Date: Mon, 23 Feb 2009 12:07:01 -0200 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/132007: [maintainer-update] update biology/fasta3 Message-ID: <520894aa0902230607y767fad7cr2acd66c61224d163@mail.gmail.com> Resent-Message-ID: <200902231410.n1NEA4wI099119@freefall.freebsd.org>
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>Number: 132007 >Category: ports >Synopsis: [maintainer-update] update biology/fasta3 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Mon Feb 23 14:10:04 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.3-RELEASE-p1 i386 >Organization: IIB-UNSAM >Environment: FreeBSD gama.iib.unsam.edu.ar 6.3-RELEASE-p1 FreeBSD 6.3-RELEASE-p1 #0: Wed Apr 2 18:37:14 ART 2008 fernan@gama.iib.unsam.edu.ar:/usr/obj/freebsd/freebsd-6.3/src/sys/GAMA i386 <machine, os, target, libraries (multiple lines)> >Description: <precise description of the problem (multiple lines)> Update fasta3 to the latest release >How-To-Repeat: <code/input/activities to reproduce the problem (multiple lines)> >Fix: <how to correct or work around the problem, if known (multiple lines)> --- fasta3.diff begins here --- diff -ruN --exclude CVS /usr/ports/biology/fasta3/Makefile fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile 2008-04-17 09:50:40.000000000 -0300 +++ fasta3/Makefile 2009-02-23 11:03:04.000000000 -0300 @@ -7,7 +7,7 @@ # PORTNAME= fasta3 -PORTVERSION= 35.3.6 +PORTVERSION= 35.4.4 CATEGORIES= biology MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta3/ DISTNAME= fasta-${PORTVERSION} @@ -17,6 +17,8 @@ NO_CDROM= May not be sold or incorporated into a commercial product WRKSRC= ${WRKDIR}/${DISTNAME} +BUILD_WRKSRC= ${WRKSRC}/src +INSTALL_WRKSRC= ${BUILD_WRKSRC} SUB_FILES= pkg-message MAKEFILE= Makefile.freebsd @@ -26,19 +28,26 @@ MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \ FASTA_HOST='"${FASTA_HOST}"' -FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \ - fasta20.doc fasta_func.doc readme.* fasta.defaults -DATA= *.mat -EXAMPLES= *.aa *.lc *.seq - -MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1 -MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \ - fasta3.1 fasty3.1 fasta3.1 tfasty3.1 fasta3.1 ssearch3.1 \ - fastf3.1 tfastf3.1 fasts3.1 tfasts3.1 +FASTA3_DOCS= README.versions fasta3x.me fasta3x.doc \ + fasta20.doc fasta_func.doc readme.* fasta.defaults \ + fasta.options fasta_versions.html changes*.html +DATA= data/*.mat +EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib + +MAN1= fasta35.1 fastf3.1 fasts3.1 map_db.1 prss3.1 ps_lav.1 \ + pvcomp.1 +MLINKS= fasta35.1 tfasta35.1 fasta35.1 fastx35.1 fasta35.1 tfastx35.1 \ + fasta35.1 fasty35.1 fasta35.1 tfasty35.1 fasta35.1 ssearch35.1 \ + fasta35.1 fastf35.1 fasta35.1 fasts35.1 fasta35.1 tfasts35.1 \ + fasta35.1 fastm35.1 fasta35.1 fastf35.1 fasta35.1 ggsearch35.1 \ + fasta35.1 lalign35.1 fasta35.1 prss35.1 fasta35.1 prfx35.1 PLIST_SUB= VER=${PORTVERSION:R:R} +post-patch: + @ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/ post-install: - ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample + ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/ + ${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample @ ${MKDIR} ${DATADIR} .for data in ${DATA} ${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR} @@ -48,12 +57,15 @@ ${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR} .endfor .for manpage in ${MAN1} - @ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/ + @ ${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/ .endfor .if !defined(NOPORTDOCS) @ ${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR} .for docfile in ${FASTA3_DOCS} - @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR} + @ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR} .endfor .endif @ ${CAT} ${PKGMESSAGE} diff -ruN --exclude CVS /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo 2008-04-17 09:50:40.000000000 -0300 +++ fasta3/distinfo 2009-02-22 23:27:01.000000000 -0300 @@ -1,3 +1,3 @@ -MD5 (fasta-35.3.6.tar.gz) = d324f94fc90a78e7d0c8d97bacdd448a -SHA256 (fasta-35.3.6.tar.gz) = 4525232e2a1a42388921760d75c5ece6e058d9ce2c35cba074ce544d6e56df15 -SIZE (fasta-35.3.6.tar.gz) = 614606 +MD5 (fasta-35.4.4.tar.gz) = a96d498fc548c8b65b07f13b9548a36d +SHA256 (fasta-35.4.4.tar.gz) = 744911dd6524e57f63c32d76016bd071e16b7c39c34277b2a4d79a601e74d258 +SIZE (fasta-35.4.4.tar.gz) = 612851 diff -ruN --exclude CVS /usr/ports/biology/fasta3/files/patch-Makefile.pcom fasta3/files/patch-Makefile.pcom --- /usr/ports/biology/fasta3/files/patch-Makefile.pcom 1969-12-31 21:00:00.000000000 -0300 +++ fasta3/files/patch-Makefile.pcom 2009-02-22 23:57:42.000000000 -0300 @@ -0,0 +1,11 @@ +--- make/Makefile.pcom.orig 2009-02-22 23:56:26.000000000 -0300 ++++ make/Makefile.pcom 2009-02-22 23:57:17.000000000 -0300 +@@ -42,7 +42,7 @@ + rm -f *.o $(PROGS) $(APROGS); rm -rf $(BIN)/* + + install: $(PROGS) +- pushd $(BIN); cp $(PROGS) $(XDIR); popd ++ cd $(BIN); cp $(PROGS) $(XDIR); cd ../src + + uinstall: $(PROGS) + pushd $(BIN); mv $(PROGS) $(UDIR); popd diff -ruN --exclude CVS /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist --- /usr/ports/biology/fasta3/pkg-plist 2008-04-17 09:50:40.000000000 -0300 +++ fasta3/pkg-plist 2009-02-23 11:05:40.000000000 -0300 @@ -17,6 +17,7 @@ bin/lalign%%VER%% bin/lav2ps bin/lav2svg +bin/map_db bin/ssearch%%VER%% bin/ssearch%%VER%%_t bin/tfastf%%VER%% @@ -32,6 +33,7 @@ %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST +%%PORTDOCS%%%%DOCSDIR%%/README.versions %%PORTDOCS%%%%DOCSDIR%%/fasta3x.me %%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc %%PORTDOCS%%%%DOCSDIR%%/fasta20.doc @@ -51,25 +53,21 @@ %%PORTDOCS%%%%DOCSDIR%%/readme.v35 %%PORTDOCS%%%%DOCSDIR%%/readme.w32 %%PORTDOCS%%%%DOCSDIR%%/fasta.defaults -%%EXAMPLESDIR%%/bovgh.seq -%%EXAMPLESDIR%%/bovprl.seq +%%PORTDOCS%%%%DOCSDIR%%/fasta.options +%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html %%EXAMPLESDIR%%/egmsmg.aa -%%EXAMPLESDIR%%/gst.seq %%EXAMPLESDIR%%/gstt1_drome.aa %%EXAMPLESDIR%%/gtm1_human.aa %%EXAMPLESDIR%%/gtt1_drome.aa %%EXAMPLESDIR%%/h10_human.aa %%EXAMPLESDIR%%/hahu.aa -%%EXAMPLESDIR%%/hsgstm1b.seq -%%EXAMPLESDIR%%/humgstd.seq %%EXAMPLESDIR%%/lcbo.aa %%EXAMPLESDIR%%/m1r.aa %%EXAMPLESDIR%%/m2.aa %%EXAMPLESDIR%%/mchu.aa %%EXAMPLESDIR%%/mgstm1.aa -%%EXAMPLESDIR%%/mgstm1.lc -%%EXAMPLESDIR%%/mgstm1.seq -%%EXAMPLESDIR%%/mgtt2_x.seq %%EXAMPLESDIR%%/ms1.aa %%EXAMPLESDIR%%/musplfm.aa %%EXAMPLESDIR%%/mwkw.aa @@ -86,10 +84,22 @@ %%EXAMPLESDIR%%/prio_atepa.aa %%EXAMPLESDIR%%/qrhuld.aa %%EXAMPLESDIR%%/titin_hum.aa -%%EXAMPLESDIR%%/titin_hum.seq %%EXAMPLESDIR%%/xurt8c.aa -%%EXAMPLESDIR%%/xurt8c.lc %%EXAMPLESDIR%%/xurtg.aa +%%EXAMPLESDIR%%/mgstm1.lc +%%EXAMPLESDIR%%/xurt8c.lc +%%EXAMPLESDIR%%/bovgh.seq +%%EXAMPLESDIR%%/bovprl.seq +%%EXAMPLESDIR%%/gst.seq +%%EXAMPLESDIR%%/hsgstm1b.seq +%%EXAMPLESDIR%%/humgstd.seq +%%EXAMPLESDIR%%/mgstm1.seq +%%EXAMPLESDIR%%/mgtt2_x.seq +%%EXAMPLESDIR%%/titin_hum.seq +%%EXAMPLESDIR%%/mu.lib +%%EXAMPLESDIR%%/n2_fs.lib +%%EXAMPLESDIR%%/n_fs.lib +%%EXAMPLESDIR%%/prot_test.lib %%DATADIR%%/blosum45.mat %%DATADIR%%/blosum50.mat %%DATADIR%%/blosum62.mat --- fasta3.diff ends here --- -- fernan >Release-Note: >Audit-Trail: >Unformatted:
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