:50:43 UTC ++++ makefile @@ -1,5 +1,5 @@ #uncomment and locally adapt next line to fix the full helpfile path name -HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\" -+HELPFILENAME = -DHELPFILENAME=\"$(LOCALBASE)/doc/njplot/njplot.help\" ++HELPFILENAME = -DHELPFILENAME=\"${DATADIR}/njplot.help\" #comment out next line and uncomment next 2 to use the PDFLib Lite library NO_PDF = -DNO_PDF -@@ -7,43 +7,45 @@ +@@ -7,27 +7,31 @@ NO_PDF = -DNO_PDF #PDFLIB = -L$(PDF) -lpdf # c compiler and linker -CC = gcc -+CC ?= gcc ++CC ?= cc - # Vibrant top directory --VIBRANT = /banques0/ncbiJun04 -+#VIBRANT = /banques0/ncbiJun04 +-# Vibrant top directory +-VIBRANT = /usr/include/ncbi +NCBIINC = $(LOCALBASE)/include/ncbi +NCBILIB = $(LOCALBASE)/lib/ncbi - - # X11 include directory --X11INCL = /usr/X11R6/include -+X11INCL = $(LOCALBASE)/include - - # motif library directory --MOTIFLIB = /sw/lib --MOTIFINCL = /sw/include -+#MOTIFLIB = /sw/lib -+#MOTIFINCL = /sw/include - OBJECTS = njplot-vib.o OBJUNROOTED = unrooted-vib.o preptree.o ++CFLAGS = -c -DWIN_MOTIF -Dunix -I${LOCALBASE}/include -I$(NCBIINC) $(HELPFILENAME) $(NO_PDF) -Wimplicit-function-declaration --CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ -- -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ -- -Wimplicit-function-declaration -g -+CFLAGS = -c -DWIN_MOTIF -Dunix -I$(NCBIINC) \ -+ -I$(X11INCL) $(HELPFILENAME) $(NO_PDF) \ -+ -Wimplicit-function-declaration - +-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT) $(HELPFILENAME) $(NO_PDF) +- all: njplot unrooted newicktops newicktotxt njplot : $(OBJECTS) - $(CC) -g -o njplot $(OBJECTS) \ -- -L$(VIBRANT)/lib \ -+ -L$(NCBILIB) \ - -lvibrant -lncbi \ - $(PDFLIB) \ -- -L$(MOTIFLIB) -lXm \ -- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm -+ $(MOTIFLIB) \ -+ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm - + $(CC) -o njplot $(OBJECTS) \ +- -lvibrant -lncbi -lXm -lXt +- ++ -L$(NCBILIB) \ ++ -lvibrant -lncbi \ ++ $(MOTIFLIB) \ ++ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm ++ unrooted : $(OBJUNROOTED) - $(CC) -g -o unrooted $(OBJUNROOTED) \ -- -L$(VIBRANT)/lib -lvibrant -lncbi \ -- -L$(MOTIFLIB) -lXm \ -- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm + $(CC) -o unrooted $(OBJUNROOTED) \ +- -lvibrant -lncbi -lXm -lXt + -L$(NCBILIB) -lvibrant -lncbi \ -+ $(MOTIFLIB) \ -+ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm ++ $(MOTIFLIB) \ ++ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm newicktops: njplot-vib.c $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm
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