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Message-Id: <200503180721.j2I7LJcG058999@merolae.biol.s.u-tokyo.ac.jp>
Date: Fri, 18 Mar 2005 16:21:19 +0900 (JST)
From: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Reply-To: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: Update port: biology/ncbi-toolkit to 2004.10.20
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         78979
>Category:       ports
>Synopsis:       Update port: biology/ncbi-toolkit to 2004.10.20
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    pav
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Fri Mar 18 07:30:02 GMT 2005
>Closed-Date:    Sat Mar 19 18:27:23 GMT 2005
>Last-Modified:  Sat Mar 19 18:27:23 GMT 2005
>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:
State-Changed-From-To: open->feedback 
State-Changed-By: pav 
State-Changed-When: Sat Mar 19 16:49:58 GMT 2005 
State-Changed-Why:  
Asked maintainer for approval. 


Responsible-Changed-From-To: freebsd-ports-bugs->pav 
Responsible-Changed-By: pav 
Responsible-Changed-When: Sat Mar 19 16:49:58 GMT 2005 
Responsible-Changed-Why:  
Handle. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=78979 

From: Pav Lucistnik <pav@FreeBSD.org>
To: tonym@biolateral.com.au, freebsd-gnats-submit@FreeBSD.org
Cc:  
Subject: Re: ports/78979: Update port: biology/ncbi-toolkit to 2004.10.20
Date: Sat, 19 Mar 2005 17:49:55 +0100

 Dear maintainer of FreeBSD port biology/ncbi-toolkit, please take a look
 at
 
 http://www.freebsd.org/cgi/query-pr.cgi?q=78979
 
 Do you approve this update?
 
 -- 
 Pav Lucistnik <pav@oook.cz>
               <pav@FreeBSD.org>
 
 > With a 10 MHz 386 the downloading speed would most likely drop to a crawl
 > or stop with the decoding process etc.
 I think most 10MHz 386 users are quite accustomed to things dropping
 to a crawl.
State-Changed-From-To: feedback->closed 
State-Changed-By: pav 
State-Changed-When: Sat Mar 19 18:26:59 GMT 2005 
State-Changed-Why:  
Submitter called to cancel this patch in favour of 67735 

http://www.freebsd.org/cgi/query-pr.cgi?pr=78979 
>Unformatted:
