ports/177243: science/gromacs: Update to version 4.6.1

[KATO Tsuguru]

>Number:         177243
>Category:       ports
>Synopsis:       science/gromacs: Update to version 4.6.1
>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:   Fri Mar 22 18:40:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 7.4-RELEASE-p10 i386
>Organization:
>Environment:
>Description:
- Update to version 4.6.1

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/science/gromacs/Makefile science/gromacs/Makefile
--- /usr/ports/science/gromacs/Makefile	2013-02-10 22:27:35.000000000 +0900
+++ science/gromacs/Makefile	2013-03-10 17:37:17.000000000 +0900
@@ -2,7 +2,7 @@
 # $FreeBSD: head/science/gromacs/Makefile 312002 2013-02-10 07:56:49Z miwi $
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6
+PORTVERSION=	4.6.1
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -127,7 +127,7 @@
 	@${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \
 		${REINPLACE_CMD} -e \
 		's|share/man|man| ; \
-		 s|-lpthread|${PTHREAD_LIBS}| ; \
+		 s|-lpthread|-pthread| ; \
 		 /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|'
 	@${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \
 		's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \
diff -urN /usr/ports/science/gromacs/distinfo science/gromacs/distinfo
--- /usr/ports/science/gromacs/distinfo	2013-02-10 22:27:35.000000000 +0900
+++ science/gromacs/distinfo	2013-03-10 16:23:11.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.6.tar.gz) = f695ea814b10cb9afa8d69241fed703c6e20156bab96ed4b25f817ad85a8dbde
-SIZE (gromacs-4.6.tar.gz) = 10098687
+SHA256 (gromacs-4.6.1.tar.gz) = a0514b2a04ecac7461a67fc8edefa2b8eeaf22a25cd61c3348042dd077b077e6
+SIZE (gromacs-4.6.1.tar.gz) = 9975315
diff -urN /usr/ports/science/gromacs/pkg-plist science/gromacs/pkg-plist
--- /usr/ports/science/gromacs/pkg-plist	2013-02-10 22:27:35.000000000 +0900
+++ science/gromacs/pkg-plist	2013-03-10 17:43:09.000000000 +0900
@@ -343,13 +343,13 @@
 include/gromacs/xtcio.h
 include/gromacs/xvgr.h
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.8
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.8
 lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so.8
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.8
 libdata/pkgconfig/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
@@ -431,6 +431,8 @@
 %%DATADIR%%/html/online/g_dipoles.html
 %%DATADIR%%/html/online/g_disre.html
 %%DATADIR%%/html/online/g_dist.html
+%%DATADIR%%/html/online/g_dos.html
+%%DATADIR%%/html/online/g_dyecoupl.html
 %%DATADIR%%/html/online/g_dyndom.html
 %%DATADIR%%/html/online/g_enemat.html
 %%DATADIR%%/html/online/g_energy.html
@@ -440,6 +442,8 @@
 %%DATADIR%%/html/online/g_hbond.html
 %%DATADIR%%/html/online/g_helix.html
 %%DATADIR%%/html/online/g_helixorient.html
+%%DATADIR%%/html/online/g_hydorder.html
+%%DATADIR%%/html/online/g_kinetics.html
 %%DATADIR%%/html/online/g_lie.html
 %%DATADIR%%/html/online/g_mdmat.html
 %%DATADIR%%/html/online/g_membed.html
@@ -449,7 +453,9 @@
 %%DATADIR%%/html/online/g_nmeig.html
 %%DATADIR%%/html/online/g_nmens.html
 %%DATADIR%%/html/online/g_nmtraj.html
+%%DATADIR%%/html/online/g_options.html
 %%DATADIR%%/html/online/g_order.html
+%%DATADIR%%/html/online/g_pme_error.html
 %%DATADIR%%/html/online/g_polystat.html
 %%DATADIR%%/html/online/g_potential.html
 %%DATADIR%%/html/online/g_principal.html
@@ -462,6 +468,7 @@
 %%DATADIR%%/html/online/g_rotacf.html
 %%DATADIR%%/html/online/g_rotmat.html
 %%DATADIR%%/html/online/g_saltbr.html
+%%DATADIR%%/html/online/g_sans.html
 %%DATADIR%%/html/online/g_sas.html
 %%DATADIR%%/html/online/g_select.html
 %%DATADIR%%/html/online/g_sgangle.html
>Release-Note:
>Audit-Trail:
>Unformatted: