From owner-freebsd-ports Mon Jan 29 6:41: 3 2001 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 7F26037B6AB for ; Mon, 29 Jan 2001 06:40:01 -0800 (PST) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.1/8.11.1) id f0TEe1w97990; Mon, 29 Jan 2001 06:40:01 -0800 (PST) (envelope-from gnats) Received: from fling.sanbi.ac.za (fling.sanbi.ac.za [196.38.142.119]) by hub.freebsd.org (Postfix) with ESMTP id E4ED937B6A4 for ; Mon, 29 Jan 2001 06:34:32 -0800 (PST) Received: from johann by fling.sanbi.ac.za with local (Exim 3.13 #4) id 14NFO1-0006v8-00 for FreeBSD-gnats-submit@freebsd.org; Mon, 29 Jan 2001 16:34:29 +0200 Message-Id: Date: Mon, 29 Jan 2001 16:34:29 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.2 Subject: ports/24717: Port update/fix: biology/emboss (MAINTAINER) Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk X-Loop: FreeBSD.org >Number: 24717 >Category: ports >Synopsis: Port update/fix: biology/emboss (MAINTAINER) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jan 29 06:40:01 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1 - Update the EMBASSY package EMNU from 1.0.2 to 1.0.3 - Merged the four pkg-plist* files into one - EMBOSS now looks for its databases in sensible default locations - this is a bigger deal than it may sound! :-) - Fixed a broken patch - EMBOSS now correctly looks for its configuration file in ${PREFIX}/etc - Added some sensible defaults to the sample configuration file which is installed to ${PREFIX}/etc - Files added: - files/patch-configure - files/patch-emboss-acd-emboss.default - Files deleted: - pkg-plist.EMNU - pkg-plist.MSE - pkg-plist.PHYLIP - pkg-plist.TOPO - Only tested on -CURRENT; I know there are still issues with ncurses on 3-STABLE >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Mon Jan 29 16:27:10 2001 +++ emboss/Makefile Fri Jan 26 11:17:12 2001 @@ -6,10 +6,11 @@ # PORTNAME= emboss -PORTVERSION= 1.9.0 +PORTVERSION= 1.9.1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ + ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} DIST_SUBDIR= ${PORTNAME} @@ -24,7 +25,6 @@ USE_LIBTOOL= yes USE_XLIB= yes USE_MOTIF= yes -PLIST= ${WRKDIR}/pkg-plist PKGMESSAGE= ${WRKDIR}/pkg-message .if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc) @@ -33,29 +33,30 @@ CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \ LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib" - SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ - MKDIR="${MKDIR}" \ - RM="${RM}" + MKDIR="${MKDIR}" RM="${RM}" WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -EMNU_VERSION= 1.0.2 +EMNU_VERSION= 1.0.3 MSE_VERSION= 0.0.4 TOPO_VERSION= 0.1 PHYLIP_VERSION= 3.573c +DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html + .for app in EMNU MSE PHYLIP TOPO SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" .if defined(WITH_${app}) APPLIST+= ${app} -PLISTS+= ${PKGDIR}/pkg-plist.${app} ${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} ${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} DISTFILES+= ${${app}_DISTFILE} +PLIST_${app}= "" +.else +PLIST_${app}= "@comment " .endif +PLIST_SUB+= PLIST_${app}=${PLIST_${app}} .endfor -PLISTS+= ${PKGDIR}/pkg-plist -DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html pre-fetch: @ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME} @@ -74,7 +75,7 @@ post-patch: .for DIR in ${DOC_DIRS} @ ${PERL} -pi.orig -e \ - "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \ + 's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \ ${WRKSRC}/${DIR}/Makefile.in .endfor @@ -96,9 +97,6 @@ ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ ${MAKE_ARGS}) .endfor - -pre-install: - @ ${CAT} ${PLISTS} > ${PLIST} post-install: .for app in ${APPLIST} diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Mon Jan 29 16:27:10 2001 +++ emboss/distinfo Fri Jan 26 10:25:48 2001 @@ -1,5 +1,5 @@ -MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c -MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b -MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f -MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3 -MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29 +MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9 +MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678 +MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f +MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834 diff -ruN emboss.bak/files/patch-aa emboss/files/patch-aa --- emboss.bak/files/patch-aa Mon Jan 29 16:27:10 2001 +++ emboss/files/patch-aa Thu Jan 25 16:08:08 2001 @@ -17,7 +17,7 @@ + if (!prefixRootFile) + { + ajFmtPrintS (&namRootStr, "%s/etc/%s.default", -+ namInstallRoot, prefixCap, prefix); ++ namInstallRoot, prefix); + prefixRootFile = fopen (ajStrStr(namRootStr), "r"); + } + diff -ruN emboss.bak/files/patch-configure emboss/files/patch-configure --- emboss.bak/files/patch-configure Thu Jan 1 02:00:00 1970 +++ emboss/files/patch-configure Thu Jan 25 19:08:09 2001 @@ -0,0 +1,11 @@ +--- configure.orig Mon Jan 22 23:28:17 2001 ++++ configure Thu Jan 25 19:07:33 2001 +@@ -1473,7 +1473,7 @@ + + + +-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" ++AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\"" + + #AC_PROG_CXX + for ac_prog in mawk gawk nawk awk diff -ruN emboss.bak/files/patch-emboss-acd-emboss.default emboss/files/patch-emboss-acd-emboss.default --- emboss.bak/files/patch-emboss-acd-emboss.default Thu Jan 1 02:00:00 1970 +++ emboss/files/patch-emboss-acd-emboss.default Mon Jan 29 16:24:53 2001 @@ -0,0 +1,32 @@ +--- emboss/acd/emboss.default.orig Mon Jan 22 23:26:54 2001 ++++ emboss/acd/emboss.default Mon Jan 29 16:23:15 2001 +@@ -1,9 +1,26 @@ +-SET emboss_tempdata /nfs/WWW/data/EMBOSS/test ++##################################################### ++### Configuration options for FreeBSD EMBOSS port ### ++##################################################### + +-# Logfile - set this to a file that any user can append to +-# and EMBOSS applications will automatically write log information ++# This is the compiled-in default. Change only if ++# you know what you're doing! ++# ++#SET emboss_data /usr/local/share/EMBOSS/data + ++# This is where your local databases reside ++# (this will differ from site to site): ++# ++SET emboss_tempdata /var/db/bio ++ ++# Logfile - set this to a file that any user can append to and EMBOSS ++# applications will automatically write log information ++# + #SET emboss_logfile /packages/emboss/emboss/log ++ ++ ++########################################### ++### Configuration options for databases ### ++########################################### + + # swissprot (Puffer fish entries) + # ========= diff -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Mon Jan 29 16:27:10 2001 +++ emboss/pkg-plist Fri Jan 26 10:37:26 2001 @@ -1,3 +1,61 @@ +%%PLIST_EMNU%%bin/emnu +%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd +%%PLIST_MSE%%bin/mse +%%PLIST_MSE%%lib/libckit.a +%%PLIST_MSE%%lib/libckit.la +%%PLIST_MSE%%lib/libckit.so +%%PLIST_MSE%%lib/libckit.so.1 +%%PLIST_MSE%%share/EMBOSS/acd/mse.acd +%%PLIST_PHYLIP%%bin/eclique +%%PLIST_PHYLIP%%bin/econsense +%%PLIST_PHYLIP%%bin/econtml +%%PLIST_PHYLIP%%bin/econtrast +%%PLIST_PHYLIP%%bin/ednacomp +%%PLIST_PHYLIP%%bin/ednadist +%%PLIST_PHYLIP%%bin/ednainvar +%%PLIST_PHYLIP%%bin/ednaml +%%PLIST_PHYLIP%%bin/ednamlk +%%PLIST_PHYLIP%%bin/ednapars +%%PLIST_PHYLIP%%bin/ednapenny +%%PLIST_PHYLIP%%bin/edollop +%%PLIST_PHYLIP%%bin/edolpenny +%%PLIST_PHYLIP%%bin/efactor +%%PLIST_PHYLIP%%bin/efitch +%%PLIST_PHYLIP%%bin/egendist +%%PLIST_PHYLIP%%bin/ekitsch +%%PLIST_PHYLIP%%bin/emix +%%PLIST_PHYLIP%%bin/eneighbor +%%PLIST_PHYLIP%%bin/epenny +%%PLIST_PHYLIP%%bin/eprotdist +%%PLIST_PHYLIP%%bin/eprotpars +%%PLIST_PHYLIP%%bin/erestml +%%PLIST_PHYLIP%%bin/eseqboot +%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd +%%PLIST_TOPO%%bin/topo +%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd bin/abiview bin/acdc bin/antigenic diff -ruN emboss.bak/pkg-plist.EMNU emboss/pkg-plist.EMNU --- emboss.bak/pkg-plist.EMNU Mon Jan 29 16:27:10 2001 +++ emboss/pkg-plist.EMNU Thu Jan 1 02:00:00 1970 @@ -1,2 +0,0 @@ -bin/emnu -share/EMBOSS/acd/emnu.acd diff -ruN emboss.bak/pkg-plist.MSE emboss/pkg-plist.MSE --- emboss.bak/pkg-plist.MSE Mon Jan 29 16:27:10 2001 +++ emboss/pkg-plist.MSE Thu Jan 1 02:00:00 1970 @@ -1,6 +0,0 @@ -bin/mse -lib/libckit.a -lib/libckit.la -lib/libckit.so -lib/libckit.so.1 -share/EMBOSS/acd/mse.acd diff -ruN emboss.bak/pkg-plist.PHYLIP emboss/pkg-plist.PHYLIP --- emboss.bak/pkg-plist.PHYLIP Mon Jan 29 16:27:10 2001 +++ emboss/pkg-plist.PHYLIP Thu Jan 1 02:00:00 1970 @@ -1,48 +0,0 @@ -bin/eclique -bin/econsense -bin/econtml -bin/econtrast -bin/ednacomp -bin/ednadist -bin/ednainvar -bin/ednaml -bin/ednamlk -bin/ednapars -bin/ednapenny -bin/edollop -bin/edolpenny -bin/efactor -bin/efitch -bin/egendist -bin/ekitsch -bin/emix -bin/eneighbor -bin/epenny -bin/eprotdist -bin/eprotpars -bin/erestml -bin/eseqboot -share/EMBOSS/acd/eclique.acd -share/EMBOSS/acd/econsense.acd -share/EMBOSS/acd/econtml.acd -share/EMBOSS/acd/econtrast.acd -share/EMBOSS/acd/ednacomp.acd -share/EMBOSS/acd/ednadist.acd -share/EMBOSS/acd/ednainvar.acd -share/EMBOSS/acd/ednaml.acd -share/EMBOSS/acd/ednamlk.acd -share/EMBOSS/acd/ednapars.acd -share/EMBOSS/acd/ednapenny.acd -share/EMBOSS/acd/edollop.acd -share/EMBOSS/acd/edolpenny.acd -share/EMBOSS/acd/efactor.acd -share/EMBOSS/acd/efitch.acd -share/EMBOSS/acd/egendist.acd -share/EMBOSS/acd/ekitsch.acd -share/EMBOSS/acd/emix.acd -share/EMBOSS/acd/eneighbor.acd -share/EMBOSS/acd/epenny.acd -share/EMBOSS/acd/eprotdist.acd -share/EMBOSS/acd/eprotpars.acd -share/EMBOSS/acd/erestml.acd -share/EMBOSS/acd/eseqboot.acd diff -ruN emboss.bak/pkg-plist.TOPO emboss/pkg-plist.TOPO --- emboss.bak/pkg-plist.TOPO Mon Jan 29 16:27:10 2001 +++ emboss/pkg-plist.TOPO Thu Jan 1 02:00:00 1970 @@ -1,2 +0,0 @@ -bin/topo -share/EMBOSS/acd/topo.acd >Release-Note: >Audit-Trail: >Unformatted: To 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