From owner-cvs-all@FreeBSD.ORG Fri Mar 31 09:43:23 2006 Return-Path: X-Original-To: cvs-all@FreeBSD.org Delivered-To: cvs-all@FreeBSD.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 8240116A401; Fri, 31 Mar 2006 09:43:23 +0000 (UTC) (envelope-from thierry@FreeBSD.org) Received: from repoman.freebsd.org (repoman.freebsd.org [216.136.204.115]) by mx1.FreeBSD.org (Postfix) with ESMTP id 3C4EC43D55; Fri, 31 Mar 2006 09:43:23 +0000 (GMT) (envelope-from thierry@FreeBSD.org) Received: from repoman.freebsd.org (localhost [127.0.0.1]) by repoman.freebsd.org (8.13.1/8.13.1) with ESMTP id k2V9hMfA056491; Fri, 31 Mar 2006 09:43:23 GMT (envelope-from thierry@repoman.freebsd.org) Received: (from thierry@localhost) by repoman.freebsd.org (8.13.1/8.13.1/Submit) id k2V9hMo1056490; Fri, 31 Mar 2006 09:43:22 GMT (envelope-from thierry) Message-Id: <200603310943.k2V9hMo1056490@repoman.freebsd.org> From: Thierry Thomas Date: Fri, 31 Mar 2006 09:43:22 +0000 (UTC) To: ports-committers@FreeBSD.org, cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org X-FreeBSD-CVS-Branch: HEAD Cc: Subject: cvs commit: ports UPDATING ports/biology/emboss Makefile distinfo pkg-message pkg-plist ports/biology/emboss/files patch-ajindex.c patch-ajindex.h patch-ajpdb.c patch-ajseqdb.c patch-dbxfasta.c patch-dbxflat.c patch-dbxgcg.c patch-embindex.c patch-embindex.h ... X-BeenThere: cvs-all@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: CVS commit messages for the entire tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 31 Mar 2006 09:43:23 -0000 thierry 2006-03-31 09:43:22 UTC FreeBSD ports repository Modified files: . UPDATING biology/emboss Makefile distinfo pkg-plist biology/embassy Makefile distinfo pkg-plist Added files: biology/emboss/files patch-ajindex.c patch-ajindex.h patch-ajpdb.c patch-ajseqdb.c patch-dbxfasta.c patch-dbxflat.c patch-dbxgcg.c patch-embindex.c patch-embindex.h patch-emboss.default.template patch-marscan.c pkg-message.in pre-install.in Removed files: biology/emboss pkg-message biology/embassy/files domainatrix-patch-Makefile.in emnu-patch-Makefile.in Log: For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero (maintainer) Revision Changes Path 1.304 +17 -1 ports/UPDATING 1.6 +22 -18 ports/biology/embassy/Makefile 1.4 +39 -24 ports/biology/embassy/distinfo 1.2 +0 -11 ports/biology/embassy/files/domainatrix-patch-Makefile.in (dead) 1.2 +0 -11 ports/biology/embassy/files/emnu-patch-Makefile.in (dead) 1.3 +177 -124 ports/biology/embassy/pkg-plist 1.47 +15 -14 ports/biology/emboss/Makefile 1.26 +3 -3 ports/biology/emboss/distinfo 1.1 +5134 -0 ports/biology/emboss/files/patch-ajindex.c (new) 1.1 +170 -0 ports/biology/emboss/files/patch-ajindex.h (new) 1.1 +67 -0 ports/biology/emboss/files/patch-ajpdb.c (new) 1.1 +195 -0 ports/biology/emboss/files/patch-ajseqdb.c (new) 1.1 +89 -0 ports/biology/emboss/files/patch-dbxfasta.c (new) 1.1 +146 -0 ports/biology/emboss/files/patch-dbxflat.c (new) 1.1 +96 -0 ports/biology/emboss/files/patch-dbxgcg.c (new) 1.1 +115 -0 ports/biology/emboss/files/patch-embindex.c (new) 1.1 +96 -0 ports/biology/emboss/files/patch-embindex.h (new) 1.1 +20 -0 ports/biology/emboss/files/patch-emboss.default.template (new) 1.1 +72 -0 ports/biology/emboss/files/patch-marscan.c (new) 1.1 +27 -0 ports/biology/emboss/files/pkg-message.in (new) 1.1 +21 -0 ports/biology/emboss/files/pre-install.in (new) 1.7 +0 -22 ports/biology/emboss/pkg-message (dead) 1.23 +1684 -1599 ports/biology/emboss/pkg-plist