From owner-freebsd-ports Sat Jun 15 20:20:16 2002 Delivered-To: freebsd-ports@hub.freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id E653C37B407 for ; Sat, 15 Jun 2002 20:20:01 -0700 (PDT) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.6/8.11.6) id g5G3K1o43013; Sat, 15 Jun 2002 20:20:01 -0700 (PDT) (envelope-from gnats) Received: from c16703.thorn1.nsw.optusnet.com.au (c16703.thorn1.nsw.optusnet.com.au [210.49.148.69]) by hub.freebsd.org (Postfix) with ESMTP id B22F137B408 for ; Sat, 15 Jun 2002 20:18:21 -0700 (PDT) Received: from dt.home (localhost [127.0.0.1]) by c16703.thorn1.nsw.optusnet.com.au (8.12.3/8.12.3) with ESMTP id g5G3IIH9053081 for ; Sun, 16 Jun 2002 13:18:19 +1000 (EST) (envelope-from tonym@dt.home) Received: (from tonym@localhost) by dt.home (8.12.3/8.12.3/Submit) id g5G3Gvrm052887; Sun, 16 Jun 2002 13:16:57 +1000 (EST) Message-Id: <200206160316.g5G3Gvrm052887@dt.home> Date: Sun, 16 Jun 2002 13:16:57 +1000 (EST) From: Tony Maher Reply-To: Tony Maher To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/39357: Maintainer update: biology/ncbi-toolkit Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >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 - FreeBSD bio-porters +-- Tony Maher 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 >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message