Date: Sun, 16 Jun 2002 13:16:57 +1000 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/39357: Maintainer update: biology/ncbi-toolkit Message-ID: <200206160316.g5G3Gvrm052887@dt.home>
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>Number: 39357
>Category: ports
>Synopsis: Maintainer update: biology/ncbi-toolkit
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Sat Jun 15 20:20:01 PDT 2002
>Closed-Date:
>Last-Modified:
>Originator: Tony Maher
>Release: FreeBSD 4.6-RC i386
>Organization:
BioLateral
>Environment:
System: FreeBSD dt.home 4.6-RC FreeBSD 4.6-RC #5: Sat Jun 1 13:32:56 EST 2002 root@dt.home:/usr/obj/usr/src/sys/DT i386
>Description:
Update ncbi-toolkit to version 2002.04.26.
Use the new ${REINPLACE_CMD} while I am here.
Update patch-aa
a) to remove a file that is not actually an executable
b) not list all the libraries explicitly, just copy
all library files we can find. This simplifies
future updates and we already know (or will update)
what they are via pkg-plist.
Update emails in pkg-descr.
Fix typo and unnecessary blank lines in pkg-message.
>How-To-Repeat:
>Fix:
diff -u ncbi-toolkit.orig/Makefile ncbi-toolkit/Makefile
--- ncbi-toolkit.orig/Makefile Sat Jun 8 10:40:10 2002
+++ ncbi-toolkit/Makefile Sun Jun 16 11:56:45 2002
@@ -6,7 +6,7 @@
#
PORTNAME= ncbi-toolkit
-PORTVERSION= 2001.12.20
+PORTVERSION= 2002.04.26
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME= ncbi
@@ -36,7 +36,7 @@
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 -u ncbi-toolkit.orig/distinfo ncbi-toolkit/distinfo
--- ncbi-toolkit.orig/distinfo Fri Feb 22 18:57:05 2002
+++ ncbi-toolkit/distinfo Sat Jun 15 09:57:51 2002
@@ -1 +1 @@
-MD5 (ncbi.tar.gz) = 8038afb3f5502b3b8ade4f221eebe46e
+MD5 (ncbi.tar.gz) = 7278c10b227b0298f00a5ed5dde58bc4
Common subdirectories: ncbi-toolkit.orig/files and ncbi-toolkit/files
diff -u ncbi-toolkit.orig/pkg-descr ncbi-toolkit/pkg-descr
--- ncbi-toolkit.orig/pkg-descr Thu Jun 21 00:25:54 2001
+++ ncbi-toolkit/pkg-descr Sat Jun 15 09:57:51 2002
@@ -16,5 +16,4 @@
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 -u ncbi-toolkit.orig/pkg-message ncbi-toolkit/pkg-message
--- ncbi-toolkit.orig/pkg-message Fri Feb 22 18:57:05 2002
+++ ncbi-toolkit/pkg-message Sat Jun 15 09:57:51 2002
@@ -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 -u ncbi-toolkit.orig/pkg-plist ncbi-toolkit/pkg-plist
--- ncbi-toolkit.orig/pkg-plist Fri Feb 22 18:57:05 2002
+++ ncbi-toolkit/pkg-plist Sat Jun 15 09:57:51 2002
@@ -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/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/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 @@
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_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
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