From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Jan 24 15:30:14 2011 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id BEF8B1065674 for ; Mon, 24 Jan 2011 15:30:14 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 81D528FC14 for ; Mon, 24 Jan 2011 15:30:14 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.4/8.14.4) with ESMTP id p0OFUENr062515 for ; Mon, 24 Jan 2011 15:30:14 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.4/8.14.4/Submit) id p0OFUEej062506; Mon, 24 Jan 2011 15:30:14 GMT (envelope-from gnats) Resent-Date: Mon, 24 Jan 2011 15:30:14 GMT Resent-Message-Id: <201101241530.p0OFUEej062506@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, Fernan Aguero Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 82BEE1065670; Mon, 24 Jan 2011 15:30:02 +0000 (UTC) (envelope-from fernan.aguero@gmail.com) Received: from mail-iw0-f182.google.com (mail-iw0-f182.google.com [209.85.214.182]) by mx1.freebsd.org (Postfix) with ESMTP id 3558F8FC14; Mon, 24 Jan 2011 15:30:01 +0000 (UTC) Received: by iwn39 with SMTP id 39so4216620iwn.13 for ; Mon, 24 Jan 2011 07:30:01 -0800 (PST) Received: by 10.231.40.13 with SMTP id i13mr4888006ibe.190.1295881113977; Mon, 24 Jan 2011 06:58:33 -0800 (PST) Received: by 10.231.205.142 with HTTP; Mon, 24 Jan 2011 06:58:03 -0800 (PST) Message-Id: Date: Mon, 24 Jan 2011 11:58:03 -0300 From: Fernan Aguero To: FreeBSD-gnats-submit@FreeBSD.org Cc: erwin@FreeBSD.org Subject: ports/154267: [maintainer-update] upgrade biology/fasta3 to v36, fix fetch issue X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jan 2011 15:30:14 -0000 >Number: 154267 >Category: ports >Synopsis: [maintainer-update] upgrade biology/fasta3 to v36, fix fetch issue >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Mon Jan 24 15:30:13 UTC 2011 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.3-RELEASE-p1 i386 >Organization: IIB-UNSAM >Environment: FreeBSD gama.iib.unsam.edu.ar 6.3-RELEASE-p1 FreeBSD 6.3-RELEASE-p1 #0: Wed Apr 2 18:37:14 ART 2008 fernan@gama.iib.unsam.edu.ar:/usr/obj/freebsd/freebsd-6.3/src/sys/GAMA i386 >Description: FASTA is reportedly broken, as the old distfiles have been removed from upstream sources. http://pointyhat-west.isc.freebsd.org/errorlogs/amd64-errorlogs/a.7.4-release.20110113192327.pointyhat-west/fasta3-35.4.9.log Upgrade FASTA to latest v.36, and fix the fetch issue >How-To-Repeat: >Fix: --- fasta3.diff begins here --- diff --exclude CVS -u /usr/ports/biology/fasta3/Makefile fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile 2009-08-23 12:47:37.000000000 -0300 +++ fasta3/Makefile 2011-01-21 18:15:44.000000000 -0300 @@ -7,9 +7,9 @@ # PORTNAME= fasta3 -PORTVERSION= 35.4.9 +PORTVERSION= 36.3.2 CATEGORIES= biology -MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta3/ +MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/ DISTNAME= fasta-${PORTVERSION} MAINTAINER= fernan@iib.unsam.edu.ar @@ -34,12 +34,12 @@ DATA= data/*.mat EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib -MAN1= fasta35.1 map_db.1 ps_lav.1 pvcomp.1 -MLINKS= fasta35.1 tfasta35.1 fasta35.1 fastx35.1 fasta35.1 tfastx35.1 \ - fasta35.1 fasty35.1 fasta35.1 tfasty35.1 fasta35.1 ssearch35.1 \ - fasta35.1 fastf35.1 fasta35.1 fasts35.1 fasta35.1 tfasts35.1 \ - fasta35.1 fastm35.1 fasta35.1 tfastf35.1 fasta35.1 ggsearch35.1 \ - fasta35.1 lalign35.1 fasta35.1 prss35.1 fasta35.1 prfx35.1 +MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 +MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \ + fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \ + fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \ + fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \ + fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1 PLIST_SUB= VER=${PORTVERSION:R:R} post-patch: diff --exclude CVS -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo 2009-08-23 12:47:37.000000000 -0300 +++ fasta3/distinfo 2011-01-21 18:03:08.000000000 -0300 @@ -1,3 +1,2 @@ -MD5 (fasta-35.4.9.tar.gz) = 6bf19b771f2c64287b7713864b9f0a69 -SHA256 (fasta-35.4.9.tar.gz) = 4beaed42557572a1c8e5480e93641af175fa43c545f75c4bf06db62dced6bd39 -SIZE (fasta-35.4.9.tar.gz) = 630748 +SHA256 (fasta-36.3.2.tar.gz) = 1eddb7dac3a52311d43bac854b2153c13aa23cbb163952c9e385a75aa2b9e446 +SIZE (fasta-36.3.2.tar.gz) = 711876 Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files diff --exclude CVS -u /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist --- /usr/ports/biology/fasta3/pkg-plist 2009-06-09 04:53:37.000000000 -0300 +++ fasta3/pkg-plist 2011-01-21 18:26:39.000000000 -0300 @@ -17,7 +17,6 @@ bin/lalign%%VER%% bin/lav2ps bin/lav2svg -bin/list_db bin/map_db bin/ssearch%%VER%% bin/ssearch%%VER%%_t @@ -39,10 +38,6 @@ %%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc %%PORTDOCS%%%%DOCSDIR%%/fasta20.doc %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc -%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4 %%PORTDOCS%%%%DOCSDIR%%/readme.v30 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7 @@ -52,12 +47,14 @@ %%PORTDOCS%%%%DOCSDIR%%/readme.v33t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v34t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v35 +%%PORTDOCS%%%%DOCSDIR%%/readme.v36 %%PORTDOCS%%%%DOCSDIR%%/readme.w32 %%PORTDOCS%%%%DOCSDIR%%/fasta.defaults %%PORTDOCS%%%%DOCSDIR%%/fasta.options %%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html %%PORTDOCS%%%%DOCSDIR%%/changes_v34.html %%PORTDOCS%%%%DOCSDIR%%/changes_v35.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html %%EXAMPLESDIR%%/egmsmg.aa %%EXAMPLESDIR%%/gstt1_drome.aa %%EXAMPLESDIR%%/gtm1_human.aa @@ -95,6 +92,7 @@ %%EXAMPLESDIR%%/hsgstm1b.seq %%EXAMPLESDIR%%/humgstd.seq %%EXAMPLESDIR%%/mgstm1.seq +%%EXAMPLESDIR%%/mgstm1_genclone.seq %%EXAMPLESDIR%%/mgtt2_x.seq %%EXAMPLESDIR%%/titin_hum.seq %%EXAMPLESDIR%%/mu.lib --- fasta3.diff ends here --- --0003255763fe784d3e049a98d5d1 Content-Type: text/x-patch; charset=US-ASCII; name="fasta3.diff" 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