From owner-freebsd-ports-bugs@FreeBSD.ORG Sun Jun 12 00:40:28 2005 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id B7E0916A41F for ; Sun, 12 Jun 2005 00:40:28 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 0917443D4C for ; Sun, 12 Jun 2005 00:40:28 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.3/8.13.3) with ESMTP id j5C0eRKW018434 for ; Sun, 12 Jun 2005 00:40:27 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.3/8.13.1/Submit) id j5C0eRlA018433; Sun, 12 Jun 2005 00:40:27 GMT (envelope-from gnats) Resent-Date: Sun, 12 Jun 2005 00:40:27 GMT Resent-Message-Id: <200506120040.j5C0eRlA018433@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, George Hartzell Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 17C1A16A41C for ; Sun, 12 Jun 2005 00:40:03 +0000 (GMT) (envelope-from hartzell@ash.alerce.com) Received: from ash.alerce.com (w092.z064001164.sjc-ca.dsl.cnc.net [64.1.164.92]) by mx1.FreeBSD.org (Postfix) with ESMTP id 87F4843D1F for ; Sun, 12 Jun 2005 00:40:02 +0000 (GMT) (envelope-from hartzell@ash.alerce.com) Received: from ash.alerce.com (localhost [127.0.0.1]) by ash.alerce.com (8.13.3/8.13.1) with ESMTP id j5C0e1sY031749 for ; Sat, 11 Jun 2005 17:40:01 -0700 (PDT) (envelope-from hartzell@ash.alerce.com) Received: (from hartzell@localhost) by ash.alerce.com (8.13.3/8.13.1/Submit) id j5C0e1IS031742; Sat, 11 Jun 2005 17:40:01 -0700 (PDT) (envelope-from hartzell) Message-Id: <200506120040.j5C0e1IS031742@ash.alerce.com> Date: Sat, 11 Jun 2005 17:40:01 -0700 (PDT) From: George Hartzell To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/82154: Update port biology/primer3 to current release (1.0.0) X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: George Hartzell List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 12 Jun 2005 00:40:28 -0000 >Number: 82154 >Category: ports >Synopsis: Update port biology/primer3 to current release (1.0.0) >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: Sun Jun 12 00:40:26 GMT 2005 >Closed-Date: >Last-Modified: >Originator: George Hartzell >Release: FreeBSD 5.4-STABLE i386 >Organization: >Environment: System: FreeBSD ash.alerce.com 5.4-STABLE FreeBSD 5.4-STABLE #8: Thu Jun 9 14:35:17 PDT 2005 root@ash.alerce.com:/usr/obj/usr/src/sys/ASH i386 >Description: The attached patch updates the primer3 port (biology/primer3) to the current release (1.0.0) >How-To-Repeat: >Fix: --- primer3-diff begins here --- Index: Makefile =================================================================== RCS file: /home/ncvs/ports/biology/primer3/Makefile,v retrieving revision 1.5 diff -c -2 -r1.5 Makefile *** Makefile 27 Feb 2004 22:20:43 -0000 1.5 --- Makefile 12 Jun 2005 00:30:07 -0000 *************** *** 7,14 **** PORTNAME= primer3 ! PORTVERSION= 0.9 CATEGORIES= biology MASTER_SITES= http://frodo.wi.mit.edu/primer3/ ! DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/}_test MAINTAINER= tonym@biolateral.com.au --- 7,14 ---- PORTNAME= primer3 ! PORTVERSION= 1.0.0 CATEGORIES= biology MASTER_SITES= http://frodo.wi.mit.edu/primer3/ ! DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= tonym@biolateral.com.au *************** *** 19,24 **** CPIO= cpio --quiet -pdum -R DOCUMENTS= README example - CGI_EXAMPLES= primer3_www.cgi primer3_www_help.html \ - primer3_www_results.cgi primer3_www_results_help.html post-patch: --- 19,22 ---- *************** *** 34,40 **** @${MKDIR} ${DATADIR} @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR} - .for file in ${CGI_EXAMPLES} - @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR} - .endfor .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} --- 32,35 ---- *************** *** 42,46 **** @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR} .endfor ! @${RMDIR} ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp @${MKDIR} ${EXAMPLESDIR} @cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \ --- 37,41 ---- @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR} .endfor ! @${RM} -rf ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp @${MKDIR} ${EXAMPLESDIR} @cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \ Index: distinfo =================================================================== RCS file: /home/ncvs/ports/biology/primer3/distinfo,v retrieving revision 1.2 diff -c -2 -r1.2 distinfo *** distinfo 31 Mar 2004 03:06:20 -0000 1.2 --- distinfo 12 Jun 2005 00:12:35 -0000 *************** *** 1,2 **** ! MD5 (primer3_0_9_test.tar.gz) = 1ae09013c982eb67953cc4dd5b837088 ! SIZE (primer3_0_9_test.tar.gz) = 948375 --- 1,2 ---- ! MD5 (primer3_1.0.0.tar.gz) = 58605ee607f6218a2a775345b10d15fa ! SIZE (primer3_1.0.0.tar.gz) = 936696 Index: pkg-plist =================================================================== RCS file: /home/ncvs/ports/biology/primer3/pkg-plist,v retrieving revision 1.3 diff -c -2 -r1.3 pkg-plist *** pkg-plist 22 Oct 2003 09:29:51 -0000 1.3 --- pkg-plist 12 Jun 2005 00:28:20 -0000 *************** *** 36,45 **** %%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.rev %%PORTDOCS%%share/examples/primer3/primer1_output - %%PORTDOCS%%share/examples/primer3/primer_boundary1_formated_output %%PORTDOCS%%share/examples/primer3/primer_boundary1_input %%PORTDOCS%%share/examples/primer3/primer_boundary1_output - %%PORTDOCS%%share/examples/primer3/primer_boundary_formated_output %%PORTDOCS%%share/examples/primer3/primer_boundary_input - %%PORTDOCS%%share/examples/primer3/primer_boundary_output %%PORTDOCS%%share/examples/primer3/primer_check_input %%PORTDOCS%%share/examples/primer3/primer_check_output --- 36,42 ---- *************** *** 262,269 **** %%PORTDOCS%%share/examples/primer3/primer_human_output %%PORTDOCS%%share/examples/primer3/primer_input - %%PORTDOCS%%share/examples/primer3/primer_internal1_formated_output %%PORTDOCS%%share/examples/primer3/primer_internal1_input - %%PORTDOCS%%share/examples/primer3/primer_internal1_output - %%PORTDOCS%%share/examples/primer3/primer_internal_formated_output %%PORTDOCS%%share/examples/primer3/primer_internal_input %%PORTDOCS%%share/examples/primer3/primer_internal_output --- 259,263 ---- *************** *** 302,317 **** %%PORTDOCS%%share/examples/primer3/primer_list_last/targets_test.for %%PORTDOCS%%share/examples/primer3/primer_list_last/targets_test.rev - %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_formated_output %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_input %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_output - %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_formated_output %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_input %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_output - %%PORTDOCS%%share/examples/primer3/primer_mispriming_formated_output %%PORTDOCS%%share/examples/primer3/primer_mispriming_input %%PORTDOCS%%share/examples/primer3/primer_mispriming_long_lib_input %%PORTDOCS%%share/examples/primer3/primer_mispriming_long_lib_output %%PORTDOCS%%share/examples/primer3/primer_mispriming_output - %%PORTDOCS%%share/examples/primer3/primer_must_use_formated_output %%PORTDOCS%%share/examples/primer3/primer_must_use_input %%PORTDOCS%%share/examples/primer3/primer_must_use_output --- 296,307 ---- *************** *** 321,325 **** %%PORTDOCS%%share/examples/primer3/primer_obj_fn_output %%PORTDOCS%%share/examples/primer3/primer_output - %%PORTDOCS%%share/examples/primer3/primer_position_penalty_formated_output %%PORTDOCS%%share/examples/primer3/primer_position_penalty_input %%PORTDOCS%%share/examples/primer3/primer_position_penalty_output --- 311,314 ---- *************** *** 335,339 **** %%PORTDOCS%%share/examples/primer3/primer_syntax_input %%PORTDOCS%%share/examples/primer3/primer_syntax_output - %%PORTDOCS%%share/examples/primer3/primer_task_formated_output %%PORTDOCS%%share/examples/primer3/primer_task_input %%PORTDOCS%%share/examples/primer3/primer_task_output --- 324,327 ---- *************** *** 345,354 **** %%PORTDOCS%%share/examples/primer3/repeat_lib5 %%PORTDOCS%%share/examples/primer3/repeat_lib6 bin/primer3 share/primer3/Copyright - share/primer3/primer3_www.cgi - share/primer3/primer3_www_help.html - share/primer3/primer3_www_results.cgi - share/primer3/primer3_www_results_help.html @dirrm share/primer3 %%PORTDOCS%%@dirrm %%DOCSDIR%%/ --- 333,357 ---- %%PORTDOCS%%share/examples/primer3/repeat_lib5 %%PORTDOCS%%share/examples/primer3/repeat_lib6 + %%PORTDOCS%%share/examples/primer3/long_seq_tm_test.pl + %%PORTDOCS%%share/examples/primer3/not_for_production_Ns.lib + %%PORTDOCS%%share/examples/primer3/not_for_production_Xs.lib + %%PORTDOCS%%share/examples/primer3/primer_boundary1_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_boundary_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_boundary_output + %%PORTDOCS%%share/examples/primer3/primer_internal1_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_internal1_output + %%PORTDOCS%%share/examples/primer3/primer_internal_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_lib_amb_codes_input + %%PORTDOCS%%share/examples/primer3/primer_lib_amb_codes_output + %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_mispriming_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_must_use_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_position_penalty_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_task_formatted_output + %%PORTDOCS%%share/examples/primer3/primer_template_mispriming_input + %%PORTDOCS%%share/examples/primer3/primer_template_mispriming_output bin/primer3 share/primer3/Copyright @dirrm share/primer3 %%PORTDOCS%%@dirrm %%DOCSDIR%%/ --- primer3-diff ends here --- >Release-Note: >Audit-Trail: >Unformatted: