svn commit: r426241 - in head: . biology biology/njplot biology/njplot/files
Joseph Mingrone
jrm at FreeBSD.org
Wed Nov 16 14:52:55 UTC 2016
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 at m.u-tokyo.ac.jp
-COMMENT= Phylogenetic tree drawing program capable of interactive manipulation
+MAINTAINER= jrm at 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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