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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 <bsd.port.options.mk>
-
-.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 <bsd.port.mk>
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

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