ports/78979: Update port: biology/ncbi-toolkit to 2004.10.20
Motomichi Matsuzaki
mzaki at biol.s.u-tokyo.ac.jp
Fri Mar 18 07:30:04 UTC 2005
>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 at 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:
More information about the freebsd-ports-bugs
mailing list