upgrade to 20020426

PR:		39357
Submitted by:	maintainer

6 files changed, 16 insertions, 22 deletions

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index db24f9b14014..4a5c90f8516b 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	ncbi-toolkit
-PORTVERSION=	2001.12.20
+PORTVERSION=	2002.04.26
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
@@ -36,7 +36,7 @@ CPIO=		cpio --quiet -pdum -R
 pre-configure:
 	@${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
 	@${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR}
-	@${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;'  -e 's#netbsd#freebsd#' ${BUILDSCRIPT}
+	@${REINPLACE_CMD} -e 's#NetBSD#FreeBSD#;'  -e 's#netbsd#freebsd#' ${BUILDSCRIPT}
 
 post-install:
 	@${MKDIR} ${DATADIR}
diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo
index 599cf9943e68..bf2e6dc2f18a 100644
--- a/biology/ncbi-toolkit/distinfo
+++ b/biology/ncbi-toolkit/distinfo
@@ -1 +1 @@
-MD5 (ncbi.tar.gz) = 8038afb3f5502b3b8ade4f221eebe46e
+MD5 (ncbi.tar.gz) = 7278c10b227b0298f00a5ed5dde58bc4
diff --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa
index 3c213427f054..e2e8abb9e5a7 100644
--- a/biology/ncbi-toolkit/files/patch-aa
+++ b/biology/ncbi-toolkit/files/patch-aa
@@ -1,12 +1,12 @@
---- make/makeall.unx.orig	Thu Apr  5 09:24:30 2001
-+++ make/makeall.unx	Tue Sep 18 14:49:24 2001
-@@ -851,3 +851,51 @@
+--- make/makeall.unx.orig	Thu Mar 21 06:01:20 2002
++++ make/makeall.unx	Sat Jun  8 20:16:09 2002
+@@ -859,3 +859,46 @@
  	#load $(LDFLAGS) getmuid.c medutil.c \
  	$(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \
  	$(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl
 +
 +EXE=	Nentrez Psequin \
-+		asn2fast asn2ff asn2xml asndhuff asntool \
++		asn2ff asn2xml asndhuff asntool \
 +		bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \
 +		cdscan checksub copymat \
 +		ddv dosimple \
@@ -21,13 +21,6 @@
 +		udv vecscreen
 +
 +
-+LIB=	libncbi.a		libncbicdr.a	libncbimla.a	libncbitxc2.a \
-+		libnetentr.a	libncbiCacc.a	libncbicn3d.a	libncbimmdb.a \
-+		libnetblast.a	libvibgif.a		libncbiNacc.a	libncbidesk.a \
-+		libncbiobj.a	libnetcli.a		libvibnet.a		libncbiacc.a \
-+		libncbiid1.a	libncbitool.a	libnetcli_.a	libvibrant.a
-+
-+
 +MKDIR=	/bin/mkdir -p
 +INSTALL_PROGRAM=	/usr/bin/install -c
 +
@@ -37,7 +30,9 @@
 +
 +linstall: $(LIB)
 +	${MKDIR} ${PREFIX}/lib/ncbi
-+	${INSTALL_PROGRAM} $? ${PREFIX}/lib/ncbi
++	for file in *.a; do \
++		${INSTALL_PROGRAM} $$file ${PREFIX}/lib/ncbi; \
++	done
 +
 +iinstall::
 +	${MKDIR} ${PREFIX}/include/ncbi/connect
diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr
index 515d58ba056b..7972d3710665 100644
--- a/biology/ncbi-toolkit/pkg-descr
+++ b/biology/ncbi-toolkit/pkg-descr
@@ -16,5 +16,4 @@ From the README:
   have found it a useful and stable basis for a number of tools and
   applications.
 
--- Tony Maher <tony.maher@ebioinformatics.com>
-   FreeBSD bio-porters <bio@freebsd.net>
+-- Tony Maher <tonym@biolateral.com.au>
diff --git a/biology/ncbi-toolkit/pkg-message b/biology/ncbi-toolkit/pkg-message
index 2c9868c3c9a9..d3506163b167 100644
--- a/biology/ncbi-toolkit/pkg-message
+++ b/biology/ncbi-toolkit/pkg-message
@@ -1,8 +1,6 @@
-
-The data files are installed in "%%PREFIX%%/share/ncbi-tookit".
+The data files are installed in "%%PREFIX%%/share/ncbi-toolkit".
 To use them you need to create a .ncbirc file in your home directory
 with the following lines:
 
 [NCBI]
 Data=%%PREFIX%%/share/ncbi-toolkit/
-
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index 7aedcf5ba1f6..3f1c702ba5c0 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -37,12 +37,12 @@
 %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn19.gif
 %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn20.gif
 %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn21.gif
+%%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn22.gif
 %%PORTDOCS%%share/doc/ncbi-toolkit/ncbixml.txt
 %%PORTDOCS%%share/doc/ncbi-toolkit/sdk.doc
 %%PORTDOCS%%share/doc/ncbi-toolkit/sequin.htm
 bin/Nentrez
 bin/Psequin
-bin/asn2fast
 bin/asn2ff
 bin/asn2xml
 bin/asndhuff
@@ -87,6 +87,7 @@ bin/testobj
 bin/testval
 bin/udv
 bin/vecscreen
+lib/ncbi/libddvlib.a
 lib/ncbi/libncbi.a
 lib/ncbi/libncbiCacc.a
 lib/ncbi/libncbiNacc.a
@@ -102,7 +103,6 @@ lib/ncbi/libncbitool.a
 lib/ncbi/libncbitxc2.a
 lib/ncbi/libnetblast.a
 lib/ncbi/libnetcli.a
-lib/ncbi/libnetcli_.a
 lib/ncbi/libnetentr.a
 lib/ncbi/libvibgif.a
 lib/ncbi/libvibnet.a
@@ -110,6 +110,7 @@ lib/ncbi/libvibrant.a
 include/ncbi/connect/ncbi_ansi_ext.h
 include/ncbi/connect/ncbi_buffer.h
 include/ncbi/connect/ncbi_comm.h
+include/ncbi/connect/ncbi_config.h
 include/ncbi/connect/ncbi_connection.h
 include/ncbi/connect/ncbi_connector.h
 include/ncbi/connect/ncbi_connutil.h
@@ -117,6 +118,7 @@ include/ncbi/connect/ncbi_core.h
 include/ncbi/connect/ncbi_file_connector.h
 include/ncbi/connect/ncbi_heapmgr.h
 include/ncbi/connect/ncbi_http_connector.h
+include/ncbi/connect/ncbi_memory_connector.h
 include/ncbi/connect/ncbi_priv.h
 include/ncbi/connect/ncbi_sendmail.h
 include/ncbi/connect/ncbi_server_info.h