Date: Mon, 3 Jun 2013 02:51:28 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/179208: science/gromacs: Update to version 4.6.2 Message-ID: <20130603025128.096b8f6f8d380790dd6a6186@yahoo.com> Resent-Message-ID: <201306021810.r52IA0rR099332@freefall.freebsd.org>
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>Number: 179208 >Category: ports >Synopsis: science/gromacs: Update to version 4.6.2 >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: Sun Jun 02 18:10:00 UTC 2013 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 8.4-RELEASE i386 >Organization: >Environment: >Description: - Update to version 4.6.2 New file: files/patch-src__gmxlib__thread_mpi__atomic.c >How-To-Repeat: >Fix: diff -urN /usr/ports/science/gromacs/Makefile science/gromacs/Makefile --- /usr/ports/science/gromacs/Makefile 2013-04-24 01:03:03.000000000 +0900 +++ science/gromacs/Makefile 2013-06-03 00:00:00.000000000 +0900 @@ -2,7 +2,7 @@ # $FreeBSD: head/science/gromacs/Makefile 316355 2013-04-23 14:20:25Z bapt $ PORTNAME= gromacs -PORTVERSION= 4.6.1 +PORTVERSION= 4.6.2 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ diff -urN /usr/ports/science/gromacs/distinfo science/gromacs/distinfo --- /usr/ports/science/gromacs/distinfo 2013-03-25 04:19:44.000000000 +0900 +++ science/gromacs/distinfo 2013-06-03 00:00:00.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (gromacs-4.6.1.tar.gz) = a0514b2a04ecac7461a67fc8edefa2b8eeaf22a25cd61c3348042dd077b077e6 -SIZE (gromacs-4.6.1.tar.gz) = 9975315 +SHA256 (gromacs-4.6.2.tar.gz) = 7bcccd15f02e7163455e1f342fc13e609e9088735b962d96afe0a79aaad92d4c +SIZE (gromacs-4.6.2.tar.gz) = 10986082 diff -urN /usr/ports/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c --- /usr/ports/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c 1970-01-01 09:00:00.000000000 +0900 +++ science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c 2013-06-03 00:00:00.000000000 +0900 @@ -0,0 +1,17 @@ +--- src/gmxlib/thread_mpi/atomic.c.orig ++++ src/gmxlib/thread_mpi/atomic.c +@@ -35,6 +35,14 @@ + files. + */ + ++#ifdef HAVE_TMPI_CONFIG_H ++#include "tmpi_config.h" ++#endif ++ ++#ifdef HAVE_CONFIG_H ++#include "config.h" ++#endif ++ + #include "impl.h" + + /* This file is only needed when no intrinsic atomic operations are present. */ diff -urN /usr/ports/science/gromacs/pkg-plist science/gromacs/pkg-plist --- /usr/ports/science/gromacs/pkg-plist 2013-03-25 04:19:44.000000000 +0900 +++ science/gromacs/pkg-plist 2013-06-03 00:00:00.000000000 +0900 @@ -256,6 +256,8 @@ include/gromacs/thread_mpi.h include/gromacs/thread_mpi/atomic.h include/gromacs/thread_mpi/atomic/cycles.h +include/gromacs/thread_mpi/atomic/derived.h +include/gromacs/thread_mpi/atomic/fujitsu_sparc64.h include/gromacs/thread_mpi/atomic/gcc.h include/gromacs/thread_mpi/atomic/gcc_ia64.h include/gromacs/thread_mpi/atomic/gcc_intrinsics.h @@ -985,6 +987,27 @@ %%DATADIR%%/top/gromos53a6.ff/tip3p.itp %%DATADIR%%/top/gromos53a6.ff/tip4p.itp %%DATADIR%%/top/gromos53a6.ff/watermodels.dat +%%DATADIR%%/top/gromos54a7.ff/aminoacids.c.tdb +%%DATADIR%%/top/gromos54a7.ff/aminoacids.hdb +%%DATADIR%%/top/gromos54a7.ff/aminoacids.n.tdb +%%DATADIR%%/top/gromos54a7.ff/aminoacids.r2b +%%DATADIR%%/top/gromos54a7.ff/aminoacids.rtp +%%DATADIR%%/top/gromos54a7.ff/aminoacids.vsd +%%DATADIR%%/top/gromos54a7.ff/atomtypes.atp +%%DATADIR%%/top/gromos54a7.ff/dppc.itp +%%DATADIR%%/top/gromos54a7.ff/ff_dum.itp +%%DATADIR%%/top/gromos54a7.ff/ffbonded.itp +%%DATADIR%%/top/gromos54a7.ff/ffnonbonded.itp +%%DATADIR%%/top/gromos54a7.ff/forcefield.doc +%%DATADIR%%/top/gromos54a7.ff/forcefield.itp +%%DATADIR%%/top/gromos54a7.ff/ions.itp +%%DATADIR%%/top/gromos54a7.ff/popc.itp +%%DATADIR%%/top/gromos54a7.ff/spc.itp +%%DATADIR%%/top/gromos54a7.ff/spce.itp +%%DATADIR%%/top/gromos54a7.ff/tip3p.itp +%%DATADIR%%/top/gromos54a7.ff/tip4p.itp +%%DATADIR%%/top/gromos54a7.ff/tmcl.itp +%%DATADIR%%/top/gromos54a7.ff/watermodels.dat %%DATADIR%%/top/gurgle.dat %%DATADIR%%/top/ha-shift.dat %%DATADIR%%/top/highway.dat @@ -1042,6 +1065,7 @@ %%DATADIR%%/top/vdwradii.dat %%DATADIR%%/top/xlateat.dat @dirrm %%DATADIR%%/top/oplsaa.ff +@dirrm %%DATADIR%%/top/gromos54a7.ff @dirrm %%DATADIR%%/top/gromos53a6.ff @dirrm %%DATADIR%%/top/gromos53a5.ff @dirrm %%DATADIR%%/top/gromos45a3.ff >Release-Note: >Audit-Trail: >Unformatted:
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