Date: Fri, 12 Jan 2001 15:53:23 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24274: Port fix: textproc/py-martel (MAINTAINER) Message-ID: <E14H4dv-0000FR-00@fling.sanbi.ac.za>
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>Number: 24274 >Category: ports >Synopsis: Port fix: textproc/py-martel (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: Fri Jan 12 06:00:01 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - The patch in files/patch-Generate.py has been recalled by Martel's author. It resulted in a huge performance hit, while the problem it "fixed" turned out to be not a bug, but a limitation of Martel's design. See: http://www.biopython.org/pipermail/biopython-dev/2000-December/000215.html - File to be removed: files/patch-Generate.py - Bumped PORTREVISION >How-To-Repeat: >Fix: diff -ruN py-martel.bak/Makefile py-martel/Makefile --- py-martel.bak/Makefile Fri Jan 12 15:48:41 2001 +++ py-martel/Makefile Fri Jan 12 15:47:34 2001 @@ -7,6 +7,7 @@ PORTNAME= martel PORTVERSION= 0.5 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= textproc biology python MASTER_SITES= http://www.biopython.org/~dalke/Martel/ diff -ruN py-martel.bak/files/patch-Generate.py py-martel/files/patch-Generate.py --- py-martel.bak/files/patch-Generate.py Fri Jan 12 15:48:41 2001 +++ py-martel/files/patch-Generate.py Thu Jan 1 02:00:00 1970 @@ -1,45 +0,0 @@ -From: "Andrew Dalke" <dalke@acm.org> -To: <biopython-dev@biopython.org> -Date: Wed, 6 Dec 2000 01:12:29 -0700 - -There's a bug in Martel-0.4 and earlier versions. - -Suppose you have ([<>][ABC])+[<>]? -and want to match it against - - <A<B< - -The "<A" matches the first [<>][ABC]. The "<B" matches -the second [<>][ABC]. The parser tries to match the final -"<" against [<>][ABC] and should fail then try to match -the "<" against [<>]? . - -The bug was that it would match the "<" against the [<>] in -[<>][ABC] and fail at that point. It gives an assertion error -about "l" being greater than "r". - -Here's the patch. The only consequence should be a small hit -in performance. - - Andrew - -[ Note from port maintainer: - This patch was somehow not incorporated into Martel 0.5 ] - - ---- Generate.py.orig Wed Nov 22 09:26:48 2000 -+++ Generate.py Thu Dec 7 12:27:09 2000 -@@ -268,11 +268,11 @@ - - # Must repeat at least "i" times. - for i in range(min_count): -- result.append( (None, TT.SubTable, tuple(tagtable)) ) -+ result.append( (">ignore", TT.Table, tuple(tagtable)) ) - - # Special case for when the max count means "unbounded" - if max_count == sre_parse.MAXREPEAT: -- result.append( (None, TT.SubTable, tuple(tagtable), -+ result.append( (">ignore", TT.Table, tuple(tagtable), - +1, 0)) - elif min_count == max_count: - # Special case when i == j >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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