Index: MOVED =================================================================== --- MOVED +++ MOVED @@ -7966,7 +7966,6 @@ 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 Index: biology/Makefile =================================================================== --- biology/Makefile +++ biology/Makefile @@ -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 Index: biology/njplot/Makefile =================================================================== --- biology/njplot/Makefile +++ biology/njplot/Makefile @@ -2,52 +2,42 @@ # $FreeBSD$ 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/ -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 - -OPTIONS_DEFINE= DOCS X11 -OPTIONS_DEFAULT= DOCS X11 - -.include - -.if ${PORT_OPTIONS:MX11} -BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit -USE_XORG= x11 xt xmu xp -USES= motif -.endif - -MAKEFILE= makefile +#LICENSE= unspecified open source 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 - +MAKEFILE= makefile MAN_1= njplot.1 unrooted.1 -PLIST_FILES+= man/man1/njplot.1.gz \ +PLIST_FILES= bin/newicktops \ + bin/newicktotxt \ + man/man1/njplot.1.gz \ man/man1/unrooted.1.gz +PORTDOCS= njplot.help njplot.html njplot.gif -.if !${PORT_OPTIONS:MX11} -post-patch: +OPTIONS_DEFINE= DOCS X11 +OPTIONS_DEFAULT=DOCS X11 + +X11_BUILD_DEPENDS= blastall:biology/ncbi-toolkit +X11_USE= xorg=x11,xmu,xp,xt +X11_USES= motif +X11_VARS= BINARIES+="njplot unrooted" +X11_PLIST_FILES= bin/njplot bin/unrooted + +post-patch-X11-off: ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile -.endif do-install: ${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${MAN_1:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/man/man1 - ${MKDIR} ${STAGEDIR}${DOCSDIR} + +do-install-DOCS-on: + @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include Index: biology/njplot/distinfo =================================================================== --- biology/njplot/distinfo +++ biology/njplot/distinfo @@ -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 Index: biology/njplot/files/patch-makefile =================================================================== --- biology/njplot/files/patch-makefile +++ biology/njplot/files/patch-makefile @@ -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=\"$(LOCALBASE)/doc/njplot/njplot.help\" ++HELPFILENAME = -DHELPFILENAME=\"${DOCSDIR}njplot/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