biology/molden: update to 5.8.2

Also add do-install-{option}-on targets and shadow ${MKDIR} commands.

PR:		233060
Submitted by:	yuri

3 files changed, 45 insertions, 10 deletions

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index 46f7ca44c4e4..c8dbd154042a 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	molden
-PORTVERSION=	5.7
-PORTREVISION=	16
+DISTVERSION=	5.8.2
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
@@ -19,7 +18,7 @@ LICENSE_PERMS=	auto-accept
 
 RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable.
 
-WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
+WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION:R}
 
 USES=		fortran gl gmake
 USE_XORG=	x11
@@ -62,11 +61,15 @@ do-install:
 .for i in ambfor surf
 	(cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin)
 .endfor
-	${MKDIR} ${STAGEDIR}${DATADIR}/test
-	(cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test)
+
+do-install-DATA-on:
+	@${MKDIR} ${STAGEDIR}${DATADIR}/test
+	(cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/test)
 	${MKDIR} ${STAGEDIR}${DATADIR}/utils
-	(cd ${WRKSRC}/utils &&  ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/utils)
+	(cd ${WRKSRC}/utils && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/utils)
+
+do-install-DOCS-on:
 	${MKDIR} ${STAGEDIR}${DOCSDIR}
-	(cd ${WRKSRC}/doc && ${INSTALL_DATA} * ${STAGEDIR}${DOCSDIR})
+	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
 
 .include <bsd.port.mk>
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index c2df757b8bf0..f5bedab276c4 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1526851227
-SHA256 (molden5.7.tar.gz) = 10e3c02b63e6aa277922488f48be1bbd231e5bb111fb86fa162293a6fbc9718a
-SIZE (molden5.7.tar.gz) = 5346379
+TIMESTAMP = 1541594934
+SHA256 (molden5.8.2.tar.gz) = 65a24db9e80b4fb6038cc1e57c7d6e2457414812c9389bc651af7cb33f01dbe9
+SIZE (molden5.8.2.tar.gz) = 5770998
diff --git a/biology/molden/files/patch-xwin.c b/biology/molden/files/patch-xwin.c
new file mode 100644
index 000000000000..482160e326b6
--- /dev/null
+++ b/biology/molden/files/patch-xwin.c
@@ -0,0 +1,32 @@
+--- xwin.c.orig	2018-11-07 12:54:20 UTC
++++ xwin.c
+@@ -4218,8 +4218,12 @@ void makeRasterFont(Display *dpy);
+ #include <math.h>
+ 
+ #include <fcntl.h>
+-#if defined(__APPLE__) || defined(__FreeBSD__)
++#if defined(__APPLE__)
+ #include <copyfile.h>
++#elif defined(__FreeBSD__)
++#include <sys/types.h>
++#include <sys/socket.h>
++#include <sys/uio.h>
+ #else
+ #include <sys/sendfile.h>
+ #endif
+@@ -4238,9 +4242,14 @@ int OSCopyFile(const char* source, const
+     }
+ 
+     //Here we use kernel-space copying for performance reasons
+-#if defined(__APPLE__) || defined(__FreeBSD__)
++#if defined(__APPLE__)
+     //fcopyfile works on FreeBSD and OS X 10.5+ 
+     int result = fcopyfile(input, output, 0, COPYFILE_ALL);
++#elif defined(__FreeBSD__)
++    off_t bytesCopied = 0;
++    struct stat fileinfo = {0};
++    fstat(input, &fileinfo);
++    int result = sendfile(output, input, 0/*ofset*/, fileinfo.st_size, 0/*hdtr*/, &bytesCopied, 0/*flags*/);
+ #else
+     //sendfile will work with non-socket output (i.e. regular file) on Linux 2.6.33+
+     off_t bytesCopied = 0;