svn commit: r327709 - in head/biology: ariadne artemis avida babel biococoa biojava blast blat boinc-simap chemeq clustalw consed crux dotter embassy emboss fasta fasta3 fastdnaml finchtv fluctuate...
Baptiste Daroussin
bapt at FreeBSD.org
Fri Sep 20 15:56:02 UTC 2013
Author: bapt
Date: Fri Sep 20 15:55:44 2013
New Revision: 327709
URL: http://svnweb.freebsd.org/changeset/ports/327709
Log:
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
Modified:
head/biology/ariadne/Makefile
head/biology/artemis/Makefile
head/biology/avida/Makefile
head/biology/babel/Makefile
head/biology/biococoa/Makefile
head/biology/biojava/Makefile
head/biology/blast/Makefile
head/biology/blat/Makefile
head/biology/boinc-simap/Makefile
head/biology/chemeq/Makefile
head/biology/clustalw/Makefile
head/biology/consed/Makefile
head/biology/crux/Makefile
head/biology/dotter/Makefile
head/biology/embassy/Makefile
head/biology/emboss/Makefile
head/biology/fasta/Makefile
head/biology/fasta3/Makefile
head/biology/fastdnaml/Makefile
head/biology/finchtv/Makefile
head/biology/fluctuate/Makefile
head/biology/garlic/Makefile
head/biology/genpak/Makefile
head/biology/gff2ps/Makefile
head/biology/gmap/Makefile
head/biology/gperiodic/Makefile
head/biology/grappa/Makefile
head/biology/hmmer/Makefile
head/biology/iolib/Makefile
head/biology/jalview/Makefile
head/biology/lagan/Makefile
head/biology/lamarc/Makefile
head/biology/libgenome/Makefile
head/biology/libsbml/Makefile
head/biology/linux-foldingathome/Makefile
head/biology/mafft/Makefile
head/biology/mapm3/Makefile
head/biology/migrate/Makefile
head/biology/molden/Makefile
head/biology/mopac/Makefile
head/biology/mrbayes/Makefile
head/biology/mummer/Makefile
head/biology/muscle/Makefile
head/biology/ncbi-toolkit/Makefile
head/biology/njplot/Makefile
head/biology/ortep3/Makefile
head/biology/p5-AcePerl/Makefile
head/biology/p5-Bio-ASN1-EntrezGene/Makefile
head/biology/p5-Bio-Das-Lite/Makefile
head/biology/p5-Bio-Das/Makefile
head/biology/p5-Bio-GFF3/Makefile
head/biology/p5-Bio-Glite/Makefile
head/biology/p5-Bio-Graphics/Makefile
head/biology/p5-Bio-MAGETAB/Makefile
head/biology/p5-Bio-NEXUS/Makefile
head/biology/p5-Bio-Phylo/Makefile
head/biology/p5-Bio-SCF/Makefile
head/biology/p5-bioperl-run/Makefile
head/biology/p5-bioperl/Makefile
head/biology/paml/Makefile
head/biology/phd2fasta/Makefile
head/biology/phrap/Makefile
head/biology/phred/Makefile
head/biology/phylip/Makefile
head/biology/phyml/Makefile
head/biology/platon/Makefile
head/biology/plink/Makefile
head/biology/plinkseq/Makefile
head/biology/povchem/Makefile
head/biology/primer3/Makefile
head/biology/protomol/Makefile
head/biology/psi88/Makefile
head/biology/py-biopython/Makefile
head/biology/pycogent/Makefile
head/biology/pyfasta/Makefile
head/biology/pymol/Makefile
head/biology/python-nexus/Makefile
head/biology/rasmol/Makefile
head/biology/recombine/Makefile
head/biology/ruby-bio/Makefile
head/biology/seaview/Makefile
head/biology/seqan/Makefile
head/biology/seqio/Makefile
head/biology/sim4/Makefile
head/biology/ssaha/Makefile
head/biology/tRNAscan-SE/Makefile
head/biology/t_coffee/Makefile
head/biology/tinker/Makefile
head/biology/treepuzzle/Makefile
head/biology/treeviewx/Makefile
head/biology/ugene/Makefile
head/biology/velvet/Makefile
head/biology/wise/Makefile
head/biology/xmolwt/Makefile
Modified: head/biology/ariadne/Makefile
==============================================================================
--- head/biology/ariadne/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/ariadne/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -18,6 +18,7 @@ PORTDOCS= README
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}| ; \
s|CC =|CC ?=| ; \
Modified: head/biology/artemis/Makefile
==============================================================================
--- head/biology/artemis/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/artemis/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ JAVA_VERSION= 1.6+
NO_BUILD= yes
PLIST_SUB= PORTVERSION="${PORTVERSION}"
+NO_STAGE= yes
post-extract:
@${FIND} ${WRKSRC} -type d -name CVS -exec ${RM} -rf {} +
Modified: head/biology/avida/Makefile
==============================================================================
--- head/biology/avida/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/avida/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -30,6 +30,7 @@ DATA_FILES= analyze.cfg avida.cfg defaul
instset-heads-sex.cfg instset-heads.cfg instset-smt.cfg \
instset-transsmt.cfg
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "ia64" || ${ARCH} == "powerpc" || ${ARCH} == "sparc64"
Modified: head/biology/babel/Makefile
==============================================================================
--- head/biology/babel/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/babel/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -22,6 +22,7 @@ PORTDOCS= README.1ST
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
post-build:
${SED} -e 's%@PREFIX@%${PREFIX}%g' \
${FILESDIR}/babel.sh >${WRKSRC}/babel.sh
Modified: head/biology/biococoa/Makefile
==============================================================================
--- head/biology/biococoa/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/biococoa/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,4 +21,5 @@ USE_GNUSTEP_INSTALL= yes
WRKSRC= ${WRKDIR}/biococoa-${PORTVERSION}
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/biojava/Makefile
==============================================================================
--- head/biology/biojava/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/biojava/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -25,6 +25,7 @@ PORTEXAMPLES= demos
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
.if !defined(WITHOUT_TESTS)
+NO_STAGE= yes
regression-test:
@(cd ${BUILD_WRKSRC}; \
${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)
Modified: head/biology/blast/Makefile
==============================================================================
--- head/biology/blast/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/blast/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -32,6 +32,7 @@ BLASTA_LINKS= blastn blastp blastx tblas
XDFORMAT_LINKS= setdb pressdb
SUB_FILES= pkg-message
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == amd64
Modified: head/biology/blat/Makefile
==============================================================================
--- head/biology/blat/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/blat/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -27,6 +27,7 @@ PORTDATA= *
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
post-patch:
@${MKDIR} ${WRKSRC}/bin/${ARCH}
@${MKDIR} ${WRKSRC}/lib/${ARCH}
Modified: head/biology/boinc-simap/Makefile
==============================================================================
--- head/biology/boinc-simap/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/boinc-simap/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,6 +1,5 @@
# Created by: Pav Lucistnik <pav at FreeBSD.org>
# $FreeBSD$
-#
PORTNAME= boinc-simap
PORTVERSION= ${SIMAP_VERSION}.${HMMER_VERSION}
@@ -37,6 +36,7 @@ ONLY_FOR_ARCHS= i386 amd64
OPTIONS_DEFINE= SSE
+NO_STAGE= yes
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MSSE}
Modified: head/biology/chemeq/Makefile
==============================================================================
--- head/biology/chemeq/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/chemeq/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -24,6 +24,7 @@ PORTEXAMPLES= chemreport chemreport.pl c
OPTIONS_DEFINE= DOCS EXAMPLES
+NO_STAGE= yes
.include <bsd.port.options.mk>
do-install:
Modified: head/biology/clustalw/Makefile
==============================================================================
--- head/biology/clustalw/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/clustalw/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: clustalw
-# Date created: 6 July 2000
-# Whom: dbader at eece.unm.edu
-#
+# Created by: dbader at eece.unm.edu
# $FreeBSD$
-#
PORTNAME= clustalw
PORTVERSION= 2.1
@@ -24,6 +20,7 @@ GNU_CONFIGURE= yes
PLIST_FILES= bin/clustalw bin/clustalw2
+NO_STAGE= yes
post-install:
${LN} -sf clustalw2 ${PREFIX}/bin/clustalw
Modified: head/biology/consed/Makefile
==============================================================================
--- head/biology/consed/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/consed/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: phred
-# Date created: 8 July 2005
-# Whom: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
-#
+# Created by: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
# $FreeBSD$
-#
PORTNAME= consed
PORTVERSION= 16.0
@@ -62,6 +58,7 @@ EXAMPLES= standard autofinish assembly_v
PLIST= ${PKGDIR}/pkg-plist.examples
.endif
+NO_STAGE= yes
post-build:
(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)
Modified: head/biology/crux/Makefile
==============================================================================
--- head/biology/crux/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/crux/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ USE_PYTHON= 2.5+
OPTIONS_DEFINE= SYS_LINALG
SYS_LINALG_DESC= Enable system ATLAS/LAPACK
+NO_STAGE= yes
.include <bsd.port.pre.mk>
CPPFLAGS+= -I${LOCALBASE}/include
Modified: head/biology/dotter/Makefile
==============================================================================
--- head/biology/dotter/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/dotter/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,4 +1,4 @@
-# Created by: Fernan Aguero <fernan at iib.unsam.edu.ar>
+# Created by: Fernan Aguero <fernan at iib.unsam.edu.ar>
# $FreeBSD$
PORTNAME= dotter
@@ -22,6 +22,7 @@ ONLY_FOR_ARCHS= i386
NO_BUILD= yes
PLIST_FILES= bin/${PORTNAME} bin/${DISTNAME}
+NO_STAGE= yes
do-install:
${BRANDELF} -t Linux ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}
${INSTALL_PROGRAM} ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} \
Modified: head/biology/embassy/Makefile
==============================================================================
--- head/biology/embassy/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/embassy/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -74,6 +74,7 @@ EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HM
TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \
VIENNA MIRA IPRSCAN CBSTOOLS
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>
Modified: head/biology/emboss/Makefile
==============================================================================
--- head/biology/emboss/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/emboss/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -47,6 +47,7 @@ CONFIGURE_ARGS+= --without-x
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template
+NO_STAGE= yes
pre-install:
@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
Modified: head/biology/fasta/Makefile
==============================================================================
--- head/biology/fasta/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/fasta/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -25,6 +25,7 @@ MLINKS= fasta.1 tfasta.1 fasta.1 lfasta
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
do-extract:
@ ${RM} -rf ${WRKDIR}
@ ${MKDIR} ${WRKSRC}
Modified: head/biology/fasta3/Makefile
==============================================================================
--- head/biology/fasta3/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/fasta3/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -37,6 +37,7 @@ MLINKS= fasta36.1 tfasta35.1 fasta36.1
fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
PLIST_SUB= VER=${PORTVERSION:R:R}
+NO_STAGE= yes
post-patch:
@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
post-install:
Modified: head/biology/fastdnaml/Makefile
==============================================================================
--- head/biology/fastdnaml/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/fastdnaml/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ PORTDOCS= fastDNAml_doc_1.2.txt fastDNAm
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
.include <bsd.port.options.mk>
do-install:
Modified: head/biology/finchtv/Makefile
==============================================================================
--- head/biology/finchtv/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/finchtv/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -18,6 +18,7 @@ NO_BUILD= yes
SUB_FILES= pkg-message
STRIP=
+NO_STAGE= yes
do-install:
.if !defined(NOPORTDOCS)
@${MKDIR} ${DOCSDIR}
Modified: head/biology/fluctuate/Makefile
==============================================================================
--- head/biology/fluctuate/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/fluctuate/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -18,6 +18,7 @@ PORTDOCS= errors.doc fluctuate.doc
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
do-install:
@ ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
Modified: head/biology/garlic/Makefile
==============================================================================
--- head/biology/garlic/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/garlic/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: garlic
-# Date created: 28 July 2003
-# Whom: maho at FreeBSD.org
-#
+# Created by: maho at FreeBSD.org
# $FreeBSD$
-#
PORTNAME= garlic
PORTVERSION= 1.6
@@ -29,6 +25,7 @@ CFLAGS+= -mfancy-math-387 -mpreferred-st
.endif # i386
.endif
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g ;\
s|%%CC%%|${CC}|g ; \
Modified: head/biology/genpak/Makefile
==============================================================================
--- head/biology/genpak/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/genpak/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,10 +1,5 @@
-# ex:ts=8
-# New ports collection makefile for: genpak
-# Date created: Feb 28, 2001
-# Whom: Ying-Chieh Liao <ijliao at FreeBSD.org>
-#
+# Created by: Ying-Chieh Liao <ijliao at FreeBSD.org>
# $FreeBSD$
-#
PORTNAME= genpak
PORTVERSION= 0.26
@@ -31,4 +26,5 @@ MAN1= Genpak.1 gp_acc.1 gp_adjust.1 gp_c
INSTALL_TARGET= install docs
.endif
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/gff2ps/Makefile
==============================================================================
--- head/biology/gff2ps/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/gff2ps/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -27,6 +27,7 @@ GFF2PS_MAN= MANUAL_GFF2PS_v0.96.ps
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MDOCS}
Modified: head/biology/gmap/Makefile
==============================================================================
--- head/biology/gmap/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/gmap/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# Ports collection makefile for: gmap
-# Date created: 24 September 2006
-# Whom: Bob Zimmermann <rpz at cse.wustl.edu>
-#
+# Created by: Bob Zimmermann <rpz at cse.wustl.edu>
# $FreeBSD$
-#
PORTNAME= gmap
PORTVERSION= 2006.04.21
@@ -17,4 +13,5 @@ COMMENT= A Genomic Mapping and Alignment
USE_GMAKE= yes
GNU_CONFIGURE= yes
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/gperiodic/Makefile
==============================================================================
--- head/biology/gperiodic/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/gperiodic/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ PORTDOCS= AUTHORS ChangeLog README
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
do-build:
cd ${WRKSRC} && ${CC} ${CFLAGS} `pkg-config --cflags --libs gtk+-2.0` \
gperiodic.c -o gperiodic
Modified: head/biology/grappa/Makefile
==============================================================================
--- head/biology/grappa/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/grappa/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: grappa
-# Date created: 30 June 2001
-# Whom: dbader at ece.unm.edu
-#
+# Created by: dbader at ece.unm.edu
# $FreeBSD$
-#
PORTNAME= grappa
PORTVERSION= 2.0
@@ -18,6 +14,7 @@ USE_GMAKE= yes
PLIST_FILES= bin/grappa bin/invdist bin/distmat
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e 's/-lpthread/${PTHREAD_LIBS}/g' ${WRKSRC}/${MAKEFILE}
Modified: head/biology/hmmer/Makefile
==============================================================================
--- head/biology/hmmer/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/hmmer/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -24,6 +24,7 @@ EXAMPLES= 7LESS_DROME Pkinase.sto fn3.st
OPTIONS_DEFINE= PVM
PVM_DESC= PVM support
+NO_STAGE= yes
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MPVM}
Modified: head/biology/iolib/Makefile
==============================================================================
--- head/biology/iolib/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/iolib/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -30,4 +30,5 @@ MAN3= read_scf_header.3 read_allocate.3
read2exp.3 fread_scf.3
MAN4= Read.4
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/jalview/Makefile
==============================================================================
--- head/biology/jalview/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/jalview/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ WRKSRC= ${WRKDIR}/${PORTNAME}
DATADIR= ${JAVASHAREDIR}/${PORTNAME}
SUB_FILES= jalview.sh
+NO_STAGE= yes
do-install:
${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${PREFIX}/bin/jalview
@${MKDIR} ${DATADIR}
Modified: head/biology/lagan/Makefile
==============================================================================
--- head/biology/lagan/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/lagan/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -39,6 +39,7 @@ SCRIPTUTILS= cmerge2.pl draft.pl mextrac
READMES= README.FIRST README.chaos README.lagan README.mlagan \
README.tools README.shuffle
+NO_STAGE= yes
post-patch:
@${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \
'/^CC/s|^|#| ; \
Modified: head/biology/lamarc/Makefile
==============================================================================
--- head/biology/lamarc/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/lamarc/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -22,6 +22,7 @@ GNU_CONFIGURE= yes
PORTDOCS= *
PLIST_FILES= bin/${PORTNAME}
+NO_STAGE= yes
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MWXGTK}
Modified: head/biology/libgenome/Makefile
==============================================================================
--- head/biology/libgenome/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/libgenome/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -22,6 +22,7 @@ USE_LDCONFIG= yes
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e 's|-O2|@CXXFLAGS@|g' ${WRKSRC}/src/Makefile.in
Modified: head/biology/libsbml/Makefile
==============================================================================
--- head/biology/libsbml/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/libsbml/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -22,6 +22,7 @@ USE_LDCONFIG= yes
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
MAKE_JOBS_UNSAFE= yes
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>
Modified: head/biology/linux-foldingathome/Makefile
==============================================================================
--- head/biology/linux-foldingathome/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/linux-foldingathome/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# Ports collection makefile for: foldingathome
-# Date created: 2/8/2006
-# Whom: Yonatan <onatan at gmail.com>
-#
+# Created by: Yonatan <onatan at gmail.com>
# $FreeBSD$
-#
PORTNAME= foldingathome
PORTVERSION= 5.04
@@ -23,6 +19,7 @@ PLIST_FILES= share/${PORTNAME}/${DISTNAM
bin/FoldingAtHome
PLIST_DIRS= share/${PORTNAME}
+NO_STAGE= yes
do-extract:
${MKDIR} ${WRKSRC}
${CP} ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX} ${WRKSRC}
Modified: head/biology/mafft/Makefile
==============================================================================
--- head/biology/mafft/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/mafft/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,10 +1,5 @@
-# ex:ts=8
-# New ports collection makefile for: mafft
-# Date created: 1 Feb 2006
-# Whom: Fernan Aguero <fernan at iib.unsam.edu.ar>
-#
+# Created by: Fernan Aguero <fernan at iib.unsam.edu.ar>
# $FreeBSD$
-#
PORTNAME= mafft
PORTVERSION= 6.903
@@ -37,6 +32,7 @@ LN_FILES= einsi fftns fftnsi ginsi linsi
mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
mafft-qinsi mafft-xinsi nwns nwnsi
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "sparc64"
Modified: head/biology/mapm3/Makefile
==============================================================================
--- head/biology/mapm3/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/mapm3/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: mapm3
-# Date created: 26 March 2008
-# Whom: Tassilo Philipp <tphilipp at potion-studios.com>
-#
+# Created by: Tassilo Philipp <tphilipp at potion-studios.com>
# $FreeBSD$
-#
PORTNAME= mapm3
PORTVERSION= 3.0
@@ -21,6 +17,7 @@ COMMENT= Constructs linkage maps of mark
NO_WRKSUBDIR= yes
MAKE_JOBS_UNSAFE= yes
+NO_STAGE= yes
post-patch:
${CP} ${WRKSRC}/sun/* ${WRKSRC}
Modified: head/biology/migrate/Makefile
==============================================================================
--- head/biology/migrate/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/migrate/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -22,6 +22,7 @@ PORTDOCS= *
PORTEXAMPLES= *
PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n
+NO_STAGE= yes
.include <bsd.port.options.mk>
NOT_FOR_ARCHS= alpha
Modified: head/biology/molden/Makefile
==============================================================================
--- head/biology/molden/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/molden/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -31,6 +31,7 @@ PORTDOCS= *
PORTDATA= *
PLIST_FILES= bin/ambfor bin/gmolden bin/molden bin/surf
+NO_STAGE= yes
.include <bsd.port.options.mk>
post-patch:
Modified: head/biology/mopac/Makefile
==============================================================================
--- head/biology/mopac/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/mopac/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -29,6 +29,7 @@ PORTEXAMPLES= *
OPTIONS_DEFINE= EXAMPLES
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e '/pkgconfig/s|$$(libdir)|$$(prefix)/libdata|g' \
${WRKSRC}/Makefile.am
Modified: head/biology/mrbayes/Makefile
==============================================================================
--- head/biology/mrbayes/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/mrbayes/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: mrbayes
-# Date created: 11 December 2007
-# Whom: mzaki at biol.s.u-tokyo.ac.jp
-#
+# Created by: mzaki at biol.s.u-tokyo.ac.jp
# $FreeBSD$
-#
PORTNAME= mrbayes
PORTVERSION= 3.1.2
@@ -23,6 +19,7 @@ PLIST_FILES= bin/mb
PORTEXAMPLES= adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \
cynmix.nex kim.nex primates.nex replicase.nex
+NO_STAGE= yes
do-install:
@${INSTALL_PROGRAM} ${WRKSRC}/mb ${PREFIX}/bin/
.if !defined(NOPORTEXAMPLES)
Modified: head/biology/mummer/Makefile
==============================================================================
--- head/biology/mummer/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/mummer/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,10 +1,5 @@
-# ex:ts=8
-# New ports collection makefile for: MUMmer
-# Date created: 20 November 2007
-# Whom: Tony Maher
-#
+# Created by: Tony Maher
# $FreeBSD$
-#
PORTNAME= mummer
PORTVERSION= 3.23
@@ -24,6 +19,7 @@ SCRIPTS= dnadiff exact-tandems mapview m
nucmer2xfig promer run-mummer1 run-mummer3
DOCUMENTS= COPYRIGHT INSTALL LICENSE README
+NO_STAGE= yes
do-install:
.for program in ${PROGRAMS}
(cd ${WRKSRC} && ${INSTALL_PROGRAM} ${program} ${PREFIX}/bin)
Modified: head/biology/muscle/Makefile
==============================================================================
--- head/biology/muscle/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/muscle/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: muscle
-# Date created: 6 December 2007
-# Whom: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
-#
+# Created by: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
# $FreeBSD$
-#
PORTNAME= muscle
PORTVERSION= 3.6
@@ -31,6 +27,7 @@ USE_DOS2UNIX= *.cpp
PLIST_FILES= bin/muscle
+NO_STAGE= yes
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/muscle ${PREFIX}/bin
.if !defined(NOPORTDOCS)
Modified: head/biology/ncbi-toolkit/Makefile
==============================================================================
--- head/biology/ncbi-toolkit/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/ncbi-toolkit/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -52,6 +52,7 @@ MLINKS= blast.1 bl2seq.1 blast.1 blasta
blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
blast.1 seedtop.1 blast.1 rpsblast.1
+NO_STAGE= yes
.include <bsd.port.options.mk>
post-patch:
Modified: head/biology/njplot/Makefile
==============================================================================
--- head/biology/njplot/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/njplot/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -31,6 +31,7 @@ PORTDOCS= njplot.help njplot.html njplot
MAN1= njplot.1 unrooted.1
.ifdef (WITHOUT_X11)
+NO_STAGE= yes
post-patch:
${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile
.endif
Modified: head/biology/ortep3/Makefile
==============================================================================
--- head/biology/ortep3/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/ortep3/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -28,6 +28,7 @@ PORTEXAMPLES= *
OPTIONS_DEFINE= DOCS EXAMPLES PGPLOT
PGPLOT_DESC= Fortran subroutine package for drawing graphs
+NO_STAGE= yes
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MPGPLOT}
Modified: head/biology/p5-AcePerl/Makefile
==============================================================================
--- head/biology/p5-AcePerl/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-AcePerl/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -41,6 +41,7 @@ MAN3= Ace.3 Ace::Browser::AceSubs.3 Ace
Ace::Sequence::Homol.3 Ace::Sequence::Multi.3 \
Ace::Sequence::Transcript.3
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "amd64" || ${ARCH} == "ia64"
Modified: head/biology/p5-Bio-ASN1-EntrezGene/Makefile
==============================================================================
--- head/biology/p5-Bio-ASN1-EntrezGene/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-ASN1-EntrezGene/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: biology/p5-Bio-ASN1-EntrezGene
-# Date created: 12 October 2005
-# Whom: Mauricio Herrera Cuadra <mauricio at arareko.net>
-#
+# Created by: Mauricio Herrera Cuadra <mauricio at arareko.net>
# $FreeBSD$
-#
PORTNAME= Bio-ASN1-EntrezGene
PORTVERSION= 1.091
@@ -25,4 +21,5 @@ MAN3= Bio::ASN1::EntrezGene.3 \
Bio::ASN1::Sequence.3 \
Bio::ASN1::Sequence::Indexer.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-Das-Lite/Makefile
==============================================================================
--- head/biology/p5-Bio-Das-Lite/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-Das-Lite/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,4 +21,5 @@ USE_PERL5= modbuild
MAN3= Bio::Das::Lite.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-Das/Makefile
==============================================================================
--- head/biology/p5-Bio-Das/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-Das/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -31,4 +31,5 @@ MAN3= Bio::Das.3 Bio::Das::AGPServer::Co
Bio::Das::Request::Types.3 Bio::Das::Segment.3 Bio::Das::Stylesheet.3 \
Bio::Das::Type.3 Bio::Das::TypeHandler.3 Bio::Das::Util.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-GFF3/Makefile
==============================================================================
--- head/biology/p5-Bio-GFF3/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-GFF3/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -27,4 +27,5 @@ MAN3= Bio::GFF3::LowLevel.3 \
Bio::GFF3::LowLevel::Parser::1_0_backcompat.3 \
Bio::GFF3::Transform::FromFasta.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-Glite/Makefile
==============================================================================
--- head/biology/p5-Bio-Glite/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-Glite/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -19,4 +19,5 @@ USE_PERL5= configure
MAN3= Bio::Glite.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-Graphics/Makefile
==============================================================================
--- head/biology/p5-Bio-Graphics/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-Graphics/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -128,4 +128,5 @@ MAN3= Bio::Graphics.3 \
Bio::Graphics::Wiggle.3 \
Bio::Graphics::Wiggle::Loader.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-MAGETAB/Makefile
==============================================================================
--- head/biology/p5-Bio-MAGETAB/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-MAGETAB/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -87,6 +87,7 @@ MAN3= Bio::MAGETAB.3 \
Bio::MAGETAB::Util::Writer::SDRF.3 \
Bio::MAGETAB::Util::Writer::Tabfile.3
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e '/^auto_install;/d' ${WRKSRC}/Makefile.PL
Modified: head/biology/p5-Bio-NEXUS/Makefile
==============================================================================
--- head/biology/p5-Bio-NEXUS/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-NEXUS/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -52,4 +52,5 @@ MAN3= Bio::NEXUS.3 \
Bio::NEXUS::Util::Logger.3 \
Bio::NEXUS::WeightSet.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-Bio-Phylo/Makefile
==============================================================================
--- head/biology/p5-Bio-Phylo/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-Phylo/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -148,6 +148,7 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::Util::StackTrace.3 \
Bio::PhyloRole.3
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e '/NAME/ s|Bio-Phylo|Bio::Phylo|' ${WRKSRC}/Makefile.PL
Modified: head/biology/p5-Bio-SCF/Makefile
==============================================================================
--- head/biology/p5-Bio-SCF/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-Bio-SCF/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,4 +21,5 @@ USE_PERL5= configure
MAN3= Bio::SCF.3
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/p5-bioperl-run/Makefile
==============================================================================
--- head/biology/p5-bioperl-run/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-bioperl-run/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: p5-bioperl-run
-# Date created: 21 February 2006
-# Whom: Mauricio Herrera Cuadra <mauricio at arareko.net>
-#
+# Created by: Mauricio Herrera Cuadra <mauricio at arareko.net>
# $FreeBSD$
-#
PORTNAME= bioperl-run
PORTVERSION= 1.6.1
@@ -132,6 +128,7 @@ MAN3= Bio::Tools::Run::Phylo::Phylip::Dr
Bio::Tools::Run::Phylo::Hyphy::FEL.3
# now install all extra stuff (docs, examples, scripts)
+NO_STAGE= yes
post-install:
${MKDIR} ${DATADIR}
@${CP} -Rv ${WRKSRC}/scripts ${DATADIR}
Modified: head/biology/p5-bioperl/Makefile
==============================================================================
--- head/biology/p5-bioperl/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/p5-bioperl/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -983,6 +983,7 @@ MAN3= Bio::Align::AlignI.3 \
Bio::WebAgent.3
# now install all extra stuff (docs, examples, scripts, models)
+NO_STAGE= yes
post-install:
${MKDIR} ${DATADIR}
${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
Modified: head/biology/paml/Makefile
==============================================================================
--- head/biology/paml/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/paml/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -17,6 +17,7 @@ MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
BINARIES= baseml basemlg chi2 codeml evolver pamp yn00
DOC_FILES= MCMCtreeDoc.pdf pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
+NO_STAGE= yes
do-install:
.for f in ${BINARIES}
${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
Modified: head/biology/phd2fasta/Makefile
==============================================================================
--- head/biology/phd2fasta/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/phd2fasta/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -25,6 +25,7 @@ PLIST_FILES= bin/phd2fasta
PORTDOCS= PHD2FASTA.DOC
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.for f in ${DISTFILES}
Modified: head/biology/phrap/Makefile
==============================================================================
--- head/biology/phrap/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/phrap/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: phrap
-# Date created: 21 June 2005
-# Whom: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
-#
+# Created by: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
# $FreeBSD$
-#
PORTNAME= phrap
PORTVERSION= 0.990329
@@ -35,6 +31,7 @@ PLIST_FILES+= bin/${f}
PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq
PORTDOCS= general.doc phrap.doc swat.doc
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.for f in ${DISTFILES}
Modified: head/biology/phred/Makefile
==============================================================================
--- head/biology/phred/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/phred/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: phred
-# Date created: 6 December 2007
-# Whom: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
-#
+# Created by: Motomichi Matsuzaki <mzaki at biol.s.u-tokyo.ac.jp>
# $FreeBSD$
-#
PORTNAME= phred
PORTVERSION= 0.020425.c
@@ -38,6 +34,7 @@ PORTDATA+= ${f}.dist
PORTDOCS= NEWS PHRED.DOC DAEV.DOC
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.for f in ${DISTFILES}
Modified: head/biology/phylip/Makefile
==============================================================================
--- head/biology/phylip/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/phylip/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -29,6 +29,7 @@ USE_LDCONFIG= yes
PORTDOCS= *
PORTEXAMPLES= *
+NO_STAGE= yes
.include <bsd.port.options.mk>
post-install:
Modified: head/biology/phyml/Makefile
==============================================================================
--- head/biology/phyml/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/phyml/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -24,6 +24,7 @@ AUTOMAKE_ARGS= --add-missing
PLIST_FILES= bin/phyml
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} -e \
'/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \
Modified: head/biology/platon/Makefile
==============================================================================
--- head/biology/platon/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/platon/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# New ports collection makefile for: platon
-# Date created: 1999-04-22
-# Whom: Ryo MIYAMOTO <rmiya at cc.hirosaki-u.ac.jp>
-#
+# Created by: Ryo MIYAMOTO <rmiya at cc.hirosaki-u.ac.jp>
# $FreeBSD$
-#
PORTNAME= platon
PORTVERSION= 2007.01.09
@@ -31,6 +27,7 @@ SAMPLES= azt.dat bucky.spf c476.spf c540
TESTDATADIR= ABSORB_EXAMPLE ABSTOMPA_EXAMPLE ABSTOMPA_TEST ADDSYM_EXAMPLE \
ASYM_EXAMPLE MULABS_EXAMPLE PSICOR_EXAMPLE SQUEEZE_EXAMPLE
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "alpha"
Modified: head/biology/plink/Makefile
==============================================================================
--- head/biology/plink/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/plink/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -20,6 +20,7 @@ USE_FORTRAN= yes # Make it use the same
PLIST_FILES= bin/plink
+NO_STAGE= yes
do-install:
${MKDIR} ${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin
Modified: head/biology/plinkseq/Makefile
==============================================================================
--- head/biology/plinkseq/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/plinkseq/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -19,6 +19,7 @@ USE_LDCONFIG= yes
GNU_CONFIGURE= yes
CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
+NO_STAGE= yes
post-patch:
${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c
${REINPLACE_CMD} -e 's|-ldl||g' \
Modified: head/biology/povchem/Makefile
==============================================================================
--- head/biology/povchem/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/povchem/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -27,6 +27,7 @@ CPPFLAGS+= -DDATADIR=\"${DATADIR}\" \
PLIST_FILES= bin/povchem etc/povchem.cfg %%DATADIR%%/periodic.tab
PLIST_DIRS= %%DATADIR%%
+NO_STAGE= yes
post-extract:
@(cd ${DISTDIR}/${DIST_SUBDIR} && ${TAR} -cf - ${DISTFILES}) | \
(cd ${WRKSRC} && ${TAR} -xf -)
Modified: head/biology/primer3/Makefile
==============================================================================
--- head/biology/primer3/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/primer3/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -16,6 +16,7 @@ MAKE_ARGS= CC=${CC} CPP=${CXX}
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
PLIST_FILES= bin/primer3
+NO_STAGE= yes
post-patch:
@${REINPLACE_CMD} \
-e 's#^CFLAGS.*#CFLAGS += \$$\(CC_OPTS\)#;' \
Modified: head/biology/protomol/Makefile
==============================================================================
--- head/biology/protomol/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/protomol/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -30,6 +30,7 @@ WRKSRC= ${WRKDIR}/${PORTNAME}
OPTIONS_DEFINE= GLUT
OPTIONS_DEFAULT= GLUT
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>
Modified: head/biology/psi88/Makefile
==============================================================================
--- head/biology/psi88/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/psi88/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -19,6 +19,7 @@ PORTEXAMPLES= *
OPTIONS_DEFINE= DOCS EXAMPLES
+NO_STAGE= yes
.include <bsd.port.pre.mk>
USE_FORTRAN= yes
Modified: head/biology/py-biopython/Makefile
==============================================================================
--- head/biology/py-biopython/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/py-biopython/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,4 +21,5 @@ PYEASYINSTALL_ARCHDEP= yes
RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}reportlab>0:${PORTSDIR}/print/py-reportlab
.endif
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/pycogent/Makefile
==============================================================================
--- head/biology/pycogent/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/pycogent/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,4 +21,5 @@ USE_PYTHON= yes
USE_PYDISTUTILS= yes
PYDISTUTILS_PKGNAME= cogent
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/pyfasta/Makefile
==============================================================================
--- head/biology/pyfasta/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/pyfasta/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -15,4 +15,5 @@ RUN_DEPENDS:= ${BUILD_DEPENDS}
USE_PYTHON= 2.5+
USE_PYDISTUTILS= easy_install
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/pymol/Makefile
==============================================================================
--- head/biology/pymol/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/pymol/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,7 +1,4 @@
-# New ports collection makefile for: pymol
-# Date created: July 18, 2002
-# Whom: Nakata Maho <chat95 at mbox.kyoto-inet.or.jp>
-#
+# Created by: Nakata Maho <chat95 at mbox.kyoto-inet.or.jp>
# $FreeBSD$
PORTNAME= pymol
@@ -29,6 +26,7 @@ USE_GMAKE= yes
USE_PYTHON= yes
PLIST_SUB= PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER}
+NO_STAGE= yes
pre-build:
@${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py
Modified: head/biology/python-nexus/Makefile
==============================================================================
--- head/biology/python-nexus/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/python-nexus/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -1,9 +1,5 @@
-# Ports collection makefile for: python-nexus
-# Date created: 29 Dec, 2009
-# Whom: Wen Heping <wen at FreeBSD.org>
-#
+# Created by: Wen Heping <wen at FreeBSD.org>
# $FreeBSD$
-#
PORTNAME= python-nexus
PORTVERSION= 0.87
@@ -16,4 +12,5 @@ COMMENT= A generic nexus file format rea
USE_PYTHON= yes
USE_PYDISTUTILS= easy_install
+NO_STAGE= yes
.include <bsd.port.mk>
Modified: head/biology/rasmol/Makefile
==============================================================================
--- head/biology/rasmol/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/rasmol/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -25,6 +25,7 @@ PLIST_FILES= bin/rasmol bin/rasmol-16 bi
lib/X11/rasmol/rasmol.hlp
PLIST_DIRS= lib/X11/rasmol
+NO_STAGE= yes
do-build:
${SETENV} ${MAKE_ENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer
Modified: head/biology/recombine/Makefile
==============================================================================
--- head/biology/recombine/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/recombine/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -19,6 +19,7 @@ PORTDOCS= recombine.txt
OPTIONS_DEFINE= DOCS
+NO_STAGE= yes
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
${INSTALL_SCRIPT} ${WRKSRC}/filetran ${PREFIX}/bin/
Modified: head/biology/ruby-bio/Makefile
==============================================================================
--- head/biology/ruby-bio/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/ruby-bio/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -21,6 +21,7 @@ OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNA
USE_RUBY= yes
USE_RUBY_SETUP= yes
+NO_STAGE= yes
.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>
Modified: head/biology/seaview/Makefile
==============================================================================
--- head/biology/seaview/Makefile Fri Sep 20 15:52:44 2013 (r327708)
+++ head/biology/seaview/Makefile Fri Sep 20 15:55:44 2013 (r327709)
@@ -35,6 +35,7 @@ PLIST_DIRS= %%DATADIR%%
DESKTOP_ENTRIES="SeaView" "${COMMENT}" "" \
"${PORTNAME}" "Biology;Science;" "true"
+NO_STAGE= yes
.include <bsd.port.options.mk>
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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