Date: Thu, 26 Mar 2009 14:10:36 -0300 From: Fernan Aguero <fernan.aguero@gmail.com> To: FreeBSD-gnats-submit@freebsd.org Cc: freebsd-ports-bugs@freebsd.org, pav@freebsd.org, jcigar@ulb.ac.be Subject: [maintainer-update] update biology/ncbi-toolkit to latest version Message-ID: <520894aa0903261010n35317944o63d754b5994d2d5d@mail.gmail.com>
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--0016e6db6196da6c70046608b117 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit >Submitter-Id: current-users >Originator: Fernan Aguero >Organization: IIB-UNSAM >Confidential: no <FreeBSD PRs are public data> >Synopsis: [maintainer-update] update biology/ncbi-toolkit to latest version >Severity: non-critical >Priority: low >Category: ports >Class: maintainer-update >Release: FreeBSD 6.3-RELEASE-p1 i386 >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)> This PR updates ncbi-toolkit to the latest version. This should fix the problem reported in PR ports/128271. >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)> --- ncbi-toolkit.diff begins here --- diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/Makefile ncbi-toolkit/Makefile --- /usr/ports/biology/ncbi-toolkit/Makefile 2008-05-07 08:41:14.000000000 -0300 +++ ncbi-toolkit/Makefile 2009-03-26 09:28:03.000000000 -0300 @@ -7,8 +7,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2006.05.07 # containing BLAST v2.2.14 -PORTREVISION= 1 +PORTVERSION= 2009.03.01 # containing BLAST v2.2.19 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -34,23 +33,33 @@ # new slave ports TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \ - debruijn entrcmd fa2htgs findspl getseq getfeat getmesh \ - getpub gil2bin idfetch indexpub makeset tbl2asn vecscreen -BLAST_EXE= bl2seq blast blastall blastcl3 blastclust blastpgp copymat \ - fastacmd formatdb impala makemat megablast rpsblast seedtop -X11_EXE= Nentrez Psequin ddv entrez2 netentcf sbtedit udv + debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \ + idfetch indexpub makeset tbl2asn vecscreen demo_regexp \ + demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp +BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \ + fastacmd formatdb formatrpsdb impala makemat megablast \ + rpsblast seedtop taxblast +X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv # and these are the man pages we have -MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \ - asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \ - debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \ - fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \ - idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.1 \ +MAN1= asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 asn2xml.1 \ + asndhuff.1 asnval.1 blast.1 blastclust.1 cdscan.1 checksub.1 \ + copymat.1 ddv.1 debruijn.1 errhdr.1 fa2htgs.1 fastacmd.1 \ + findspl.1 fmerge.1 formatdb.1 getmesh.1 getpub.1 gil2bin.1 \ + idfetch.1 indexpub.1 makemat.1 makeset.1 sbtedit.1 tbl2asn.1 \ + udv.1 vecscreen.1 Psequin.1 asn2all.1 asntool.1 entrez2.1 \ + formatrpsdb.1 +MAN1= Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \ + asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \ + cdscan.1 checksub.1 copymat.1 ddv.1 \ + debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \ + fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \ + idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \ tbl2asn.1 udv.1 vecscreen.1 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 seedtop.1 blast.1 rpsblast.1 post-patch: @${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \ diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo --- /usr/ports/biology/ncbi-toolkit/distinfo 2006-06-06 09:05:19.000000000 -0300 +++ ncbi-toolkit/distinfo 2009-03-25 20:12:58.000000000 -0300 @@ -1,3 +1,3 @@ -MD5 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 1c00462385fbf382c99ff65f34c0d09a -SHA256 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129 -SIZE (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 15396356 +MD5 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = af10869758e3ea11ae12f97332742629 +SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df +SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732 diff -ruN --exclude CVS /usr/ports/biology/ncbi-toolkit/pkg-plist ncbi-toolkit/pkg-plist --- /usr/ports/biology/ncbi-toolkit/pkg-plist 2006-06-06 09:05:19.000000000 -0300 +++ ncbi-toolkit/pkg-plist 2009-03-26 09:37:01.000000000 -0300 @@ -1,5 +1,4 @@ bin/bl2seq -bin/blast bin/blastall bin/blastcl3 bin/blastclust @@ -7,11 +6,13 @@ bin/copymat bin/fastacmd bin/formatdb +bin/formatrpsdb bin/impala bin/makemat bin/megablast bin/rpsblast bin/seedtop +bin/taxblast bin/asn2ff bin/asn2gb bin/asn2idx @@ -23,8 +24,6 @@ bin/entrcmd bin/fa2htgs bin/findspl -bin/getseq -bin/getfeat bin/getmesh bin/getpub bin/ddv @@ -34,10 +33,16 @@ bin/makeset bin/tbl2asn bin/vecscreen +bin/demo_regexp +bin/demo_regexp_grep +bin/errhdr +bin/gene2xml +bin/ncbisort +bin/seqtest +bin/test_regexp bin/Nentrez bin/Psequin bin/entrez2 -bin/netentcf bin/sbtedit bin/udv include/ncbi/connect/connect_export.h @@ -48,12 +53,14 @@ include/ncbi/connect/ncbi_config.h include/ncbi/connect/ncbi_connection.h include/ncbi/connect/ncbi_connector.h +include/ncbi/connect/ncbi_connssl.h include/ncbi/connect/ncbi_connutil.h include/ncbi/connect/ncbi_core.h include/ncbi/connect/ncbi_core_c.h include/ncbi/connect/ncbi_dispd.h include/ncbi/connect/ncbi_file_connector.h include/ncbi/connect/ncbi_ftp_connector.h +include/ncbi/connect/ncbi_gnutls.h include/ncbi/connect/ncbi_heapmgr.h include/ncbi/connect/ncbi_host_info.h include/ncbi/connect/ncbi_host_infop.h @@ -68,11 +75,11 @@ include/ncbi/connect/ncbi_server_infop.h include/ncbi/connect/ncbi_service.h include/ncbi/connect/ncbi_service_connector.h -include/ncbi/connect/ncbi_service_misc.h include/ncbi/connect/ncbi_servicep.h include/ncbi/connect/ncbi_socket.h include/ncbi/connect/ncbi_socket_connector.h include/ncbi/connect/ncbi_socket_unix.h +include/ncbi/connect/ncbi_socketp.h include/ncbi/connect/ncbi_types.h include/ncbi/connect/ncbi_util.h include/ncbi/FSpCompat.h @@ -90,6 +97,8 @@ include/ncbi/accentr.h include/ncbi/accid1.h include/ncbi/accutils.h +include/ncbi/acerdapi.h +include/ncbi/aceread.h include/ncbi/actutils.h include/ncbi/algorend.h include/ncbi/alignloc.h @@ -125,11 +134,13 @@ include/ncbi/asnid0.h include/ncbi/asninsdseq.h include/ncbi/asnloc.h +include/ncbi/asnmacro.h include/ncbi/asnmdrs.h include/ncbi/asnmedli.h include/ncbi/asnmim.h include/ncbi/asnmime.h include/ncbi/asnmla.h +include/ncbi/asnmla2.h include/ncbi/asnneten.h include/ncbi/asnproj.h include/ncbi/asnprt.h @@ -139,6 +150,7 @@ include/ncbi/asnseq.h include/ncbi/asnsset.h include/ncbi/asnsubmt.h +include/ncbi/asntable.h include/ncbi/asntax1.h include/ncbi/asntax3.h include/ncbi/asntaxon.h @@ -147,6 +159,7 @@ include/ncbi/binary.h include/ncbi/biosrc.h include/ncbi/blast.h +include/ncbi/blast_dust.h include/ncbi/blastconcat.h include/ncbi/blastconcatdef.h include/ncbi/blastdef.h @@ -255,6 +268,8 @@ include/ncbi/lnfac.h include/ncbi/lookup.h include/ncbi/lsqfetch.h +include/ncbi/macroapi.h +include/ncbi/macrodlg.h include/ncbi/mapcn3d.h include/ncbi/mapgene.h include/ncbi/mapmime.h @@ -275,6 +290,8 @@ include/ncbi/mimapi.h include/ncbi/mkbioseq.h include/ncbi/mmdb1.h +include/ncbi/mla2api.h +include/ncbi/mlkludge.h include/ncbi/mmdb2.h include/ncbi/mmdb3.h include/ncbi/mmdbapi.h @@ -348,12 +365,14 @@ include/ncbi/objgen.h include/ncbi/objinsdseq.h include/ncbi/objloc.h +include/ncbi/objmacro.h include/ncbi/objmdrs.h include/ncbi/objmedli.h include/ncbi/objmgr.h include/ncbi/objmim.h include/ncbi/objmime.h include/ncbi/objmla.h +include/ncbi/objmla2.h include/ncbi/objmmdb1.h include/ncbi/objmmdb2.h include/ncbi/objmmdb3.h @@ -369,6 +388,7 @@ include/ncbi/objspell.h include/ncbi/objsset.h include/ncbi/objsub.h +include/ncbi/objtable.h include/ncbi/objtax1.h include/ncbi/objtax3.h include/ncbi/objtseq.h @@ -519,6 +539,7 @@ include/ncbi/vibforms.h include/ncbi/vibgraph.h include/ncbi/vibincld.h +include/ncbi/vibmain.h include/ncbi/vibmouse.h include/ncbi/vibpcc.h include/ncbi/vibprocs.h @@ -584,7 +605,6 @@ %%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html %%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf %%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html -%%PORTDOCS%%%%DOCSDIR%%/blast/update_blastdb.pl %%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README @@ -619,26 +639,30 @@ %%PORTDOCS%%%%DOCSDIR%%/images/update.png %%PORTDOCS%%%%DOCSDIR%%/images/validate.png %%PORTDOCS%%%%DOCSDIR%%/images/welcome.png -%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 %%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2all.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2fsa.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2idx.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 %%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 %%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asnval.1 %%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 %%PORTDOCS%%%%DOCSDIR%%/man/blast.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastall.1 +%%PORTDOCS%%%%DOCSDIR%%/man/blastall_old.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1 %%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1 %%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/cleanasn.1 %%PORTDOCS%%%%DOCSDIR%%/man/copymat.1 %%PORTDOCS%%%%DOCSDIR%%/man/ddv.1 %%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/entrcmd.1 %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1 %%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 @@ -648,20 +672,27 @@ %%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1 %%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1 %%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/formatrpsdb.1 %%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getfeat.1 +%%PORTDOCS%%%%DOCSDIR%%/man/gene2xml.1 %%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 %%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 %%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 %%PORTDOCS%%%%DOCSDIR%%/man/impala.1 %%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/insdseqget.1 %%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 %%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 %%PORTDOCS%%%%DOCSDIR%%/man/megablast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/netentcf.1 +%%PORTDOCS%%%%DOCSDIR%%/man/nps2gps.1 %%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 +%%PORTDOCS%%%%DOCSDIR%%/man/sbtedit.1 %%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 +%%PORTDOCS%%%%DOCSDIR%%/man/sortbyquote.1 +%%PORTDOCS%%%%DOCSDIR%%/man/spidey.1 %%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 +%%PORTDOCS%%%%DOCSDIR%%/man/trna2sap.1 +%%PORTDOCS%%%%DOCSDIR%%/man/trna2tbl.1 %%PORTDOCS%%%%DOCSDIR%%/man/udv.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc @@ -702,17 +733,26 @@ %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css %%PORTDOCS%%%%DOCSDIR%%/sequin.htm %%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt -%%DATADIR%%/16Score.nhr -%%DATADIR%%/16Score.nin -%%DATADIR%%/16Score.nsq +%%DATADIR%%/16SCore.nhr +%%DATADIR%%/16SCore.nin +%%DATADIR%%/16SCore.nsq %%DATADIR%%/BLOSUM45 +%%DATADIR%%/BLOSUM50 %%DATADIR%%/BLOSUM62 %%DATADIR%%/BLOSUM80 +%%DATADIR%%/BLOSUM90 +%%DATADIR%%/Combined16SrRNA.nhr +%%DATADIR%%/Combined16SrRNA.nin +%%DATADIR%%/Combined16SrRNA.nsq +%%DATADIR%%/Combined16SrRNA_2-12-2008.nhr +%%DATADIR%%/Combined16SrRNA_2-12-2008.nin +%%DATADIR%%/Combined16SrRNA_2-12-2008.nsq %%DATADIR%%/ContactPotential %%DATADIR%%/KSat.flt %%DATADIR%%/KSchoth.flt %%DATADIR%%/KSesigc.mat %%DATADIR%%/KSesigl.mat +%%DATADIR%%/PAM250 %%DATADIR%%/KSgc.flt %%DATADIR%%/KShopp.flt %%DATADIR%%/KSkyte.flt @@ -725,8 +765,14 @@ %%DATADIR%%/KSpsigl.mat %%DATADIR%%/KSpur.flt %%DATADIR%%/KSpyr.flt +%%DATADIR%%/LSURef_93.fasta.nhr +%%DATADIR%%/LSURef_93.fasta.nin +%%DATADIR%%/LSURef_93.fasta.nsq %%DATADIR%%/PAM30 %%DATADIR%%/PAM70 +%%DATADIR%%/SSURef_93.fasta.nhr +%%DATADIR%%/SSURef_93.fasta.nin +%%DATADIR%%/SSURef_93.fasta.nsq %%DATADIR%%/UniVec.nhr %%DATADIR%%/UniVec.nin %%DATADIR%%/UniVec.nsq @@ -737,11 +783,17 @@ %%DATADIR%%/blast.prt %%DATADIR%%/bstdt.prt %%DATADIR%%/bstdt.val +%%DATADIR%%/country_lat_lon.txt +%%DATADIR%%/ecnum_ambiguous.txt +%%DATADIR%%/ecnum_deleted.txt +%%DATADIR%%/ecnum_replaced.txt +%%DATADIR%%/ecnum_specific.txt %%DATADIR%%/featdef.prt %%DATADIR%%/featdef.val %%DATADIR%%/gc.prt %%DATADIR%%/gc.val %%DATADIR%%/humrep.fsa +%%DATADIR%%/institution_codes.txt %%DATADIR%%/lineages.txt %%DATADIR%%/makerpt.prt %%DATADIR%%/ncbiendo.dat @@ -751,6 +803,8 @@ %%DATADIR%%/ncbirnam.dat %%DATADIR%%/objprt.prt %%DATADIR%%/pubkey.enc +%%DATADIR%%/rRNA_blast.nal +%%DATADIR%%/rRNAstrand.nal %%DATADIR%%/seqcode.prt %%DATADIR%%/seqcode.val %%DATADIR%%/sequin.hlp --- ncbi-toolkit.diff ends here --- -- fernan --0016e6db6196da6c70046608b117 Content-Type: text/x-patch; charset=US-ASCII; name="ncbi-toolkit.diff" Content-Disposition: attachment; filename="ncbi-toolkit.diff" Content-Transfer-Encoding: base64 X-Attachment-Id: f_fsrpa07y0 ZGlmZiAtcnVOIC0tZXhjbHVkZSBDVlMgL3Vzci9wb3J0cy9iaW9sb2d5L25jYmktdG9vbGtpdC9N YWtlZmlsZSBuY2JpLXRvb2xraXQvTWFrZWZpbGUKLS0tIC91c3IvcG9ydHMvYmlvbG9neS9uY2Jp 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