diff options
| author | bapt <bapt@FreeBSD.org> | 2013-09-20 23:55:44 +0800 |
|---|---|---|
| committer | bapt <bapt@FreeBSD.org> | 2013-09-20 23:55:44 +0800 |
| commit | e0e72501367000f88aed7526756db60bf23087f3 (patch) | |
| tree | 8297dcd0b71086ee72b8499934378d51ab6f897f /biology | |
| parent | b715b89a1416d2148b4fef07ef9a3ce0c8e4d11d (diff) | |
| download | freebsd-ports-gnome-e0e72501367000f88aed7526756db60bf23087f3.tar.gz freebsd-ports-gnome-e0e72501367000f88aed7526756db60bf23087f3.tar.zst freebsd-ports-gnome-e0e72501367000f88aed7526756db60bf23087f3.zip | |
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
Diffstat (limited to 'biology')
94 files changed, 117 insertions, 114 deletions
diff --git a/biology/ariadne/Makefile b/biology/ariadne/Makefile index 44d41f2d4f55..4620887f1554 100644 --- a/biology/ariadne/Makefile +++ b/biology/ariadne/Makefile @@ -18,6 +18,7 @@ PORTDOCS= README OPTIONS_DEFINE= DOCS +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}| ; \ s|CC =|CC ?=| ; \ diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile index 880282b4ae6d..f665deffa161 100644 --- a/biology/artemis/Makefile +++ b/biology/artemis/Makefile @@ -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 {} + diff --git a/biology/avida/Makefile b/biology/avida/Makefile index acdf64508300..4d283832b17e 100644 --- a/biology/avida/Makefile +++ b/biology/avida/Makefile @@ -30,6 +30,7 @@ DATA_FILES= analyze.cfg avida.cfg default-gx.org \ 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" diff --git a/biology/babel/Makefile b/biology/babel/Makefile index 3e17f2f53f92..9bec6cbc8fa3 100644 --- a/biology/babel/Makefile +++ b/biology/babel/Makefile @@ -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 diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile index f8852192aa08..fa8e9f98e374 100644 --- a/biology/biococoa/Makefile +++ b/biology/biococoa/Makefile @@ -21,4 +21,5 @@ USE_GNUSTEP_INSTALL= yes WRKSRC= ${WRKDIR}/biococoa-${PORTVERSION} +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile index 1677031a5dbf..3115443baa3b 100644 --- a/biology/biojava/Makefile +++ b/biology/biojava/Makefile @@ -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) diff --git a/biology/blast/Makefile b/biology/blast/Makefile index 86680b36caa4..81bef22fa5b7 100644 --- a/biology/blast/Makefile +++ b/biology/blast/Makefile @@ -32,6 +32,7 @@ BLASTA_LINKS= blastn blastp blastx tblastn tblastx XDFORMAT_LINKS= setdb pressdb SUB_FILES= pkg-message +NO_STAGE= yes .include <bsd.port.pre.mk> .if ${ARCH} == amd64 diff --git a/biology/blat/Makefile b/biology/blat/Makefile index 6010ffc4bf0d..d887d1df9fc9 100644 --- a/biology/blat/Makefile +++ b/biology/blat/Makefile @@ -27,6 +27,7 @@ PORTDATA= * OPTIONS_DEFINE= DOCS +NO_STAGE= yes post-patch: @${MKDIR} ${WRKSRC}/bin/${ARCH} @${MKDIR} ${WRKSRC}/lib/${ARCH} diff --git a/biology/boinc-simap/Makefile b/biology/boinc-simap/Makefile index 955527e2e57d..01e50a7056ec 100644 --- a/biology/boinc-simap/Makefile +++ b/biology/boinc-simap/Makefile @@ -1,6 +1,5 @@ # Created by: Pav Lucistnik <pav@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} diff --git a/biology/chemeq/Makefile b/biology/chemeq/Makefile index 96888c38b509..ea6c4aa391a8 100644 --- a/biology/chemeq/Makefile +++ b/biology/chemeq/Makefile @@ -24,6 +24,7 @@ PORTEXAMPLES= chemreport chemreport.pl chemtest chemtest.pl test.stuff OPTIONS_DEFINE= DOCS EXAMPLES +NO_STAGE= yes .include <bsd.port.options.mk> do-install: diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index 24f5a2fde83b..3ddb03097b5f 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: clustalw -# Date created: 6 July 2000 -# Whom: dbader@eece.unm.edu -# +# Created by: dbader@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 diff --git a/biology/consed/Makefile b/biology/consed/Makefile index 9dc71cb3c238..93979f541942 100644 --- a/biology/consed/Makefile +++ b/biology/consed/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: phred -# Date created: 8 July 2005 -# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> -# +# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> # $FreeBSD$ -# PORTNAME= consed PORTVERSION= 16.0 @@ -62,6 +58,7 @@ EXAMPLES= standard autofinish assembly_view polyphred 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} ${CFLAGS} sff2scf.c -o sff2scf) diff --git a/biology/crux/Makefile b/biology/crux/Makefile index b5bda2d650eb..c0a7cbd0b49f 100644 --- a/biology/crux/Makefile +++ b/biology/crux/Makefile @@ -20,6 +20,7 @@ USE_PYTHON= 2.5+ OPTIONS_DEFINE= SYS_LINALG SYS_LINALG_DESC= Enable system ATLAS/LAPACK +NO_STAGE= yes .include <bsd.port.pre.mk> CPPFLAGS+= -I${LOCALBASE}/include diff --git a/biology/dotter/Makefile b/biology/dotter/Makefile index 7d4f14570e79..cdfdaf7792d2 100644 --- a/biology/dotter/Makefile +++ b/biology/dotter/Makefile @@ -1,4 +1,4 @@ -# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar> +# Created by: Fernan Aguero <fernan@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} \ diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile index 282860cda02b..6a3b695cffe5 100644 --- a/biology/embassy/Makefile +++ b/biology/embassy/Makefile @@ -74,6 +74,7 @@ EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEMENEW MSE PHYLIPNEW \ TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \ VIENNA MIRA IPRSCAN CBSTOOLS +NO_STAGE= yes .include <bsd.port.pre.mk> .include <bsd.port.options.mk> diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 997874ce9309..a44e339ab1a5 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -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} diff --git a/biology/fasta/Makefile b/biology/fasta/Makefile index cc33f3d61f25..ef539f2171aa 100644 --- a/biology/fasta/Makefile +++ b/biology/fasta/Makefile @@ -25,6 +25,7 @@ MLINKS= fasta.1 tfasta.1 fasta.1 lfasta.1 fasta.1 plfasta.1 \ OPTIONS_DEFINE= DOCS +NO_STAGE= yes do-extract: @ ${RM} -rf ${WRKDIR} @ ${MKDIR} ${WRKSRC} diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile index 1242345d8cc8..6415d90b8247 100644 --- a/biology/fasta3/Makefile +++ b/biology/fasta3/Makefile @@ -37,6 +37,7 @@ MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \ fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1 PLIST_SUB= VER=${PORTVERSION:R:R} +NO_STAGE= yes post-patch: @ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/ post-install: diff --git a/biology/fastdnaml/Makefile b/biology/fastdnaml/Makefile index 6b9c969ef438..4ed24a0d5de6 100644 --- a/biology/fastdnaml/Makefile +++ b/biology/fastdnaml/Makefile @@ -20,6 +20,7 @@ PORTDOCS= fastDNAml_doc_1.2.txt fastDNAml_scripts.txt OPTIONS_DEFINE= DOCS +NO_STAGE= yes .include <bsd.port.options.mk> do-install: diff --git a/biology/finchtv/Makefile b/biology/finchtv/Makefile index 8a3b19a01e01..f0fbf6bb57bc 100644 --- a/biology/finchtv/Makefile +++ b/biology/finchtv/Makefile @@ -18,6 +18,7 @@ NO_BUILD= yes SUB_FILES= pkg-message STRIP= +NO_STAGE= yes do-install: .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile index a222e959e781..727b6ddaca96 100644 --- a/biology/fluctuate/Makefile +++ b/biology/fluctuate/Makefile @@ -18,6 +18,7 @@ PORTDOCS= errors.doc fluctuate.doc OPTIONS_DEFINE= DOCS +NO_STAGE= yes do-install: @ ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/ diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile index 44dfe4068689..e6260cf07ed6 100644 --- a/biology/garlic/Makefile +++ b/biology/garlic/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: garlic -# Date created: 28 July 2003 -# Whom: maho@FreeBSD.org -# +# Created by: maho@FreeBSD.org # $FreeBSD$ -# PORTNAME= garlic PORTVERSION= 1.6 @@ -29,6 +25,7 @@ CFLAGS+= -mfancy-math-387 -mpreferred-stack-boundary=3 .endif # i386 .endif +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g ;\ s|%%CC%%|${CC}|g ; \ diff --git a/biology/genpak/Makefile b/biology/genpak/Makefile index a34caddd030f..c59485f5c7e1 100644 --- a/biology/genpak/Makefile +++ b/biology/genpak/Makefile @@ -1,10 +1,5 @@ -# ex:ts=8 -# New ports collection makefile for: genpak -# Date created: Feb 28, 2001 -# Whom: Ying-Chieh Liao <ijliao@FreeBSD.org> -# +# Created by: Ying-Chieh Liao <ijliao@FreeBSD.org> # $FreeBSD$ -# PORTNAME= genpak PORTVERSION= 0.26 @@ -31,4 +26,5 @@ MAN1= Genpak.1 gp_acc.1 gp_adjust.1 gp_cdndev.1 gp_cusage.1 gp_digest.1 \ INSTALL_TARGET= install docs .endif +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/gff2ps/Makefile b/biology/gff2ps/Makefile index c5073acc68f6..efb4b00f2392 100644 --- a/biology/gff2ps/Makefile +++ b/biology/gff2ps/Makefile @@ -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} diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile index 6c9fe208305c..7a4e678d1cd7 100644 --- a/biology/gmap/Makefile +++ b/biology/gmap/Makefile @@ -1,9 +1,5 @@ -# Ports collection makefile for: gmap -# Date created: 24 September 2006 -# Whom: Bob Zimmermann <rpz@cse.wustl.edu> -# +# Created by: Bob Zimmermann <rpz@cse.wustl.edu> # $FreeBSD$ -# PORTNAME= gmap PORTVERSION= 2006.04.21 @@ -17,4 +13,5 @@ COMMENT= A Genomic Mapping and Alignment Program for mRNA and EST Sequences USE_GMAKE= yes GNU_CONFIGURE= yes +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/gperiodic/Makefile b/biology/gperiodic/Makefile index 9d70d954fa0d..013af8531d21 100644 --- a/biology/gperiodic/Makefile +++ b/biology/gperiodic/Makefile @@ -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 diff --git a/biology/grappa/Makefile b/biology/grappa/Makefile index 2dc45814d54c..75554c818dbe 100644 --- a/biology/grappa/Makefile +++ b/biology/grappa/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: grappa -# Date created: 30 June 2001 -# Whom: dbader@ece.unm.edu -# +# Created by: dbader@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} diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile index b89ef0a3f5c8..5f48d163ccc7 100644 --- a/biology/hmmer/Makefile +++ b/biology/hmmer/Makefile @@ -24,6 +24,7 @@ EXAMPLES= 7LESS_DROME Pkinase.sto fn3.sto globins4.sto minifam.h3f minifam.h3p \ OPTIONS_DEFINE= PVM PVM_DESC= PVM support +NO_STAGE= yes .include <bsd.port.options.mk> .if ${PORT_OPTIONS:MPVM} diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile index 40e47c27dc92..c47066958bca 100644 --- a/biology/iolib/Makefile +++ b/biology/iolib/Makefile @@ -30,4 +30,5 @@ MAN3= read_scf_header.3 read_allocate.3 ExperimentFile.3 \ read2exp.3 fread_scf.3 MAN4= Read.4 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile index cccf2fa026ee..1135d0a92a13 100644 --- a/biology/jalview/Makefile +++ b/biology/jalview/Makefile @@ -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} ${DATADIR} diff --git a/biology/lagan/Makefile b/biology/lagan/Makefile index 8132c9422519..94992ee37f08 100644 --- a/biology/lagan/Makefile +++ b/biology/lagan/Makefile @@ -39,6 +39,7 @@ SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \ READMES= README.FIRST README.chaos README.lagan README.mlagan \ README.tools README.shuffle +NO_STAGE= yes post-patch: @${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \ '/^CC/s|^|#| ; \ diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile index a96e939ea102..288a2b767283 100644 --- a/biology/lamarc/Makefile +++ b/biology/lamarc/Makefile @@ -22,6 +22,7 @@ GNU_CONFIGURE= yes PORTDOCS= * PLIST_FILES= bin/${PORTNAME} +NO_STAGE= yes .include <bsd.port.options.mk> .if ${PORT_OPTIONS:MWXGTK} diff --git a/biology/libgenome/Makefile b/biology/libgenome/Makefile index 2bab38abe999..e8418c5ad2ac 100644 --- a/biology/libgenome/Makefile +++ b/biology/libgenome/Makefile @@ -22,6 +22,7 @@ USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e 's|-O2|@CXXFLAGS@|g' ${WRKSRC}/src/Makefile.in diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index ea6926109c35..7ca564480b09 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -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> diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index 417f87089a94..54ac1b8a267f 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -1,9 +1,5 @@ -# Ports collection makefile for: foldingathome -# Date created: 2/8/2006 -# Whom: Yonatan <onatan@gmail.com> -# +# Created by: Yonatan <onatan@gmail.com> # $FreeBSD$ -# PORTNAME= foldingathome PORTVERSION= 5.04 @@ -23,6 +19,7 @@ PLIST_FILES= share/${PORTNAME}/${DISTNAME}${EXTRACT_SUFX} \ bin/FoldingAtHome PLIST_DIRS= share/${PORTNAME} +NO_STAGE= yes do-extract: ${MKDIR} ${WRKSRC} ${CP} ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX} ${WRKSRC} diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile index 954937c8eef2..95c9055ff890 100644 --- a/biology/mafft/Makefile +++ b/biology/mafft/Makefile @@ -1,10 +1,5 @@ -# ex:ts=8 -# New ports collection makefile for: mafft -# Date created: 1 Feb 2006 -# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> -# +# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar> # $FreeBSD$ -# PORTNAME= mafft PORTVERSION= 6.903 @@ -37,6 +32,7 @@ LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \ 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" diff --git a/biology/mapm3/Makefile b/biology/mapm3/Makefile index cf5d4d61354d..bfcacc0a3418 100644 --- a/biology/mapm3/Makefile +++ b/biology/mapm3/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: mapm3 -# Date created: 26 March 2008 -# Whom: Tassilo Philipp <tphilipp@potion-studios.com> -# +# Created by: Tassilo Philipp <tphilipp@potion-studios.com> # $FreeBSD$ -# PORTNAME= mapm3 PORTVERSION= 3.0 @@ -21,6 +17,7 @@ COMMENT= Constructs linkage maps of markers segregating in experimental crosses NO_WRKSUBDIR= yes MAKE_JOBS_UNSAFE= yes +NO_STAGE= yes post-patch: ${CP} ${WRKSRC}/sun/* ${WRKSRC} diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile index 81feb424d647..098efac0bb95 100644 --- a/biology/migrate/Makefile +++ b/biology/migrate/Makefile @@ -22,6 +22,7 @@ PORTDOCS= * PORTEXAMPLES= * PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n +NO_STAGE= yes .include <bsd.port.options.mk> NOT_FOR_ARCHS= alpha diff --git a/biology/molden/Makefile b/biology/molden/Makefile index a0e9bdd0f466..47b601da582f 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -31,6 +31,7 @@ PORTDOCS= * PORTDATA= * PLIST_FILES= bin/ambfor bin/gmolden bin/molden bin/surf +NO_STAGE= yes .include <bsd.port.options.mk> post-patch: diff --git a/biology/mopac/Makefile b/biology/mopac/Makefile index dc1d46a02f6a..9d5c5c76a083 100644 --- a/biology/mopac/Makefile +++ b/biology/mopac/Makefile @@ -29,6 +29,7 @@ PORTEXAMPLES= * OPTIONS_DEFINE= EXAMPLES +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e '/pkgconfig/s|$$(libdir)|$$(prefix)/libdata|g' \ ${WRKSRC}/Makefile.am diff --git a/biology/mrbayes/Makefile b/biology/mrbayes/Makefile index 8b6d02774b56..a4da98f72ec9 100644 --- a/biology/mrbayes/Makefile +++ b/biology/mrbayes/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: mrbayes -# Date created: 11 December 2007 -# Whom: mzaki@biol.s.u-tokyo.ac.jp -# +# Created by: mzaki@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) diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index fa6324fb7a07..6879eb0929ec 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -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 mummerplot nucmer \ 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) diff --git a/biology/muscle/Makefile b/biology/muscle/Makefile index 7e716e11b54c..eb39f1a540bb 100644 --- a/biology/muscle/Makefile +++ b/biology/muscle/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: muscle -# Date created: 6 December 2007 -# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> -# +# Created by: Motomichi Matsuzaki <mzaki@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) diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index 1f5b7cf28ae5..7d396f94fd3a 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -52,6 +52,7 @@ MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ 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: diff --git a/biology/njplot/Makefile b/biology/njplot/Makefile index 03a9ed3d55d3..cab4713c7424 100644 --- a/biology/njplot/Makefile +++ b/biology/njplot/Makefile @@ -31,6 +31,7 @@ PORTDOCS= njplot.help njplot.html njplot.gif MAN1= njplot.1 unrooted.1 .ifdef (WITHOUT_X11) +NO_STAGE= yes post-patch: ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile .endif diff --git a/biology/ortep3/Makefile b/biology/ortep3/Makefile index 2738864608c6..86213775f337 100644 --- a/biology/ortep3/Makefile +++ b/biology/ortep3/Makefile @@ -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} diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile index d8707a71ce82..b50f77d6db7c 100644 --- a/biology/p5-AcePerl/Makefile +++ b/biology/p5-AcePerl/Makefile @@ -41,6 +41,7 @@ MAN3= Ace.3 Ace::Browser::AceSubs.3 Ace::Browser::SearchSubs.3 \ 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" diff --git a/biology/p5-Bio-ASN1-EntrezGene/Makefile b/biology/p5-Bio-ASN1-EntrezGene/Makefile index 11a94ac25c46..219287123d19 100644 --- a/biology/p5-Bio-ASN1-EntrezGene/Makefile +++ b/biology/p5-Bio-ASN1-EntrezGene/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: biology/p5-Bio-ASN1-EntrezGene -# Date created: 12 October 2005 -# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net> -# +# Created by: Mauricio Herrera Cuadra <mauricio@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> diff --git a/biology/p5-Bio-Das-Lite/Makefile b/biology/p5-Bio-Das-Lite/Makefile index 8b45ce3a499f..185d44ca21c7 100644 --- a/biology/p5-Bio-Das-Lite/Makefile +++ b/biology/p5-Bio-Das-Lite/Makefile @@ -21,4 +21,5 @@ USE_PERL5= modbuild MAN3= Bio::Das::Lite.3 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile index 27a3fda93f13..9877aa0468c5 100644 --- a/biology/p5-Bio-Das/Makefile +++ b/biology/p5-Bio-Das/Makefile @@ -31,4 +31,5 @@ MAN3= Bio::Das.3 Bio::Das::AGPServer::Config.3 Bio::Das::AGPServer::Daemon.3 \ 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> diff --git a/biology/p5-Bio-GFF3/Makefile b/biology/p5-Bio-GFF3/Makefile index 010ba01705c7..535053c0ccdb 100644 --- a/biology/p5-Bio-GFF3/Makefile +++ b/biology/p5-Bio-GFF3/Makefile @@ -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> diff --git a/biology/p5-Bio-Glite/Makefile b/biology/p5-Bio-Glite/Makefile index 87d806a97994..4f4ae3f0fd05 100644 --- a/biology/p5-Bio-Glite/Makefile +++ b/biology/p5-Bio-Glite/Makefile @@ -19,4 +19,5 @@ USE_PERL5= configure MAN3= Bio::Glite.3 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile index 6b0e1019cecd..7f92acae59db 100644 --- a/biology/p5-Bio-Graphics/Makefile +++ b/biology/p5-Bio-Graphics/Makefile @@ -128,4 +128,5 @@ MAN3= Bio::Graphics.3 \ Bio::Graphics::Wiggle.3 \ Bio::Graphics::Wiggle::Loader.3 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/p5-Bio-MAGETAB/Makefile b/biology/p5-Bio-MAGETAB/Makefile index 37d33cf68720..8b08469ad962 100644 --- a/biology/p5-Bio-MAGETAB/Makefile +++ b/biology/p5-Bio-MAGETAB/Makefile @@ -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' ${WRKSRC}/Makefile.PL diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile index 31a50449e440..e479cadfc206 100644 --- a/biology/p5-Bio-NEXUS/Makefile +++ b/biology/p5-Bio-NEXUS/Makefile @@ -52,4 +52,5 @@ MAN3= Bio::NEXUS.3 \ Bio::NEXUS::Util::Logger.3 \ Bio::NEXUS::WeightSet.3 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile index 90d546eaa382..ad88ec6ef496 100644 --- a/biology/p5-Bio-Phylo/Makefile +++ b/biology/p5-Bio-Phylo/Makefile @@ -148,6 +148,7 @@ MAN3= Bio::Phylo.3 \ Bio::Phylo::Util::StackTrace.3 \ Bio::PhyloRole.3 +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e '/NAME/ s|Bio-Phylo|Bio::Phylo|' ${WRKSRC}/Makefile.PL diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile index fc9ac1ff9afd..cd1931d3130d 100644 --- a/biology/p5-Bio-SCF/Makefile +++ b/biology/p5-Bio-SCF/Makefile @@ -21,4 +21,5 @@ USE_PERL5= configure MAN3= Bio::SCF.3 +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile index 80a257afce72..2227b8cbde04 100644 --- a/biology/p5-bioperl-run/Makefile +++ b/biology/p5-bioperl-run/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: p5-bioperl-run -# Date created: 21 February 2006 -# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net> -# +# Created by: Mauricio Herrera Cuadra <mauricio@arareko.net> # $FreeBSD$ -# PORTNAME= bioperl-run PORTVERSION= 1.6.1 @@ -132,6 +128,7 @@ MAN3= Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \ 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} diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile index d876b0575614..e48e04b7d8f2 100644 --- a/biology/p5-bioperl/Makefile +++ b/biology/p5-bioperl/Makefile @@ -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 ${DATADIR} diff --git a/biology/paml/Makefile b/biology/paml/Makefile index f4404bf85d84..5f982ec42193 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -17,6 +17,7 @@ MAKE_ARGS= CC="${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 diff --git a/biology/phd2fasta/Makefile b/biology/phd2fasta/Makefile index f376b2662e64..1301596f0719 100644 --- a/biology/phd2fasta/Makefile +++ b/biology/phd2fasta/Makefile @@ -25,6 +25,7 @@ PLIST_FILES= bin/phd2fasta PORTDOCS= PHD2FASTA.DOC +NO_STAGE= yes .include <bsd.port.pre.mk> .for f in ${DISTFILES} diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile index e3eb88633611..adb56a79cb9e 100644 --- a/biology/phrap/Makefile +++ b/biology/phrap/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: phrap -# Date created: 21 June 2005 -# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> -# +# Created by: Motomichi Matsuzaki <mzaki@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} diff --git a/biology/phred/Makefile b/biology/phred/Makefile index 91431de93669..99ab3f200deb 100644 --- a/biology/phred/Makefile +++ b/biology/phred/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: phred -# Date created: 6 December 2007 -# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> -# +# Created by: Motomichi Matsuzaki <mzaki@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 ${DISTFILES} diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index 9011687664f3..93af0d8eaa54 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -29,6 +29,7 @@ USE_LDCONFIG= yes PORTDOCS= * PORTEXAMPLES= * +NO_STAGE= yes .include <bsd.port.options.mk> post-install: diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile index ebcc40893cd7..1354621998f3 100644 --- a/biology/phyml/Makefile +++ b/biology/phyml/Makefile @@ -24,6 +24,7 @@ AUTOMAKE_ARGS= --add-missing PLIST_FILES= bin/phyml +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e \ '/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \ diff --git a/biology/platon/Makefile b/biology/platon/Makefile index aa579e47268e..640505ba9e5e 100644 --- a/biology/platon/Makefile +++ b/biology/platon/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: platon -# Date created: 1999-04-22 -# Whom: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> -# +# Created by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> # $FreeBSD$ -# PORTNAME= platon PORTVERSION= 2007.01.09 @@ -31,6 +27,7 @@ SAMPLES= azt.dat bucky.spf c476.spf c540.cart3d check.def cubane.spf \ 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" diff --git a/biology/plink/Makefile b/biology/plink/Makefile index 3972649775f7..7fac9fea37eb 100644 --- a/biology/plink/Makefile +++ b/biology/plink/Makefile @@ -20,6 +20,7 @@ USE_FORTRAN= yes # Make it use the same compiler as lapack PLIST_FILES= bin/plink +NO_STAGE= yes do-install: ${MKDIR} ${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin diff --git a/biology/plinkseq/Makefile b/biology/plinkseq/Makefile index d2ecf2352fd7..8d3b9caab28f 100644 --- a/biology/plinkseq/Makefile +++ b/biology/plinkseq/Makefile @@ -19,6 +19,7 @@ USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE} +NO_STAGE= yes post-patch: ${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c ${REINPLACE_CMD} -e 's|-ldl||g' \ diff --git a/biology/povchem/Makefile b/biology/povchem/Makefile index 4f44b747a8e0..e9f6802472df 100644 --- a/biology/povchem/Makefile +++ b/biology/povchem/Makefile @@ -27,6 +27,7 @@ CPPFLAGS+= -DDATADIR=\"${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} && ${TAR} -xf -) diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile index 217e7db3d458..23da9545a63b 100644 --- a/biology/primer3/Makefile +++ b/biology/primer3/Makefile @@ -16,6 +16,7 @@ MAKE_ARGS= CC=${CC} CPP=${CXX} WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src PLIST_FILES= bin/primer3 +NO_STAGE= yes post-patch: @${REINPLACE_CMD} \ -e 's#^CFLAGS.*#CFLAGS += \$$\(CC_OPTS\)#;' \ diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile index 3fe7f97fff3d..52e8e658299b 100644 --- a/biology/protomol/Makefile +++ b/biology/protomol/Makefile @@ -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> diff --git a/biology/psi88/Makefile b/biology/psi88/Makefile index fa1f901c4897..e9682ee96b9b 100644 --- a/biology/psi88/Makefile +++ b/biology/psi88/Makefile @@ -19,6 +19,7 @@ PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES +NO_STAGE= yes .include <bsd.port.pre.mk> USE_FORTRAN= yes diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index ffc13df67880..3ee5a58b0f20 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -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> diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile index 0f620c546a9b..affcfed4b520 100644 --- a/biology/pycogent/Makefile +++ b/biology/pycogent/Makefile @@ -21,4 +21,5 @@ USE_PYTHON= yes USE_PYDISTUTILS= yes PYDISTUTILS_PKGNAME= cogent +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/pyfasta/Makefile b/biology/pyfasta/Makefile index 38ebb8176646..6f628a0e09d2 100644 --- a/biology/pyfasta/Makefile +++ b/biology/pyfasta/Makefile @@ -15,4 +15,5 @@ RUN_DEPENDS:= ${BUILD_DEPENDS} USE_PYTHON= 2.5+ USE_PYDISTUTILS= easy_install +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index c2d28bdbd788..b57e88b617a9 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -1,7 +1,4 @@ -# New ports collection makefile for: pymol -# Date created: July 18, 2002 -# Whom: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> -# +# Created by: Nakata Maho <chat95@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 diff --git a/biology/python-nexus/Makefile b/biology/python-nexus/Makefile index 02c43c487e57..b2e2a9213dd1 100644 --- a/biology/python-nexus/Makefile +++ b/biology/python-nexus/Makefile @@ -1,9 +1,5 @@ -# Ports collection makefile for: python-nexus -# Date created: 29 Dec, 2009 -# Whom: Wen Heping <wen@FreeBSD.org> -# +# Created by: Wen Heping <wen@FreeBSD.org> # $FreeBSD$ -# PORTNAME= python-nexus PORTVERSION= 0.87 @@ -16,4 +12,5 @@ COMMENT= A generic nexus file format reader for python USE_PYTHON= yes USE_PYDISTUTILS= easy_install +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/rasmol/Makefile b/biology/rasmol/Makefile index 6e9bbe173788..bd1dd9ece9ac 100644 --- a/biology/rasmol/Makefile +++ b/biology/rasmol/Makefile @@ -25,6 +25,7 @@ PLIST_FILES= bin/rasmol bin/rasmol-16 bin/rasmol-32 bin/rasmol-8 \ lib/X11/rasmol/rasmol.hlp PLIST_DIRS= lib/X11/rasmol +NO_STAGE= yes do-build: ${SETENV} ${MAKE_ENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer diff --git a/biology/recombine/Makefile b/biology/recombine/Makefile index d60827a3a3c4..aeb27c53d208 100644 --- a/biology/recombine/Makefile +++ b/biology/recombine/Makefile @@ -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/ diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile index 436a34aff152..7d655897fa3e 100644 --- a/biology/ruby-bio/Makefile +++ b/biology/ruby-bio/Makefile @@ -21,6 +21,7 @@ OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNAME}/options USE_RUBY= yes USE_RUBY_SETUP= yes +NO_STAGE= yes .include <bsd.port.pre.mk> .include <bsd.port.options.mk> diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index de03867264db..ccb78d7e2b16 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -35,6 +35,7 @@ PLIST_DIRS= %%DATADIR%% DESKTOP_ENTRIES="SeaView" "${COMMENT}" "" \ "${PORTNAME}" "Biology;Science;" "true" +NO_STAGE= yes .include <bsd.port.options.mk> .if ${PORT_OPTIONS:MPDFLIB} diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile index ab38bc1812c5..462b57e59d9a 100644 --- a/biology/seqan/Makefile +++ b/biology/seqan/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: seqan -# Date created: 3 May 2012 -# Whom: h2 -# +# Created by: h2 # $FreeBSD$ -# PORTNAME= seqan PORTVERSION= 1.3.1 @@ -29,6 +25,7 @@ MAKE_JOB_SAFE= yes SUB_FILES= pkg-message PKG_MESSAGE= ${WRKDIR}/pkg-message +NO_STAGE= yes .include <bsd.port.pre.mk> .if ${ARCH} == i386 diff --git a/biology/seqio/Makefile b/biology/seqio/Makefile index 75a307c70efd..ad1cc5561560 100644 --- a/biology/seqio/Makefile +++ b/biology/seqio/Makefile @@ -22,6 +22,7 @@ PORTDOCS= * OPTIONS_DEFINE= DOCS EXAMPLES +NO_STAGE= yes .include <bsd.port.options.mk> do-install: diff --git a/biology/sim4/Makefile b/biology/sim4/Makefile index 235fb6fd2d4f..dc5087c67698 100644 --- a/biology/sim4/Makefile +++ b/biology/sim4/Makefile @@ -18,6 +18,7 @@ WRKSRC= ${WRKDIR}/sim4.${PORTVERSION:S/./-/g} ALL_TARGET= sim4 PLIST_FILES= bin/sim4 +NO_STAGE= yes post-patch: ${REINPLACE_CMD} -e 's|^CC=|CC?=|g ; \ s|^CFLAGS=|CFLAGS+=|g' ${WRKSRC}/Makefile diff --git a/biology/ssaha/Makefile b/biology/ssaha/Makefile index fa6a58b06cf1..3e050b5d1348 100644 --- a/biology/ssaha/Makefile +++ b/biology/ssaha/Makefile @@ -21,6 +21,7 @@ ALL_TARGET= ssaha DATA_FILES= test.fasta test_extract.fasta test_filter.fail \ test_filter.fastq test_protein.fasta README +NO_STAGE= yes do-install: ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/ssaha ${PREFIX}/bin @${MKDIR} ${DATADIR} diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile index 1abcbce8aacf..02ea508f3554 100644 --- a/biology/tRNAscan-SE/Makefile +++ b/biology/tRNAscan-SE/Makefile @@ -24,6 +24,7 @@ PORTDOCS= Manual.ps OPTIONS_DEFINE= DOCS +NO_STAGE= yes post-patch: @${REINPLACE_CMD} -e 's|tRNAscanSE setpaths|tRNAscanSE|g ; \ s|if tRNAscan-SE|if ./tRNAscan-SE|g' ${WRKSRC}/Makefile diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile index cac221e8a045..d73d922f8dc9 100644 --- a/biology/t_coffee/Makefile +++ b/biology/t_coffee/Makefile @@ -27,6 +27,7 @@ MAKEFILE= makefile PORTEXAMPLES= * PLIST_FILES= bin/TMalign bin/t_coffee +NO_STAGE= yes .include <bsd.port.options.mk> do-install: diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index 29705bcb3d2d..b73d044d955e 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -27,6 +27,7 @@ INSTALL_TARGET= rename SUB_FILES= pkg-message +NO_STAGE= yes .include <bsd.port.pre.mk> .if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} diff --git a/biology/treepuzzle/Makefile b/biology/treepuzzle/Makefile index 365e42ae21f6..0f16bbd98629 100644 --- a/biology/treepuzzle/Makefile +++ b/biology/treepuzzle/Makefile @@ -1,9 +1,5 @@ -# Ports collection makefile for: treepuzzle -# Date created: 26 August 2002 -# Whom: lentferj -# +# Created by: lentferj # $FreeBSD$ -# PORTNAME= treepuzzle PORTVERSION= 5.2 @@ -17,6 +13,7 @@ COMMENT= Maximum likelihood phylogeny reconstruction using quartets GNU_CONFIGURE= yes PLIST_FILES= bin/puzzle +NO_STAGE= yes pre-configure: @${ECHO_MSG} "---------------------------------------------" @${ECHO_MSG} "" diff --git a/biology/treeviewx/Makefile b/biology/treeviewx/Makefile index e4644088d39b..61ec1a3e422e 100644 --- a/biology/treeviewx/Makefile +++ b/biology/treeviewx/Makefile @@ -18,4 +18,5 @@ GNU_CONFIGURE= yes PLIST_FILES= bin/tv +NO_STAGE= yes .include <bsd.port.mk> diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index ec2b37eee708..324afd10c12a 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -25,6 +25,7 @@ INSTALLS_ICONS= yes MAN1= ${PORTNAME}.1 MANCOMPRESSED= yes +NO_STAGE= yes .include <bsd.port.pre.mk> .if ${ARCH} == "amd64" diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile index de5eae20a9c6..5287ed1022da 100644 --- a/biology/velvet/Makefile +++ b/biology/velvet/Makefile @@ -1,9 +1,5 @@ -# New ports collection makefile for: velvet -# Date created: 27 Oct 2009 -# Whom: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> -# +# Created by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> # $FreeBSD$ -# PORTNAME= velvet PORTVERSION= 1.1.04 @@ -62,6 +58,7 @@ PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T} PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf +NO_STAGE= yes post-patch: .for f in ${SCRIPTS} ${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f} diff --git a/biology/wise/Makefile b/biology/wise/Makefile index 9eab34677e27..a6af80d84a0c 100644 --- a/biology/wise/Makefile +++ b/biology/wise/Makefile @@ -43,6 +43,7 @@ DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \ human.stats idenity.bla methods pb.gf pombe.gf tm.pri \ wise.2 wise.per worm.gf +NO_STAGE= yes .include <bsd.port.options.mk> post-patch: diff --git a/biology/xmolwt/Makefile b/biology/xmolwt/Makefile index 52edde304bbd..45c2a6e599eb 100644 --- a/biology/xmolwt/Makefile +++ b/biology/xmolwt/Makefile @@ -19,6 +19,7 @@ ALL_TARGET= gmolwt PORTDOCS= * PLIST_FILES= bin/gmolwt bin/molwt +NO_STAGE= yes .include <bsd.port.options.mk> .if ${PORT_OPTIONS:MGTK2} |