Date: Fri, 20 Sep 2013 15:55:44 +0000 (UTC) From: Baptiste Daroussin <bapt@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: 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... Message-ID: <201309201555.r8KFtiX6052145@svn.freebsd.org>
next in thread | raw e-mail | index | archive | help
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@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@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 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@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_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@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} \ 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@FreeBSD.org -# +# Created by: maho@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@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_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@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 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@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} 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@gmail.com> -# +# Created by: Yonatan <onatan@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@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-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@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 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@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) 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@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) 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@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> 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@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::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@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} 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@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 ${DISTFILES} Modified: head/biology/phylip/Makefile ============================================================================== --- head/biology/phylip/Makefile Fri Sep 20 15:52:44 2013 (r327708) +++ head/biology/phylip/Makefile Fri Sep 20 15:55:44 2013 (r327709) @@ -29,6 +29,7 @@ USE_LDCONFIG= yes PORTDOCS= * PORTEXAMPLES= * +NO_STAGE= yes .include <bsd.port.options.mk> post-install: Modified: head/biology/phyml/Makefile ============================================================================== --- head/biology/phyml/Makefile Fri Sep 20 15:52:44 2013 (r327708) +++ head/biology/phyml/Makefile Fri Sep 20 15:55:44 2013 (r327709) @@ -24,6 +24,7 @@ AUTOMAKE_ARGS= --add-missing PLIST_FILES= bin/phyml +NO_STAGE= yes post-patch: @${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@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 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@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 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@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 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 ***
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201309201555.r8KFtiX6052145>