svn commit: r310361 - in head/biology/t_coffee: . files
Marcelo Araujo
araujo at FreeBSD.org
Mon Jan 14 08:04:39 UTC 2013
Author: araujo
Date: Mon Jan 14 08:04:38 2013
New Revision: 310361
URL: http://svnweb.freebsd.org/changeset/ports/310361
Log:
- Update to 9.03.
PR: ports/172499
Submitted by: KATO Tsuguru <tkato432 at yahoo.com>
Added:
head/biology/t_coffee/files/patch-dev3.c (contents, props changed)
Deleted:
head/biology/t_coffee/files/patch-Makefile
head/biology/t_coffee/pkg-plist
Modified:
head/biology/t_coffee/Makefile
head/biology/t_coffee/distinfo (contents, props changed)
Modified: head/biology/t_coffee/Makefile
==============================================================================
--- head/biology/t_coffee/Makefile Mon Jan 14 07:17:13 2013 (r310360)
+++ head/biology/t_coffee/Makefile Mon Jan 14 08:04:38 2013 (r310361)
@@ -2,36 +2,40 @@
# $FreeBSD$
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}${DISTVERSIONSUFFIX}
MAINTAINER= ports at FreeBSD.org
COMMENT= A multiple DNA or protein sequence alignment package
-BUILD_DEPENDS= clustalw:${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 <bsd.port.options.mk>
+
+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 <bsd.port.mk>
Modified: head/biology/t_coffee/distinfo
==============================================================================
--- head/biology/t_coffee/distinfo Mon Jan 14 07:17:13 2013 (r310360)
+++ head/biology/t_coffee/distinfo Mon Jan 14 08:04:38 2013 (r310361)
@@ -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
Added: head/biology/t_coffee/files/patch-dev3.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/t_coffee/files/patch-dev3.c Mon Jan 14 08:04:38 2013 (r310361)
@@ -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 <math.h>
+ #include <stdarg.h>
+ #include <string.h>
++#include <sys/types.h>
+ #include <sys/sysctl.h>
+ #include "dev3_lib_header.h"
+ /******************************COPYRIGHT NOTICE*******************************/
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