Date: Fri, 18 Mar 2005 16:21:19 +0900 (JST) From: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/78979: Update port: biology/ncbi-toolkit to 2004.10.20 Message-ID: <200503180721.j2I7LJcG058999@merolae.biol.s.u-tokyo.ac.jp> Resent-Message-ID: <200503180730.j2I7U3F8011994@freefall.freebsd.org>
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>Number: 78979 >Category: ports >Synopsis: Update port: biology/ncbi-toolkit to 2004.10.20 >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Fri Mar 18 07:30:02 GMT 2005 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: FreeBSD 5.2.1-SECURITY i386 >Organization: the University of Tokyo >Environment: System: FreeBSD merolae.biol.s.u-tokyo.ac.jp 5.2.1-SECURITY FreeBSD 5.2.1-SECURITY #0: Wed Dec 1 10:56:06 GMT 2004 root@builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC i386 >Description: Changes are as follows: * update (PORTVERSION & distinfo) * install manpages * install additional executables (this will close ports/67735) * discard patch-ncbilcl.fbd * adjust pkg-plist >How-To-Repeat: >Fix: diff -ruN biology/ncbi-toolkit/Makefile biology/ncbi-toolkit/Makefile --- biology/ncbi-toolkit/Makefile Tue Nov 2 10:23:15 2004 +++ biology/ncbi-toolkit/Makefile Thu Mar 17 21:55:58 2005 @@ -6,7 +6,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2004.06.16 +PORTVERSION= 2004.10.20 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -16,6 +16,26 @@ USE_MOTIF= yes +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 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 rpsblast.1 \ + blast.1 seedtop.1 + # # In the files directory we have: # @@ -39,9 +59,10 @@ @for file in ${WRKSRC}/data/*; do \ ${INSTALL_DATA} $$file ${DATADIR}; \ done + (cd ${WRKSRC}/doc/man/; ${INSTALL_MAN} ${MAN1} ${MAN1PREFIX}/man/man1/) .if !defined(NOPORTDOCS) ${MKDIR} ${DOCDIR} - cd ${WRKSRC}/doc && ${FIND} * | \ + cd ${WRKSRC}/doc && ${FIND} * ! -name man -and ! -path man/\* | \ ${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR} .endif @${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE} diff -ruN biology/ncbi-toolkit/distinfo biology/ncbi-toolkit/distinfo --- biology/ncbi-toolkit/distinfo Tue Nov 2 10:23:15 2004 +++ biology/ncbi-toolkit/distinfo Thu Nov 4 13:26:02 2004 @@ -1,2 +1,2 @@ -MD5 (ncbi.tar.gz) = 12320f853acb397a14729fb0da0b09df -SIZE (ncbi.tar.gz) = 13680457 +MD5 (ncbi.tar.gz) = 3f82bce2a3ce549f055ff989a4b825ed +SIZE (ncbi.tar.gz) = 13867811 diff -ruN biology/ncbi-toolkit/files/patch-aa biology/ncbi-toolkit/files/patch-aa --- biology/ncbi-toolkit/files/patch-aa Tue Nov 2 10:23:15 2004 +++ biology/ncbi-toolkit/files/patch-aa Thu Mar 17 19:33:56 2005 @@ -6,18 +6,18 @@ $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl + +EXE= Nentrez Psequin \ -+ asn2ff asn2gb asn2xml asndhuff asntool \ -+ blastall blastcl3 blastclust blastpgp \ ++ asn2ff asn2gb asn2idx asn2xml asndhuff asntool \ ++ bl2seq blast blastall blastcl3 blastclust blastpgp \ + cdscan checksub copymat \ -+ ddv demo_regexp demo_regexp_grep dosimple \ -+ entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb \ -+ getfeat getmesh getpub getseq gil2bin \ ++ ddv debruijn demo_regexp demo_regexp_grep dosimple \ ++ entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb formatrpsdb \ ++ gbseqget getfeat getmesh getpub getseq gil2bin \ + idfetch impala indexpub \ + makemat makeset megablast \ + ncbisort netentcf \ + rpsblast \ -+ seedtop seqtest \ -+ tbl2asn testcore testobj testval \ ++ seedtop seqtest sortbyquote \ ++ tbl2asn test_regexp testcore testobj testval \ + udv vecscreen + + diff -ruN biology/ncbi-toolkit/files/patch-ncbilcl.fbd biology/ncbi-toolkit/files/patch-ncbilcl.fbd --- biology/ncbi-toolkit/files/patch-ncbilcl.fbd Mon May 5 21:24:08 2003 +++ biology/ncbi-toolkit/files/patch-ncbilcl.fbd Thu Jan 1 09:00:00 1970 @@ -1,18 +0,0 @@ ---- corelib/ncbilcl.fbd.orig Sat Nov 23 07:05:04 2002 -+++ corelib/ncbilcl.fbd Sat May 3 10:06:18 2003 -@@ -67,6 +67,7 @@ - /*----------------------------------------------------------------------*/ - #define SYSV_IPC_AVAIL /* System V Interprocess Communication available */ - #define _POSIX_C_SOURCE 199309L -+#define _XOPEN_SOURCE 600 /* req. for 5.0 */ - #define HAVE_STRCASECMP 1 - #define HAVE_STRDUP 1 - -@@ -87,6 +88,7 @@ - #include <errno.h> - #include <float.h> - #include <unistd.h> -+#include <sys/select.h> /* req. for 5.0. fd_set def. moved from types.h */ - - /* Check if there are POSIX threads available */ - #ifdef _POSIX_THREADS diff -ruN biology/ncbi-toolkit/pkg-plist biology/ncbi-toolkit/pkg-plist --- biology/ncbi-toolkit/pkg-plist Tue Nov 2 10:23:16 2004 +++ biology/ncbi-toolkit/pkg-plist Thu Mar 17 21:41:39 2005 @@ -2,9 +2,12 @@ bin/Psequin bin/asn2ff bin/asn2gb +bin/asn2idx bin/asn2xml bin/asndhuff bin/asntool +bin/bl2seq +bin/blast bin/blastall bin/blastcl3 bin/blastclust @@ -13,6 +16,7 @@ bin/checksub bin/copymat bin/ddv +bin/debruijn bin/demo_regexp bin/demo_regexp_grep bin/dosimple @@ -23,6 +27,8 @@ bin/fastacmd bin/findspl bin/formatdb +bin/formatrpsdb +bin/gbseqget bin/getfeat bin/getmesh bin/getpub @@ -40,6 +46,7 @@ bin/seedtop bin/seqtest bin/tbl2asn +bin/test_regexp bin/testcore bin/testobj bin/testval @@ -109,6 +116,7 @@ include/ncbi/asnsset.h include/ncbi/asnsubmt.h include/ncbi/asntax1.h +include/ncbi/asntax3.h include/ncbi/asntaxon.h include/ncbi/asntseq.h include/ncbi/bandalgn.h @@ -121,6 +129,7 @@ include/ncbi/blastkar.h include/ncbi/blastpat.h include/ncbi/blastpri.h +include/ncbi/blfmtutl.h include/ncbi/blocks.h include/ncbi/blstspc.h include/ncbi/blstxml.h @@ -131,7 +140,6 @@ include/ncbi/cdd.h include/ncbi/cddapi.h include/ncbi/cddposutil.h -include/ncbi/cddsrv.h include/ncbi/cddutil.h include/ncbi/cdentrez.h include/ncbi/cdnewlib.h @@ -243,7 +251,6 @@ include/ncbi/jzcoll.h include/ncbi/jzmisc.h include/ncbi/layout.h -include/ncbi/lbapi.h include/ncbi/legend.h include/ncbi/list.h include/ncbi/lnfac.h @@ -368,6 +375,7 @@ include/ncbi/objsset.h include/ncbi/objsub.h include/ncbi/objtax1.h +include/ncbi/objtax3.h include/ncbi/objtseq.h include/ncbi/odlbox.h include/ncbi/panels.h @@ -453,6 +461,7 @@ include/ncbi/sugmap.h include/ncbi/sugprefx.h include/ncbi/tax1map.h +include/ncbi/tax3api.h include/ncbi/taxblast.h include/ncbi/taxext.h include/ncbi/taxinc.h @@ -524,8 +533,6 @@ include/ncbi/vsmfile.h include/ncbi/vsmpriv.h include/ncbi/vsmutil.h -include/ncbi/wrpsb.h -include/ncbi/wrpsbtool.h include/ncbi/wwwblast.h include/ncbi/xmlblast.h lib/ncbi/libblast.a @@ -567,6 +574,7 @@ %%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html %%PORTDOCS%%%%DOCSDIR%%/blast/filter.html %%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html +%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html %%PORTDOCS%%%%DOCSDIR%%/blast/impala.html %%PORTDOCS%%%%DOCSDIR%%/blast/index.html %%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html @@ -603,50 +611,6 @@ %%PORTDOCS%%%%DOCSDIR%%/images/seqn20.png %%PORTDOCS%%%%DOCSDIR%%/images/seqn21.png %%PORTDOCS%%%%DOCSDIR%%/images/seqn22.png -%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastall.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 -%%PORTDOCS%%%%DOCSDIR%%/man/cdscan.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/fastacmd.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fa2htgs.1 -%%PORTDOCS%%%%DOCSDIR%%/man/findspl.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1 -%%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1 -%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getfeat.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 -%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 -%%PORTDOCS%%%%DOCSDIR%%/man/impala.1 -%%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 -%%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 -%%PORTDOCS%%%%DOCSDIR%%/man/megablast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 -%%PORTDOCS%%%%DOCSDIR%%/man/netentcf.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 -%%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 -%%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/udv.1 -%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc %%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif @@ -733,7 +697,6 @@ %%DATADIR%%/taxlist.txt @dirrm %%DATADIR%% %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install -%%PORTDOCS%%@dirrm %%DOCSDIR%%/man %%PORTDOCS%%@dirrm %%DOCSDIR%%/images %%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs %%PORTDOCS%%@dirrm %%DOCSDIR%%/blast >Release-Note: >Audit-Trail: >Unformatted:
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