ports/51709: Port update (maintainer): biology/ncbi-toolkit

Tony Maher tonymaher at optushome.com.au
Sat May 3 02:30:15 UTC 2003 

>Number:         51709
>Category:       ports
>Synopsis:       Port update (maintainer): biology/ncbi-toolkit
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Fri May 02 19:30:12 PDT 2003
>Closed-Date:
>Last-Modified:
>Originator:     Tony Maher
>Release:        FreeBSD 4.8-STABLE i386
>Organization:
>Environment:
System: FreeBSD dt.home 4.8-STABLE FreeBSD 4.8-STABLE #2: Wed Apr 16 13:00:01 EST 2003 root at dt.home:/usr/obj/usr/src/sys/DT i386


>Description:
	Update port to version 2003.04.21
	Thanks to Brad Chapman who alerted me to the new version and supplied
	patches though I did not apply them directly.

	o compiles on 4-stable *and* now on 5-current (Brad's fixes)
	o NCBI now support FreeBSD (4-stable) directly therefore no longer require
		files/freebsd.ncbi.mk files/patch-ab and files/patch-ac
	o now link against the thread library (but I am not sure if it helps)

	Tested a single blastn and get identical results on 5.0-current (02-05-03)
	and 4.8-stable (16-04-03).  I do not currently have access to large/varied
	data sets so testing is very limited.

	Please delete files/freebsd.ncbi.mk files/patch-ab and files/patch-ac

>How-To-Repeat:

>Fix:

diff -ruN ncbi-toolkit.orig/Makefile ncbi-toolkit/Makefile
--- ncbi-toolkit.orig/Makefile	Tue Feb 25 18:50:46 2003
+++ ncbi-toolkit/Makefile	Thu May  1 14:54:58 2003
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2002.04.26
+PORTVERSION=	2003.04.21
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -15,16 +15,12 @@
 COMMENT=	NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
 
 USE_MOTIF=	yes
-USE_REINPLACE=	yes
 
 #
 # In the files directory we have:
 #
 
 DUMMYMAKE=	Makefile
-PLATFORMDIR=	${WRKSRC}/platform
-BUILDSCRIPT=	${WRKSRC}/make/makedis.csh
-
 DOCDIR=		${PREFIX}/share/doc/${PORTNAME}
 CPIO=		cpio --quiet -pdum -R
 
@@ -37,8 +33,6 @@
 
 pre-configure:
 	@${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
-	@${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR}
-	@${REINPLACE_CMD} -e 's#NetBSD#FreeBSD#;'  -e 's#netbsd#freebsd#' ${BUILDSCRIPT}
 
 post-install:
 	@${MKDIR} ${DATADIR}
diff -ruN ncbi-toolkit.orig/distinfo ncbi-toolkit/distinfo
--- ncbi-toolkit.orig/distinfo	Sat Sep 21 21:11:22 2002
+++ ncbi-toolkit/distinfo	Thu May  1 11:23:11 2003
@@ -1 +1 @@
-MD5 (ncbi.tar.gz) = 7278c10b227b0298f00a5ed5dde58bc4
+MD5 (ncbi.tar.gz) = 96208e10f92b2163f5dcc3c5cf74dd44
diff -ruN ncbi-toolkit.orig/files/freebsd.ncbi.mk ncbi-toolkit/files/freebsd.ncbi.mk
--- ncbi-toolkit.orig/files/freebsd.ncbi.mk	Fri Feb 22 18:57:07 2002
+++ ncbi-toolkit/files/freebsd.ncbi.mk	Thu Jan  1 10:00:00 1970
@@ -1,31 +0,0 @@
-#
-# $Id$ freebsd.ncbi.mk
-#
-# That platform is not supported and is contributed to NCBI by 
-#                     freebsd-bio at freebsd.net
-#
-NCBI_DEFAULT_LCL = bsd
-NCBI_MAKE_SHELL = /bin/sh
-NCBI_CC = cc
-NCBI_CFLAGS1 = ${CFLAGS} -c
-NCBI_LDFLAGS1 = -O
-NCBI_OPTFLAG =
-NCBI_BIN_MASTER = /home/coremake/ncbi/bin
-NCBI_BIN_COPY = /home/coremake/ncbi/bin
-NCBI_INCDIR = /home/coremake/ncbi/include
-NCBI_LIBDIR = /home/coremake/ncbi/lib
-NCBI_ALTLIB = /home/coremake/ncbi/altlib
-#will work only when you have Motif installed!
-NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF
-NCBI_VIBLIBS = -lXm -lXmu -lXp -lXpm -lXt -lX11 -lXext 
-NCBI_DISTVIBLIBS = -L/usr/X11R6/lib /usr/X11R6/lib/libXm.a /usr/X11R6/lib/libXp.a /usr/X11R6/lib/libXpm.a -lXmu -lXt -lX11 -lXext
-NCBI_OTHERLIBS = -lm
-NCBI_RANLIB = ranlib
-# Used by makedis.csh
-NCBI_MT_OTHERLIBS = 
-NCBI_THREAD_OBJ = ncbithr.o
-NETENTREZVERSION = 2.02c2ASN1SPEC6
-
-NCBI_LBSM_SRC = ncbi_service_lbsmd_stub.c
-NCBI_LBSM_OBJ = ncbi_service_lbsmd_stub.o
-
diff -ruN ncbi-toolkit.orig/files/patch-aa ncbi-toolkit/files/patch-aa
--- ncbi-toolkit.orig/files/patch-aa	Sat Sep 21 21:11:22 2002
+++ ncbi-toolkit/files/patch-aa	Thu May  1 12:02:23 2003
@@ -6,11 +6,11 @@
  	$(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl
 +
 +EXE=	Nentrez Psequin \
-+		asn2ff asn2xml asndhuff asntool \
-+		bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \
++		asn2ff asn2gb asn2xml asndhuff asntool \
++		blastall blastcl3 blastclust blastpgp \
 +		cdscan checksub copymat \
-+		ddv dosimple \
-+		entrcmd errhdr fa2htgs fastacmd findspl fmerge formatdb \
++		ddv demo_regexp demo_regexp_grep dosimple \
++		entrcmd entrez2 errhdr fa2htgs fastacmd findspl fmerge formatdb \
 +		getfeat getmesh getpub getseq gil2bin \
 +		idfetch impala indexpub \
 +		makemat makeset megablast \
diff -ruN ncbi-toolkit.orig/files/patch-ab ncbi-toolkit/files/patch-ab
--- ncbi-toolkit.orig/files/patch-ab	Mon Oct 30 00:56:24 2000
+++ ncbi-toolkit/files/patch-ab	Thu Jan  1 10:00:00 1970
@@ -1,19 +0,0 @@
---- corelib/ncbilcl.bsd.orig	Mon Apr  3 08:50:57 2000
-+++ corelib/ncbilcl.bsd	Mon Apr  3 08:51:55 2000
-@@ -74,7 +74,6 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <string.h>
--#include <malloc.h>
- #include <memory.h>
- #include <stdlib.h>
- #include <math.h>
-@@ -84,7 +83,7 @@
- 
- /* Check if there are POSIX threads available */
- #ifdef _POSIX_THREADS
--#define POSIX_THREADS_AVAIL
-+#define POSIX_THREADS_AVAIL_broken
- #endif
- 
- 
diff -ruN ncbi-toolkit.orig/files/patch-ac ncbi-toolkit/files/patch-ac
--- ncbi-toolkit.orig/files/patch-ac	Mon Oct 30 00:56:24 2000
+++ ncbi-toolkit/files/patch-ac	Thu Jan  1 10:00:00 1970
@@ -1,11 +0,0 @@
---- corelib/ncbienv.c.orig	Tue Jan 25 08:16:49 2000
-+++ corelib/ncbienv.c	Mon Apr  3 08:56:02 2000
-@@ -183,6 +183,8 @@
- 
- #ifdef OS_UNIX
- #include <pwd.h>
-+#include <sys/param.h>
-+#define LOGNAME_MAX MAXLOGNAME
- #endif /* OS_UNIX */
- #ifdef OS_MAC
- #include <Gestalt.h>
diff -ruN ncbi-toolkit.orig/files/patch-ncbilcl.fbd ncbi-toolkit/files/patch-ncbilcl.fbd
--- ncbi-toolkit.orig/files/patch-ncbilcl.fbd	Thu Jan  1 10:00:00 1970
+++ ncbi-toolkit/files/patch-ncbilcl.fbd	Sat May  3 11:11:19 2003
@@ -0,0 +1,18 @@
+--- 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 ncbi-toolkit.orig/pkg-plist ncbi-toolkit/pkg-plist
--- ncbi-toolkit.orig/pkg-plist	Sat Sep 21 21:11:22 2002
+++ ncbi-toolkit/pkg-plist	Thu May  1 13:55:15 2003
@@ -1,7 +1,9 @@
 %%PORTDOCS%%share/doc/ncbi-toolkit/FAQ.txt
+%%PORTDOCS%%share/doc/ncbi-toolkit/README-qm
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.asn2xml
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.bcl
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.bls
+%%PORTDOCS%%share/doc/ncbi-toolkit/README.fastacmd
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.formatdb
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.imp
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.mbl
@@ -9,11 +11,13 @@
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.pbl
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.rps
 %%PORTDOCS%%share/doc/ncbi-toolkit/README.sdk
+%%PORTDOCS%%share/doc/ncbi-toolkit/asn2gb.txt
+%%PORTDOCS%%share/doc/ncbi-toolkit/asn2gph.txt
+%%PORTDOCS%%share/doc/ncbi-toolkit/dispatcher.html
 %%PORTDOCS%%share/doc/ncbi-toolkit/fa2htgs/README
 %%PORTDOCS%%share/doc/ncbi-toolkit/fa2htgs/updateHtgsDoc
 %%PORTDOCS%%share/doc/ncbi-toolkit/firedialog.gif
 %%PORTDOCS%%share/doc/ncbi-toolkit/firewall.html
-%%PORTDOCS%%share/doc/ncbi-toolkit/firewall.txt
 %%PORTDOCS%%share/doc/ncbi-toolkit/fwd_check.sh
 %%PORTDOCS%%share/doc/ncbi-toolkit/images/ncbi_sequin.css
 %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn01.gif
@@ -41,14 +45,14 @@
 %%PORTDOCS%%share/doc/ncbi-toolkit/ncbixml.txt
 %%PORTDOCS%%share/doc/ncbi-toolkit/sdk.doc
 %%PORTDOCS%%share/doc/ncbi-toolkit/sequin.htm
+%%PORTDOCS%%share/doc/ncbi-toolkit/tbl2asn.txt
 bin/Nentrez
 bin/Psequin
 bin/asn2ff
+bin/asn2gb
 bin/asn2xml
 bin/asndhuff
 bin/asntool
-bin/bl2seq
-bin/blast.REAL
 bin/blastall
 bin/blastcl3
 bin/blastclust
@@ -57,8 +61,11 @@
 bin/checksub
 bin/copymat
 bin/ddv
+bin/demo_regexp
+bin/demo_regexp_grep
 bin/dosimple
 bin/entrcmd
+bin/entrez2
 bin/errhdr
 bin/fa2htgs
 bin/fastacmd
@@ -104,9 +111,11 @@
 lib/ncbi/libnetblast.a
 lib/ncbi/libnetcli.a
 lib/ncbi/libnetentr.a
+lib/ncbi/libregexp.a
 lib/ncbi/libvibgif.a
 lib/ncbi/libvibnet.a
 lib/ncbi/libvibrant.a
+include/ncbi/connect/connect_export.h
 include/ncbi/connect/ncbi_ansi_ext.h
 include/ncbi/connect/ncbi_buffer.h
 include/ncbi/connect/ncbi_comm.h
@@ -115,9 +124,14 @@
 include/ncbi/connect/ncbi_connector.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_heapmgr.h
+include/ncbi/connect/ncbi_host_info.h
+include/ncbi/connect/ncbi_host_infop.h
 include/ncbi/connect/ncbi_http_connector.h
+include/ncbi/connect/ncbi_lbsmd.h
 include/ncbi/connect/ncbi_memory_connector.h
 include/ncbi/connect/ncbi_priv.h
 include/ncbi/connect/ncbi_sendmail.h
@@ -126,12 +140,17 @@
 include/ncbi/connect/ncbi_service.h
 include/ncbi/connect/ncbi_service_connector.h
 include/ncbi/connect/ncbi_servicep.h
-include/ncbi/connect/ncbi_servicep_dispd.h
-include/ncbi/connect/ncbi_servicep_lbsmd.h
 include/ncbi/connect/ncbi_socket.h
 include/ncbi/connect/ncbi_socket_connector.h
 include/ncbi/connect/ncbi_types.h
 include/ncbi/connect/ncbi_util.h
+include/ncbi/FSpCompat.h
+include/ncbi/FullPath.h
+include/ncbi/MoreCarbonAccessors.h
+include/ncbi/MoreFilesExtras.h
+include/ncbi/MoreFilesX.h
+include/ncbi/Optimization.h
+include/ncbi/OptimizationEnd.h
 include/ncbi/PubStructAsn.h
 include/ncbi/a2ferr.h
 include/ncbi/a2ferrdf.h
@@ -161,7 +180,11 @@
 include/ncbi/asn2graphic.h
 include/ncbi/asn2graphicp.h
 include/ncbi/asnacces.h
+include/ncbi/asngbseq.h
+include/ncbi/asntseq.h
 include/ncbi/blast.h
+include/ncbi/blastconcat.h
+include/ncbi/blastconcatdef.h
 include/ncbi/asnalign.h
 include/ncbi/asnbibli.h
 include/ncbi/asnblock.h
@@ -382,6 +405,7 @@
 include/ncbi/objentr.h
 include/ncbi/objfdef.h
 include/ncbi/objfeat.h
+include/ncbi/objgbseq.h
 include/ncbi/objgen.h
 include/ncbi/objloc.h
 include/ncbi/objmdrs.h
@@ -404,9 +428,14 @@
 include/ncbi/objsset.h
 include/ncbi/objsub.h
 include/ncbi/objtax1.h
+include/ncbi/objtseq.h
 include/ncbi/odlbox.h
 include/ncbi/panels.h
 include/ncbi/parsegb.h
+include/ncbi/pcre.h
+include/ncbi/pcre_config.h
+include/ncbi/pcre_internal.h
+include/ncbi/pcreposix.h
 include/ncbi/pdiagnos.h
 include/ncbi/pgppop.h
 include/ncbi/pictur3d.h
@@ -457,6 +486,7 @@
 include/ncbi/seqgrphx.h
 include/ncbi/seqmgr.h
 include/ncbi/seqmtrx.h
+include/ncbi/seqpanel.h
 include/ncbi/seqpcc.h
 include/ncbi/seqport.h
 include/ncbi/seqscrl.h
@@ -552,7 +582,6 @@
 include/ncbi/vsmutil.h
 include/ncbi/wrpsb.h
 include/ncbi/wrpsbtool.h
-include/ncbi/wwwblast.h
 include/ncbi/xmlblast.h
 share/ncbi-toolkit/BLOSUM45
 share/ncbi-toolkit/BLOSUM62

>Release-Note:
>Audit-Trail:
>Unformatted:

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