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Message-Id: <20131217025038.8750bc121a8ca18e3f5f261b@yahoo.com>
Date: Tue, 17 Dec 2013 02:50:38 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: science/gromacs: Update to version 4.6.5

>Number:         184903
>Category:       ports
>Synopsis:       science/gromacs: Update to version 4.6.5
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    danilo
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Dec 16 18:10:29 UTC 2013
>Closed-Date:    Tue Dec 17 20:36:58 UTC 2013
>Last-Modified:  Tue Dec 17 20:40:00 UTC 2013
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p4 i386
>Organization:
>Environment:
>Description:
- Update to version 4.6.5

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/science/gromacs/Makefile science/gromacs/Makefile
--- /usr/ports/science/gromacs/Makefile	2013-11-27 16:18:41.000000000 +0900
+++ science/gromacs/Makefile	2013-12-17 00:00:00.000000000 +0900
@@ -2,7 +2,7 @@
 # $FreeBSD: head/science/gromacs/Makefile 334960 2013-11-26 17:45:42Z wg $
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6.4
+PORTVERSION=	4.6.5
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -22,7 +22,7 @@
 MPICH_DESC=	MPI support using net/mpich2
 OMPI_DESC=	MPI support using net/openmpi
 
-USES=		cmake pkgconfig shebangfix perl5
+USES=		cmake perl5 pkgconfig shebangfix
 SHEBANG_FILES=	admin/*.pl scripts/*.pl scripts/*.sh src/gmxlib/selection/*.sh
 bash_CMD=	${SH}
 USE_FORTRAN=	yes
diff -urN /usr/ports/science/gromacs/distinfo science/gromacs/distinfo
--- /usr/ports/science/gromacs/distinfo	2013-11-27 16:18:41.000000000 +0900
+++ science/gromacs/distinfo	2013-12-17 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.6.4.tar.gz) = 4d4f15e6d10e97aff7a21d3bb5536283cf8ba669589310c456c1bb22bdfe7d8e
-SIZE (gromacs-4.6.4.tar.gz) = 10990996
+SHA256 (gromacs-4.6.5.tar.gz) = a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09
+SIZE (gromacs-4.6.5.tar.gz) = 10991576
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->danilo 
Responsible-Changed-By: danilo 
Responsible-Changed-When: Tue Dec 17 19:11:43 UTC 2013 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184903 
State-Changed-From-To: open->closed 
State-Changed-By: danilo 
State-Changed-When: Tue Dec 17 20:36:57 UTC 2013 
State-Changed-Why:  
Committed, with minor changes. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184903 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/184903: commit references a PR
Date: Tue, 17 Dec 2013 20:36:46 +0000 (UTC)

 Author: danilo
 Date: Tue Dec 17 20:36:38 2013
 New Revision: 336762
 URL: http://svnweb.freebsd.org/changeset/ports/336762
 
 Log:
   - Update from 4.6.4 to 4.6.5 [1]
   - Convert some "if's" in options helpers
   
   PR:		ports/184903
   Submitted by:	KATO Tsuguru <tkato432@yahoo.com> [1]
 
 Modified:
   head/science/gromacs/Makefile
   head/science/gromacs/distinfo
 
 Modified: head/science/gromacs/Makefile
 ==============================================================================
 --- head/science/gromacs/Makefile	Tue Dec 17 20:35:25 2013	(r336761)
 +++ head/science/gromacs/Makefile	Tue Dec 17 20:36:38 2013	(r336762)
 @@ -2,7 +2,7 @@
  # $FreeBSD$
  
  PORTNAME=	gromacs
 -PORTVERSION=	4.6.4
 +PORTVERSION=	4.6.5
  CATEGORIES=	science
  MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
  
 @@ -16,13 +16,15 @@ OPTIONS_DEFAULT=	FLOAT GSL X11
  OPTIONS_RADIO=	MPI
  OPTIONS_RADIO_MPI=	MPICH OMPI
  
 +OPTIONS_SUB=	yes
 +
  ATLAS_DESC=	Use ATLAS for BLAS and LAPACK
  FLOAT_DESC=	Use single instead of double precision
  GSL_DESC=	Extra analysis using math/gsl
  MPICH_DESC=	MPI support using net/mpich2
  OMPI_DESC=	MPI support using net/openmpi
  
 -USES=		cmake pkgconfig shebangfix perl5
 +USES=		cmake perl5 pkgconfig shebangfix
  SHEBANG_FILES=	admin/*.pl scripts/*.pl scripts/*.sh src/gmxlib/selection/*.sh
  bash_CMD=	${SH}
  USE_FORTRAN=	yes
 @@ -30,6 +32,16 @@ CMAKE_ARGS=	-DBLAS_LIBRARIES:FILEPATH="$
  		-DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}"
  USE_LDCONFIG=	yes
  
 +GSL_LIB_DEPENDS=	libgsl.so:${PORTSDIR}/math/gsl
 +GSL_CMAKE_ON=		-DGMX_GSL:BOOL=ON
 +GSL_CMAKE_OFF=		-DGMX_GSL:BOOL=OFF
 +
 +SIMD_CMAKE_OFF=		-DGMX_CPU_ACCELERATION:STRING="None"
 +
 +X11_USE=		XORG=xext,x11
 +X11_CMAKE_ON=		-DGMX_X11:BOOL=ON
 +X11_CMAKE_OFF=		-DGMX_X11:BOOL=OFF
 +
  .include <bsd.port.options.mk>
  
  .if ${PORT_OPTIONS:MATLAS}
 @@ -54,26 +66,6 @@ CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=ON
  PLIST_SUB+=	SUFFIX_D="_d"
  .endif
  
 -.if ${PORT_OPTIONS:MGSL}
 -LIB_DEPENDS+=	libgsl.so:${PORTSDIR}/math/gsl
 -CMAKE_ARGS+=	-DGMX_GSL:BOOL=ON
 -.else
 -CMAKE_ARGS+=	-DGMX_GSL:BOOL=OFF
 -.endif
 -
 -.if empty(PORT_OPTIONS:MSIMD)
 -CMAKE_ARGS+=	-DGMX_CPU_ACCELERATION:STRING="None"
 -.endif
 -
 -.if ${PORT_OPTIONS:MX11}
 -USE_XORG=	xext x11
 -CMAKE_ARGS+=	-DGMX_X11:BOOL=ON
 -PLIST_SUB+=	X11=""
 -.else
 -CMAKE_ARGS+=	-DGMX_X11:BOOL=OFF
 -PLIST_SUB+=	X11="@comment "
 -.endif
 -
  .if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI}
  CMAKE_ARGS+=	-DGMX_MPI:BOOL=ON \
  		-DMPI_C_COMPILER:FILEPATH="${MPICC}"
 
 Modified: head/science/gromacs/distinfo
 ==============================================================================
 --- head/science/gromacs/distinfo	Tue Dec 17 20:35:25 2013	(r336761)
 +++ head/science/gromacs/distinfo	Tue Dec 17 20:36:38 2013	(r336762)
 @@ -1,2 +1,2 @@
 -SHA256 (gromacs-4.6.4.tar.gz) = 4d4f15e6d10e97aff7a21d3bb5536283cf8ba669589310c456c1bb22bdfe7d8e
 -SIZE (gromacs-4.6.4.tar.gz) = 10990996
 +SHA256 (gromacs-4.6.5.tar.gz) = a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09
 +SIZE (gromacs-4.6.5.tar.gz) = 10991576
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>Unformatted:
