Date: Thu, 27 Jul 2000 18:33:41 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/20223: New port: biology/p5-AcePerl Message-ID: <E13HqbN-0002k7-00@fling.sanbi.ac.za>
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>Number: 20223 >Category: ports >Synopsis: New port: biology/p5-AcePerl >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: Thu Jul 27 09:40:01 PDT 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 3.5-STABLE i386 >Organization: Electric Genetics >Environment: FreeBSD fling.sanbi.ac.za 3.5-STABLE FreeBSD 3.5-STABLE #2: Fri Jul 14 17:30:00 SAST 2000 toor@fling.sanbi.ac.za:/usr/src/sys/compile/FLING i386 >Description: New port of a Perl interface to the ACEDB genome database system >How-To-Repeat: N/A >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # p5-AcePerl # p5-AcePerl/pkg # p5-AcePerl/pkg/PLIST # p5-AcePerl/pkg/DESCR # p5-AcePerl/pkg/COMMENT # p5-AcePerl/patches # p5-AcePerl/patches/patch-ab # p5-AcePerl/patches/patch-aa # p5-AcePerl/Makefile # p5-AcePerl/files # p5-AcePerl/files/md5 # p5-AcePerl/files/FREEBSD_DEF # echo c - p5-AcePerl mkdir -p p5-AcePerl > /dev/null 2>&1 echo c - p5-AcePerl/pkg mkdir -p p5-AcePerl/pkg > /dev/null 2>&1 echo x - p5-AcePerl/pkg/PLIST sed 's/^X//' >p5-AcePerl/pkg/PLIST << 'END-of-p5-AcePerl/pkg/PLIST' Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.bs Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.so Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isTimestamp.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace END-of-p5-AcePerl/pkg/PLIST echo x - p5-AcePerl/pkg/DESCR sed 's/^X//' >p5-AcePerl/pkg/DESCR << 'END-of-p5-AcePerl/pkg/DESCR' XAcePerl is an object-oriented Perl interface for the ACEDB genome database Xsystem. It provides functionality for connecting to remote ACEDB databases, Xperforming queries, fetching ACE objects, and updating databases. X XWWW: http://stein.cshl.org/AcePerl/ X X- Johann Xjohann@egenetics.com END-of-p5-AcePerl/pkg/DESCR echo x - p5-AcePerl/pkg/COMMENT sed 's/^X//' >p5-AcePerl/pkg/COMMENT << 'END-of-p5-AcePerl/pkg/COMMENT' XPerl interface to the ACEDB genome database system END-of-p5-AcePerl/pkg/COMMENT echo c - p5-AcePerl/patches mkdir -p p5-AcePerl/patches > /dev/null 2>&1 echo x - p5-AcePerl/patches/patch-ab sed 's/^X//' >p5-AcePerl/patches/patch-ab << 'END-of-p5-AcePerl/patches/patch-ab' X--- ace/memsubs.c.orig Mon Jan 11 02:01:29 1999 X+++ ace/memsubs.c Thu Jul 27 17:18:45 2000 X@@ -21,7 +21,7 @@ X #if defined(NEXT) || defined(HP) || defined(MACINTOSH) X extern void* malloc(mysize_t size) ; X #elif !defined(WIN32) X-#include <malloc.h> /* normal machines */ X+#include <stdlib.h> /* normal machines */ X #endif X X /********** primary type definition **************/ END-of-p5-AcePerl/patches/patch-ab echo x - p5-AcePerl/patches/patch-aa sed 's/^X//' >p5-AcePerl/patches/patch-aa << 'END-of-p5-AcePerl/patches/patch-aa' X--- ace/wh/mystdlib.h.orig Fri Jul 2 23:04:55 1999 X+++ ace/wh/mystdlib.h Thu Jul 27 17:20:19 2000 X@@ -161,7 +161,7 @@ X #endif X X #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \ X- defined(HP) || defined(WIN32) X+ defined(HP) || defined(WIN32) || defined(FREEBSD) X X #ifdef WIN32 X #include <mbctype.h> X--- ace/wh/mydirent.h.orig Mon Jan 11 01:51:40 1999 X+++ ace/wh/mydirent.h Thu Jul 27 17:20:41 2000 X@@ -55,7 +55,7 @@ X extern char *getwd(char *pathname) ; X #endif /* HP || SOLARIS || WIN32 */ X X-#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) X+#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined(FREEBSD) X #include <dirent.h> X typedef struct dirent MYDIRENT ; X #endif END-of-p5-AcePerl/patches/patch-aa echo x - p5-AcePerl/Makefile sed 's/^X//' >p5-AcePerl/Makefile << 'END-of-p5-AcePerl/Makefile' X# New ports collection makefile for: p5-AcePerl X# Date created: 26 July 2000 X# Whom: Johann Visagie <johann@egenetics.com> X# X# $FreeBSD$ X# X XPORTNAME= AcePerl XPORTVERSION= 1.62 XCATEGORIES= biology databases perl5 XMASTER_SITES= http://stein.cshl.org/AcePerl/archive/ \ X ${MASTER_SITE_PERL_CPAN} XMASTER_SITE_SUBDIR=Ace XPKGNAMEPREFIX= p5- X XMAINTAINER= johann@egenetics.com X XUSE_PERL5= YES X XMAN3= Ace::Sequence::Feature.3 \ X Ace::Sequence.3 \ X Ace.3 \ X Ace::Sequence::FeatureList.3 \ X Ace::Sequence::Multi.3 \ X Ace::Sequence::Homol.3 \ X Ace::Object.3 \ X Ace::Local.3 \ X Ace::Iterator.3 \ X Ace::Model.3 X XMANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION} X Xdo-configure: X ${CP} ${FILESDIR}/FREEBSD_DEF ${WRKSRC}/ace/wmake/ X @ cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL X X.include <bsd.port.mk> END-of-p5-AcePerl/Makefile echo c - p5-AcePerl/files mkdir -p p5-AcePerl/files > /dev/null 2>&1 echo x - p5-AcePerl/files/md5 sed 's/^X//' >p5-AcePerl/files/md5 << 'END-of-p5-AcePerl/files/md5' XMD5 (AcePerl-1.62.tar.gz) = d9978077a8e1857b94216d5a28bc38ef END-of-p5-AcePerl/files/md5 echo x - p5-AcePerl/files/FREEBSD_DEF sed 's/^X//' >p5-AcePerl/files/FREEBSD_DEF << 'END-of-p5-AcePerl/files/FREEBSD_DEF' X################################################################# X############### acedb: R.Durbin and J.Thierry-Mieg ############## X################################################################# X X################################################################# X########### This file is included by wmake/truemake ############# X###### Edit this file to adapt the ACeDB to a new machine ###### X##### following the explanations given in wmake/truemake ##### X################################################################# X XCFLAGS+= -g -Wall -O2 -DACEDB4 XNAME = FREEBSD XCOMPILER = gcc ${CFLAGS} XLINKER = gcc -g X XLIBS = -lm XXt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11 XLEX_LIBS = X XRPCGEN_FLAGS = -b -I -K -1 X X################################################################# X################################################################# END-of-p5-AcePerl/files/FREEBSD_DEF exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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