update to latest release. Fix: diff -ruN --exclude=CVS /usr/ports/biology/emboss/Makefile emboss/Makefile --- /usr/ports/biology/emboss/Makefile Mon Jun 18 20:28:09 2007 +++ emboss/Makefile Fri Aug 17 12:05:27 2007 @@ -6,26 +6,20 @@ # PORTNAME= emboss -PORTVERSION= 3.0.0 -PORTREVISION= 1 +PORTVERSION= 5.0.0 +RELEASE= ${PORTNAME:U}-${PORTVERSION} CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \ - ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ - ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ -DISTNAME= ${PORTNAME:U}-${PORTVERSION} -DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} +DISTNAME= ${RELEASE} +DISTFILES= ${RELEASE}${EXTRACT_SUFX} DIST_SUBDIR= ${PORTNAME} -PATCH_WRKSRC= ${WRKDIR} - MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A collection of open source tools for genetic sequence analysis BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \ primer3:${PORTSDIR}/biology/primer3 -LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \ - png.5:${PORTSDIR}/graphics/png CONFLICTS= qmail-ldap-[0-9]* digest-[0-9]* @@ -41,20 +35,21 @@ SUB_FILES= pkg-message SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR} -DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U} +DOCSDIR= ${PREFIX}/share/${PORTNAME:U}/doc DATADIR= ${PREFIX}/share/${PORTNAME:U} -DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html -CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template +CONFIGURE_ARGS+= --with-docroot=${DOCSDIR} -post-patch: -.if !defined(NOPORTDOCS) -.for DIR in ${DOC_DIRS} - @ ${REINPLACE_CMD} -e \ - 's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \ - ${WRKSRC}/${DIR}/Makefile.in -.endfor +.if defined(WITHOUT_X11) +USE_XLIB= yes +USE_MOTIF= yes +LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \ + png.5:${PORTSDIR}/graphics/png +CONFIGURE_ARGS+= --without-x .endif + +DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html +CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template pre-install: @ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE} diff -ruN --exclude=CVS /usr/ports/biology/emboss/distinfo emboss/distinfo --- /usr/ports/biology/emboss/distinfo Fri Mar 31 06:43:20 2006 +++ emboss/distinfo Fri Jul 20 23:38:22 2007 @@ -1,3 +1,3 @@ -MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc -SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea -SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908 +MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b +SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae +SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560 diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-descr emboss/pkg-descr --- /usr/ports/biology/emboss/pkg-descr Fri Aug 3 08:32:41 2001 +++ emboss/pkg-descr Wed Feb 7 11:49:31 2007 @@ -12,12 +12,8 @@ EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution -for licensing or other reasons. This port includes the currently available -EMBASSY applications. During an interactive install the user will be asked -to choose which of these will be installed (default: all). Note that the -EMBASSY versions of PHYLIP and HMMER should not clash with the standalone -versions (also in ports/biology) due to the fact that their binaries have been -renamed. +for licensing or other reasons. The EMBASSY packages live in the +biology/embassy port. WWW: http://www.emboss.org/ diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist --- /usr/ports/biology/emboss/pkg-plist Fri Mar 31 06:43:20 2006 +++ emboss/pkg-plist Fri Aug 17 11:07:25 2007 @@ -6,6 +6,7 @@ bin/acdtrace bin/acdvalid bin/antigenic +bin/backtranambig bin/backtranseq bin/banana bin/biosed @@ -43,6 +44,7 @@ bin/dotpath bin/dottup bin/dreg +bin/edialign bin/einverted bin/embossdata bin/embossversion @@ -54,6 +56,7 @@ bin/equicktandem bin/est2genome bin/etandem +bin/extractalign bin/extractfeat bin/extractseq bin/findkm @@ -73,6 +76,8 @@ bin/jembossctl bin/lindna bin/listor +bin/makenucseq +bin/makeprotseq bin/marscan bin/maskfeat bin/maskseq @@ -138,11 +143,11 @@ bin/sirna bin/sixpack bin/skipseq -bin/syco bin/splitter bin/stretcher bin/stssearch bin/supermatcher +bin/syco bin/tcode bin/textsearch bin/tfextract @@ -160,22 +165,29 @@ bin/whichdb bin/wobble bin/wordcount +bin/wordfinder bin/wordmatch bin/wossname bin/yank bin/runJemboss.csh -include/drivers.h -include/pdf.h -include/plcore.h -include/plevent.h -include/plplotP.h -include/plxwd.h -include/metadefs.h -include/plConfig.h -include/pldebug.h -include/plplot.h -include/plstrm.h -include/plDevs.h +include/eplplot/drivers.h +include/eplplot/pdf.h +include/eplplot/plcore.h +include/eplplot/plevent.h +include/eplplot/plplotP.h +include/eplplot/plxwd.h +include/eplplot/metadefs.h +include/eplplot/plConfig.h +include/eplplot/pldebug.h +include/eplplot/plplot.h +include/eplplot/plstrm.h +include/eplplot/plDevs.h +include/eplplot/disptab.h +include/eplplot/pldll.h +include/eplplot/plhershey-unicode.h +include/eplplot/ps.h +include/eplplot/plunicode-type1.h +include/eplplot/plfci-type1.h include/ajax.h include/ajarch.h include/ajdefine.h @@ -188,6 +200,7 @@ include/ajcod.h include/ajdan.h include/ajdmx.h +include/ajdom.h include/ajdomain.h include/ajexcept.h include/ajfeat.h @@ -207,6 +220,7 @@ include/ajmess.h include/ajnam.h include/ajnexus.h +include/ajpat.h 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-%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz %%DATADIR%%/plstnd5.fnt %%DATADIR%%/plxtnd5.fnt %%DATADIR%%/acd/needle.acd @@ -977,6 +304,8 @@ %%DATADIR%%/acd/nthseq.acd %%DATADIR%%/acd/octanol.acd %%DATADIR%%/acd/oddcomp.acd +%%DATADIR%%/acd/origsplitter.acd +%%DATADIR%%/acd/origunion.acd %%DATADIR%%/acd/palindrome.acd %%DATADIR%%/acd/pasteseq.acd %%DATADIR%%/acd/patmatdb.acd @@ -1010,8 +339,8 @@ %%DATADIR%%/acd/redata.acd %%DATADIR%%/acd/remap.acd %%DATADIR%%/acd/restover.acd -%%DATADIR%%/acd/revseq.acd %%DATADIR%%/acd/restrict.acd +%%DATADIR%%/acd/revseq.acd %%DATADIR%%/acd/seealso.acd %%DATADIR%%/acd/seqinfo.acd %%DATADIR%%/acd/seqmatchall.acd @@ -1057,11 +386,13 @@ %%DATADIR%%/acd/whichdb.acd %%DATADIR%%/acd/wobble.acd %%DATADIR%%/acd/wordcount.acd +%%DATADIR%%/acd/wordfinder.acd %%DATADIR%%/acd/wordmatch.acd %%DATADIR%%/acd/wossname.acd %%DATADIR%%/acd/yank.acd %%DATADIR%%/acd/codes.english %%DATADIR%%/acd/groups.standard +%%DATADIR%%/acd/keywords.standard %%DATADIR%%/acd/knowntypes.standard %%DATADIR%%/acd/sections.standard %%DATADIR%%/acd/variables.standard @@ -1077,11 +408,12 @@ %%DATADIR%%/acd/ajfeatest.acd %%DATADIR%%/acd/ajtest.acd %%DATADIR%%/acd/antigenic.acd +%%DATADIR%%/acd/backtranambig.acd %%DATADIR%%/acd/backtranseq.acd -%%DATADIR%%/acd/cai.acd %%DATADIR%%/acd/banana.acd %%DATADIR%%/acd/biosed.acd %%DATADIR%%/acd/btwisted.acd +%%DATADIR%%/acd/cai.acd %%DATADIR%%/acd/chaos.acd %%DATADIR%%/acd/charge.acd %%DATADIR%%/acd/checktrans.acd @@ -1107,6 +439,7 @@ %%DATADIR%%/acd/dbxfasta.acd %%DATADIR%%/acd/dbxflat.acd %%DATADIR%%/acd/dbxgcg.acd +%%DATADIR%%/acd/dbxstat.acd %%DATADIR%%/acd/degapseq.acd %%DATADIR%%/acd/demoalign.acd %%DATADIR%%/acd/demofeatures.acd @@ -1114,6 +447,7 @@ %%DATADIR%%/acd/demoreport.acd %%DATADIR%%/acd/demosequence.acd %%DATADIR%%/acd/demostring.acd +%%DATADIR%%/acd/demostringnew.acd %%DATADIR%%/acd/demotable.acd %%DATADIR%%/acd/descseq.acd %%DATADIR%%/acd/diffseq.acd @@ -1123,9 +457,9 @@ %%DATADIR%%/acd/dotpath.acd %%DATADIR%%/acd/dottup.acd %%DATADIR%%/acd/dreg.acd +%%DATADIR%%/acd/edialign.acd %%DATADIR%%/acd/einverted.acd %%DATADIR%%/acd/embossdata.acd -%%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/embossversion.acd %%DATADIR%%/acd/emma.acd %%DATADIR%%/acd/emowse.acd @@ -1136,6 +470,7 @@ %%DATADIR%%/acd/equicktandem.acd %%DATADIR%%/acd/est2genome.acd %%DATADIR%%/acd/etandem.acd +%%DATADIR%%/acd/extractalign.acd %%DATADIR%%/acd/extractfeat.acd %%DATADIR%%/acd/extractseq.acd %%DATADIR%%/acd/findkm.acd @@ -1148,16 +483,17 @@ %%DATADIR%%/acd/getorf.acd %%DATADIR%%/acd/giep.acd %%DATADIR%%/acd/helixturnhelix.acd -%%DATADIR%%/acd/hmoment.acd %%DATADIR%%/acd/histogramtest.acd +%%DATADIR%%/acd/hmoment.acd +%%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/infoalign.acd %%DATADIR%%/acd/infoseq.acd %%DATADIR%%/acd/intconv.acd %%DATADIR%%/acd/isochore.acd -%%DATADIR%%/acd/kmrsplitter.acd -%%DATADIR%%/acd/kmrunion.acd %%DATADIR%%/acd/lindna.acd %%DATADIR%%/acd/listor.acd +%%DATADIR%%/acd/makenucseq.acd +%%DATADIR%%/acd/makeprotseq.acd %%DATADIR%%/acd/marscan.acd %%DATADIR%%/acd/maskfeat.acd %%DATADIR%%/acd/maskseq.acd @@ -1526,6 +862,8 @@ %%DATADIR%%/data/Efeatures.embl %%DATADIR%%/data/Efeatures.emboss %%DATADIR%%/data/Efeatures.gff +%%DATADIR%%/data/Efeatures.gff3 +%%DATADIR%%/data/Efeatures.gffprotein %%DATADIR%%/data/Efeatures.pir %%DATADIR%%/data/Efeatures.protein %%DATADIR%%/data/Efeatures.swiss @@ -1546,6 +884,8 @@ 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+%%DATADIR%%/test/data/104k.nbrf %%DATADIR%%/test/data/aligna.dna %%DATADIR%%/test/data/alignapart.dna %%DATADIR%%/test/data/alignb.dna %%DATADIR%%/test/data/aligna.prot %%DATADIR%%/test/data/alignapart.prot %%DATADIR%%/test/data/alignb.prot +%%DATADIR%%/test/data/nucseq.pat +%%DATADIR%%/test/data/nucsimple.pat %%DATADIR%%/test/data/tranalign.pep %%DATADIR%%/test/data/tranalign.seq +%%DATADIR%%/test/data/vtest.seq +%%DATADIR%%/test/data/opsd.msf +%%DATADIR%%/test/data/untrimmed.seq %%DATADIR%%/test/embl/acnum.hit %%DATADIR%%/test/embl/acnum.trg %%DATADIR%%/test/embl/division.lkp @@ -1670,22 +1021,6 @@ %%DATADIR%%/test/genbank/gbsts1.seq %%DATADIR%%/test/genbank/gbvrl1.seq %%DATADIR%%/test/genbank/gbvrt.seq -%%DATADIR%%/test/gb/acnum.hit -%%DATADIR%%/test/gb/acnum.trg -%%DATADIR%%/test/gb/division.lkp -%%DATADIR%%/test/gb/entrynam.idx -%%DATADIR%%/test/gb/seqvn.hit -%%DATADIR%%/test/gb/seqvn.trg -%%DATADIR%%/test/gb/des.hit -%%DATADIR%%/test/gb/des.trg -%%DATADIR%%/test/gb/keyword.hit 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Responsible Changed From-To: freebsd-ports-bugs->rafan I'll take it.
State Changed From-To: open->feedback There are patches failed during make patch. Please look at it and submit a new diff. Thanks!
> There are patches failed during make patch. Please look at it and > submit a new diff. Thanks! Let me know if it's fixed now. Thanks! -- fernan
On Sat, Apr 05, 2008 at 10:43:14AM -0300, Fernan Aguero wrote: > > There are patches failed during make patch. Please look at it and > > submit a new diff. Thanks! > > Let me know if it's fixed now. Thanks! $ make patch ===> Extracting for emboss-5.0.0 => MD5 Checksum OK for emboss/EMBOSS-5.0.0.tar.gz. => SHA256 Checksum OK for emboss/EMBOSS-5.0.0.tar.gz. ===> Patching for emboss-5.0.0 ===> Applying FreeBSD patches for emboss-5.0.0 Ignoring previously applied (or reversed) patch. 32 out of 32 hunks ignored--saving rejects to ajax/ajindex.c.rej => Patch patch-ajindex.c failed to apply cleanly. *** Error code 1 Stop in /home/rafan/work/FreeBSD/ports/biology/emboss. *** Error code 1 Stop in /home/rafan/work/FreeBSD/ports/biology/emboss. In addition, this part looks strange to me: .if defined(WITHOUT_X11) USE_XLIB= yes USE_MOTIF= yes LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \ png.5:${PORTSDIR}/graphics/png CONFIGURE_ARGS+= --without-x .endif USE_XLIB when WITHOUT_X11 is defined? Regards, Rong-En Fan > > -- > fernan
rafan 2008-04-13 07:21:16 UTC FreeBSD ports repository Modified files: biology/emboss pkg-plist Log: - Sort pkg-plist before updating to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Revision Changes Path 1.24 +940 -940 ports/biology/emboss/pkg-plist _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
rafan 2008-04-13 07:22:21 UTC FreeBSD ports repository Modified files: biology/emboss Makefile distinfo pkg-descr pkg-plist Removed files: biology/emboss/files patch-ajindex.c patch-ajindex.h patch-ajpdb.c patch-ajseqdb.c patch-dbxfasta.c patch-dbxflat.c patch-dbxgcg.c patch-embindex.c patch-embindex.h patch-marscan.c Log: - Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer) Revision Changes Path 1.50 +17 -19 ports/biology/emboss/Makefile 1.27 +3 -3 ports/biology/emboss/distinfo 1.2 +0 -5134 ports/biology/emboss/files/patch-ajindex.c (dead) 1.2 +0 -170 ports/biology/emboss/files/patch-ajindex.h (dead) 1.2 +0 -67 ports/biology/emboss/files/patch-ajpdb.c (dead) 1.2 +0 -195 ports/biology/emboss/files/patch-ajseqdb.c (dead) 1.2 +0 -89 ports/biology/emboss/files/patch-dbxfasta.c (dead) 1.2 +0 -146 ports/biology/emboss/files/patch-dbxflat.c (dead) 1.2 +0 -96 ports/biology/emboss/files/patch-dbxgcg.c (dead) 1.2 +0 -115 ports/biology/emboss/files/patch-embindex.c (dead) 1.2 +0 -96 ports/biology/emboss/files/patch-embindex.h (dead) 1.2 +0 -72 ports/biology/emboss/files/patch-marscan.c (dead) 1.6 +2 -6 ports/biology/emboss/pkg-descr 1.25 +341 -562 ports/biology/emboss/pkg-plist _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
rafan 2008-04-13 07:22:42 UTC FreeBSD ports repository Modified files: biology/embassy Makefile distinfo pkg-plist Log: - Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer) Revision Changes Path 1.10 +12 -10 ports/biology/embassy/Makefile 1.5 +42 -39 ports/biology/embassy/distinfo 1.4 +290 -32 ports/biology/embassy/pkg-plist _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
State Changed From-To: feedback->closed Committed with minor changes. Thanks!