From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Oct 8 18:10:17 2012 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 84285106566C for ; Mon, 8 Oct 2012 18:10:17 +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 C3ABB8FC2F for ; Mon, 8 Oct 2012 18:10:16 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.5/8.14.5) with ESMTP id q98IAF0D086328 for ; Mon, 8 Oct 2012 18:10:15 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.5/8.14.5/Submit) id q98IAF29086327; Mon, 8 Oct 2012 18:10:15 GMT (envelope-from gnats) Resent-Date: Mon, 8 Oct 2012 18:10:15 GMT Resent-Message-Id: <201210081810.q98IAF29086327@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, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 14F70106566B for ; Mon, 8 Oct 2012 18:00:35 +0000 (UTC) (envelope-from tkato432@yahoo.com) Received: from msa102lp.auone-net.jp (msa102lp.auone-net.jp [222.3.140.165]) by mx1.freebsd.org (Postfix) with ESMTP id 86F688FC14 for ; Mon, 8 Oct 2012 18:00:34 +0000 (UTC) Received: from localhost.localdomain (ZT030227.ppp.dion.ne.jp [59.128.30.227]) by msa102lp.auone-net.jp (au one net msa) with ESMTP id A4C004AC038 for ; Tue, 9 Oct 2012 03:00:28 +0900 (JST) Message-Id: <20121009025602.cd6f6bc4b4770cde38730f33@yahoo.com> Date: Tue, 9 Oct 2012 02:56:02 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Cc: Subject: ports/172499: biology/t_coffee: Update to version 9.03 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, 08 Oct 2012 18:10:17 -0000 >Number: 172499 >Category: ports >Synopsis: biology/t_coffee: Update to version 9.03 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Oct 08 18:10:15 UTC 2012 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 9.03 New file: files/patch-dev3.c Remove file: files/patch-Makefile pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/t_coffee/Makefile biology/t_coffee/Makefile --- /usr/ports/biology/t_coffee/Makefile 2012-10-01 23:45:16.000000000 +0900 +++ biology/t_coffee/Makefile 2012-10-04 22:23:17.000000000 +0900 @@ -2,36 +2,40 @@ # $FreeBSD: ports/biology/t_coffee/Makefile,v 1.18 2012/10/01 14:45:16 tabthorpe Exp $ PORTNAME= t_coffee -PORTVERSION= 5.68 +PORTVERSION= 9.03 +DISTVERSIONSUFFIX= .r1318 CATEGORIES= biology -MASTER_SITES= http://www.tcoffee.org/Packages/ -DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION} +MASTER_SITES= http://www.tcoffee.org/Packages/Stable/%SUBDIR%/ +MASTER_SITE_SUBDIR= Version_${PORTVERSION}${DISTVERSIONSUFFIX} +DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX} MAINTAINER= ports@FreeBSD.org COMMENT= A multiple DNA or protein sequence alignment package -BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw -RUN_DEPENDS:= ${BUILD_DEPENDS} +LICENSE= GPLv2 + +RUN_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw + +OPTIONS_DEFINE= EXAMPLES BUILD_WRKSRC= ${WRKSRC}/t_coffee_source -MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/bin \ - CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw +USE_FORTRAN= yes +MAKE_ENV= FCC="${FC} ${FFLAGS}" MAKEFILE= makefile +MAKE_JOBS_SAFE= yes -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin +PORTEXAMPLES= * +PLIST_FILES= bin/TMalign bin/t_coffee -post-install: -.if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCSDIR}/html - ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html -.endif -.if !defined(NOPORTEXAMPLES) - @ ${MKDIR} ${EXAMPLESDIR} - cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR} +.include + +do-install: + (cd ${BUILD_WRKSRC} \ + && ${INSTALL_PROGRAM} TMalign t_coffee ${PREFIX}/bin) +.if ${PORT_OPTIONS:MEXAMPLES} + @${MKDIR} ${EXAMPLESDIR} + @(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${EXAMPLESDIR}) .endif .include diff -urN /usr/ports/biology/t_coffee/distinfo biology/t_coffee/distinfo --- /usr/ports/biology/t_coffee/distinfo 2011-03-19 21:29:38.000000000 +0900 +++ biology/t_coffee/distinfo 2012-10-04 22:02:57.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de -SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438 +SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c +SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629 diff -urN /usr/ports/biology/t_coffee/files/patch-Makefile biology/t_coffee/files/patch-Makefile --- /usr/ports/biology/t_coffee/files/patch-Makefile 2006-02-10 18:45:28.000000000 +0900 +++ biology/t_coffee/files/patch-Makefile 1970-01-01 09:00:00.000000000 +0900 @@ -1,8 +0,0 @@ ---- t_coffee_source/makefile.orig Tue Feb 7 15:11:00 2006 -+++ t_coffee_source/makefile Tue Feb 7 15:10:36 2006 -@@ -1,4 +1,4 @@ --CC=cc -+#CC=cc - t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_ dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o - $(CC) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_ nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o -lm - mv t_coffee ../bin diff -urN /usr/ports/biology/t_coffee/files/patch-dev3.c biology/t_coffee/files/patch-dev3.c --- /usr/ports/biology/t_coffee/files/patch-dev3.c 1970-01-01 09:00:00.000000000 +0900 +++ biology/t_coffee/files/patch-dev3.c 2012-10-04 22:14:42.000000000 +0900 @@ -0,0 +1,10 @@ +--- t_coffee_source/dev3.c.orig 2012-07-13 02:06:31.000000000 +0900 ++++ t_coffee_source/dev3.c 2012-10-04 22:14:10.000000000 +0900 +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + #include + #include "dev3_lib_header.h" + /******************************COPYRIGHT NOTICE*******************************/ diff -urN /usr/ports/biology/t_coffee/pkg-plist biology/t_coffee/pkg-plist --- /usr/ports/biology/t_coffee/pkg-plist 2008-09-09 22:43:15.000000000 +0900 +++ biology/t_coffee/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,190 +0,0 @@ -bin/t_coffee -%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE -%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt -%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm -%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt -%%PORTDOCS%%%%DOCSDIR%%/license.txt -%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee.html -%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee4html.cgi -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2seqs.fas -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.dnd -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample2.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample3.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample4.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/b30.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block1.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block2.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cache -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/charge_relay_lib.tc_lib -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/clustalw_method.tc_method -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/command_line.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/error_report.T-COFFEE -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g0.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/x -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g10.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g15.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g5.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/kinases.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/marna.tc_lib -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p120.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p250 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p350.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.dnd -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.dnd -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.fasta -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/seq.fas -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.aln -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.html 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-%%PORTDOCS%%@dirrm %%DOCSDIR%%/html -%%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% >Release-Note: >Audit-Trail: >Unformatted: