Update to 5.3.0

Upstream changes: http://www.scilab.org/content/download/1791/19327/file/changes5.2.2-5.3.0.pdf Port changes: -Drop dependency on readline from ports - this was never removed from the 4.x port and isn't used -Make UMFPACK off by default - the only reason it was on by default was for consistency among 5.2.x versions, since I didn't expose the knob through OPTIONS properly until 5.2.2 -Update JGraphX to compatible version for Scilab 5.3.0 -Scilab does not start java in the normal way (with javavmwrapper) so the JAVA_HOME environment variable isn't set properly. Explictly set JAVA_HOME to whatever was used to build the port. This seems to correct occasional crashes on startup. -Use batik-all.jar instead of batik.jar - has some extra classes in it -Additional dependency: java/jakarta-commons-beanutils -"bsdjava" (java/jdk16) doesn't work with this version. Require diablo or openjdk. -Use COMMENT in DESKTOP_ENTRIES -Switch to a dynamic plist for include/scilab, lib/scilab, and share/scilab. These directories vary quite a bit depending on what options are set but should be exclusive to scilab. -Reorganize post-patch section so java related substitutions aren't done unless building with java -Fix NOPORTDOCS to actually do something -Silence post-patch output -Remove rename of Visual Basic demos - BSD make couldn't handle the unquoted spaces in the path names, but this port now uses GNU make -Remove unnecessary find statements in pre-install -Remove empty directories in DATADIR/modules - toolboxes don't like them -Fix where threads incorrectly detected as Linux style -A couple patches are no longer necessary -ATOMS (package manager for downloading toolboxes in binary form) is not available for FreeBSD. It tries to download a list of available packages from the Scilab website (based on uname). There is no list for FreeBSD and it HTTP 404's. Scilab misinterprets this and says "Please connect to the Internet", which is a bit misleading. Patch to indicate that this will never work. I considered faking the uname to Linux, but there are no RPMs in ports for math-type things, like fortran, blas/lapack, etc. so I doubt anything would run. Porting any desired toolboxs is probably the best route. -Fix ATOMS to use fetch instead of requiring wget or curl (Due to the previous issue, this will only be useful for 3rd party repositories) -Fix toolbox build macros to not write to PREFIX/share/scilab when building as root PR: ports/153274 Submitted by: Rob Farmer (maintainer)
svn path=/head/; revision=266579
2024-10-20 20:09:11 +00:00 · 2010-12-19 08:51:20 +00:00 · 2010-12-19 08:51:20 +00:00 · 7c78bc1595 · 2021-03-31 03:12:20 +00:00
commit 7c78bc1595
parent 6897aea8e6
15 changed files with 373 additions and 14729 deletions
--- a/math/scilab/Makefile
+++ b/math/scilab/Makefile
@ -6,13 +6,11 @@
 #

 PORTNAME=	scilab
-PORTVERSION=	5.2.2
-PORTREVISION=	4
+PORTVERSION=	5.3.0
 CATEGORIES=	math cad parallel java
 MASTER_SITES=	http://www.scilab.org/download/${PORTVERSION}/:scilab \
-		http://www.bayofrum.net/dist/jgraphx/:jgraphx \
-		http://cerberus.bayofrum.net/dist/jgraphx/:jgraphx \
-		http://www.predatorlabs.net/dl/:jgraphx
+		http://www.predatorlabs.net/dl/:jgraphx \
+		http://www.bayofrum.net/dist/jgraphx/:jgraphx
 DISTFILES=	${DISTNAME}-src.tar.gz:scilab
 EXTRACT_ONLY=	${DISTNAME}-src.tar.gz

@ -22,8 +20,7 @@ COMMENT=	Scientific software package for numerical computations
 # A partial dependencies list can be found at:
 # http://wiki.scilab.org/Dependencies_of_Scilab_5.X
 LIB_DEPENDS=	xml2.5:${PORTSDIR}/textproc/libxml2 \
-		pcre.0:${PORTSDIR}/devel/pcre \
-		readline.6:${PORTSDIR}/devel/readline
+		pcre.0:${PORTSDIR}/devel/pcre

 MAKE_JOBS_SAFE=	yes

@ -44,7 +41,7 @@ OPTIONS=	ATLAS "Use Atlas instead of Blas" OFF \
 		OCAML "Build ocaml modelica compiler (requires GUI)" OFF \
 		PVM "Parallel Virtual Machine support" OFF \
 		TK "TCL/TK support" OFF \
-		UMFPACK "Build with umfpack" ON
+		UMFPACK "Build with umfpack" OFF

 .include <bsd.port.options.mk>

@ -69,14 +66,12 @@ PLIST_SUB+=	NLS=""

 .if defined(WITHOUT_TK)
 CONFIGURE_ARGS+=	--without-tk
-PLIST_SUB+=	TK="@comment "
 .else
 USE_TK=		yes
 CONFIGURE_ARGS+=	--with-tk-library=${LOCALBASE}/lib \
 			--with-tk-include=${TK_INCLUDEDIR} \
 			--with-tcl-library=${LOCALBASE}/lib \
 			--with-tcl-include=${TCL_INCLUDEDIR}
-PLIST_SUB+=	TK=""
 .endif

 .if defined(WITHOUT_GUI)
@ -84,18 +79,16 @@ CONFIGURE_ARGS+=	--without-gui \
 			--without-javasci \
 			--without-hdf5 \
 			--disable-build-help
-PLIST_SUB+=	GUI="@comment "
-PLIST_SUB+=	NOGUI=""
-NOPORTDOCS=	YES
 .else
 DISTFILES+=	${JGRAPHX_JAR}:jgraphx
-JGRAPHX_VERSION=	1.3.0.0
+JGRAPHX_VERSION=	1.4.1.0
 JGRAPHX_JAR=	jgraphx-${JGRAPHX_VERSION:C/\./_/g}.jar

+EXTRA_PATCHES+=	${PATCHDIR}/extra-patch-bin-JAVA_HOME
+
 LIB_DEPENDS+=	hdf5.6:${PORTSDIR}/science/hdf5-18

-BUILD_DEPENDS+=	ant:${PORTSDIR}/devel/apache-ant \
-		${JAVALIBDIR}/flexdock.jar:${PORTSDIR}/devel/flexdock \
+GUI_DEPENDS=	${JAVALIBDIR}/flexdock.jar:${PORTSDIR}/devel/flexdock \
 		${JAVALIBDIR}/jogl.jar:${PORTSDIR}/graphics/jogl \
 		${JAVALIBDIR}/commons-logging.jar:${PORTSDIR}/java/jakarta-commons-logging \
 		${JAVALIBDIR}/looks.jar:${PORTSDIR}/devel/looks \
@ -104,7 +97,7 @@ BUILD_DEPENDS+=	ant:${PORTSDIR}/devel/apache-ant \
 		${JAVALIBDIR}/jhall.jar:${PORTSDIR}/java/javahelp \
 		${JAVALIBDIR}/jlatexmath.jar:${PORTSDIR}/math/jlatexmath \
 		fop:${PORTSDIR}/textproc/fop \
-		${LOCALBASE}/share/java/batik/batik.jar:${PORTSDIR}/graphics/batik \
+		${LOCALBASE}/share/java/batik/lib/batik-all.jar:${PORTSDIR}/graphics/batik \
 		foprep:${PORTSDIR}/math/jeuclid \
 		${JAVALIBDIR}/commons-io.jar:${PORTSDIR}/devel/jakarta-commons-io \
 		${JAVALIBDIR}/xmlgraphics-commons.jar:${PORTSDIR}/graphics/xmlgraphics-commons \
@ -112,31 +105,23 @@ BUILD_DEPENDS+=	ant:${PORTSDIR}/devel/apache-ant \
 		${JAVALIBDIR}/avalon-framework.jar:${PORTSDIR}/devel/avalon-framework \
 		${LOCALBASE}/share/xsl/docbook/javahelp/javahelp.xsl:${PORTSDIR}/textproc/docbook-xsl \
 		xsltproc:${PORTSDIR}/textproc/libxslt \
-		swig:${PORTSDIR}/devel/swig13 \
-		${LOCALBASE}/share/examples/saxon/data/books.dtd:${PORTSDIR}/textproc/saxon \
-		${JAVALIBDIR}/jhdf5.jar:${PORTSDIR}/science/hdf-java
+		${JAVALIBDIR}/jhdf5.jar:${PORTSDIR}/science/hdf-java \
+		${JAVALIBDIR}/commons-beanutils.jar:${PORTSDIR}/java/jakarta-commons-beanutils

-RUN_DEPENDS+=	${JAVALIBDIR}/flexdock.jar:${PORTSDIR}/devel/flexdock \
-		${JAVALIBDIR}/jogl.jar:${PORTSDIR}/graphics/jogl \
-		${JAVALIBDIR}/commons-logging.jar:${PORTSDIR}/java/jakarta-commons-logging \
-		${JAVALIBDIR}/looks.jar:${PORTSDIR}/devel/looks \
-		${JAVALIBDIR}/skinlf.jar:${PORTSDIR}/x11-toolkits/skinlf \
-		${JAVALIBDIR}/jrosetta-API.jar:${PORTSDIR}/java/jrosetta \
-		${JAVALIBDIR}/jhall.jar:${PORTSDIR}/java/javahelp \
-		${JAVALIBDIR}/jlatexmath.jar:${PORTSDIR}/math/jlatexmath \
-		fop:${PORTSDIR}/textproc/fop \
-		${LOCALBASE}/share/java/batik/batik.jar:${PORTSDIR}/graphics/batik \
-		foprep:${PORTSDIR}/math/jeuclid \
-		${JAVALIBDIR}/commons-io.jar:${PORTSDIR}/devel/jakarta-commons-io \
-		${JAVALIBDIR}/xmlgraphics-commons.jar:${PORTSDIR}/graphics/xmlgraphics-commons \
-		${JAVALIBDIR}/xml-apis-ext.jar:${PORTSDIR}/textproc/xml-commons \
-		${JAVALIBDIR}/avalon-framework.jar:${PORTSDIR}/devel/avalon-framework \
-		${LOCALBASE}/share/xsl/docbook/javahelp/javahelp.xsl:${PORTSDIR}/textproc/docbook-xsl \
-		xsltproc:${PORTSDIR}/textproc/libxslt \
-		${JAVALIBDIR}/jhdf5.jar:${PORTSDIR}/science/hdf-java
+# Can't use USE_ANT because it overrides do-build target
+BUILD_DEPENDS+=	${GUI_DEPENDS} \
+		ant:${PORTSDIR}/devel/apache-ant \
+		swig:${PORTSDIR}/devel/swig13 \
+		${LOCALBASE}/share/examples/saxon/data/books.dtd:${PORTSDIR}/textproc/saxon
+
+RUN_DEPENDS+=	${GUI_DEPENDS}

 USE_JAVA=	yes
 JAVA_VERSION=	1.5+
+# bsdjava (ie java/jdk16) doesn't have some "extra" classes that aren't in
+# the standard java. namespace, but are required by scilab, such as
+# javax.xml.bind.annotation.XmlSeeAlso
+JAVA_VENDOR=	freebsd openjdk
 JAVA_BUILD=	yes
 JAVA_RUN=	yes
 USE_XORG=	x11
@ -145,25 +130,20 @@ CONFIGURE_ARGS+=	--with-jdk=${JAVA_HOME} \
 			--with-docbook=${LOCALBASE}/share/xsl/docbook

 DESKTOP_ENTRIES=	"SciLab" \
-			"Scientific software package for numerical computations" \
+			"${COMMENT}" \
 			"${DATADIR}/icons/scilab.xpm" "scilab" \
 			"Application;Education;Math;" false

-PLIST_SUB+=	GUI=""
-PLIST_SUB+=	NOGUI="@comment "
 .endif

 .if defined(WITHOUT_FFTW)
 CONFIGURE_ARGS+=	--without-fftw
-PLIST_SUB+=	FFTW="@comment "
 .else
 LIB_DEPENDS+=	fftw3.5:${PORTSDIR}/math/fftw3
-PLIST_SUB+=	FFTW=""
 .endif

 .if defined(WITHOUT_PVM)
 CONFIGURE_ARGS+=	--without-pvm
-PLIST_SUB+=	PVM="@comment "
 .else
 BUILD_DEPENDS+=		pvm:${PORTSDIR}/net/pvm
 RUN_DEPENDS+=		pvm:${PORTSDIR}/net/pvm
@ -173,26 +153,20 @@ CONFIGURE_ARGS+=	--with-pvm-include=${LOCALBASE}/include \

 CONFIGURE_ENV=	PVM_ROOT=${LOCALBASE} \
 		PVMGETARCH=${LOCALBASE}/lib/pvm/lib/pvmgetarch
-
-PLIST_SUB+=	PVM=""
 .endif

 .if defined(WITHOUT_UMFPACK)
 CONFIGURE_ARGS+=	--without-umfpack
-PLIST_SUB+=	UMFPACK="@comment "
 .else
 LIB_DEPENDS+=	amd.1:${PORTSDIR}/math/suitesparse
 CONFIGURE_ARGS+=	--with-umfpack-include=${LOCALBASE}/include \
 			--with-umfpack-library=${LOCALBASE}/lib
-PLIST_SUB+=	UMFPACK=""
 .endif

 .if defined(WITHOUT_MATIO)
 CONFIGURE_ARGS+=	--without-matio
-PLIST_SUB+=	MATIO="@comment "
 .else
 LIB_DEPENDS+=	matio.1:${PORTSDIR}/math/matio
-PLIST_SUB+=	MATIO=""
 .endif

 .if defined(WITHOUT_OCAML)
@ -204,51 +178,76 @@ RUN_DEPENDS+=	ocaml:${PORTSDIR}/lang/ocaml
 PLIST_SUB+=	OCAML=""
 .endif

-post-patch:
-	# Configure fixes
-	${REINPLACE_CMD} -e 's|/usr/lib/java|${JAVALIBDIR}|g' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|/usr/lib64/jni|${LOCALBASE}/lib/|g' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|-ldl | |' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|-L$$with_umfpack_library|-L$$with_umfpack_library -lgfortran|' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|-lumfpack|-lumfpack -lamd -L$$with_umfpack_library -lgfortran|g' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|TCLTK_LIBS=" -ldl"|TCLTK_LIBS=" "|' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|$$jardir/batik.jar|${LOCALBASE}/share/java/batik/batik.jar|g' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|$$jardir/fop.jar|${LOCALBASE}/share/java/fop/build/fop.jar|' ${WRKSRC}/configure
-	${REINPLACE_CMD} -e 's|$$jardir/jeuclid-core*.jar|${LOCALBASE}/share/java/jeuclid/repo/jeuclid-core*.jar|' ${WRKSRC}/configure
-	${MKDIR} ${WRKSRC}/thirdparty
-.if !defined(WITHOUT_GUI)
-	${CP} ${DISTDIR}/${JGRAPHX_JAR} ${WRKSRC}/thirdparty/jgraphx.jar
-	${REINPLACE_CMD} -e 's|@JGRAPHX@|${DATADIR}/modules/jgraphx.jar|g' ${WRKSRC}/etc/classpath.xml.in
+.if defined(NOPORTDOCS)
+EXTRA_PATCHES+=	${PATCHDIR}/extra-patch-NOPORTDOCS
 .endif
-	# Build fixes
-	${REINPLACE_CMD} -e 's|$$(CFLAGS:-O%=)|-I${LOCALBASE}/include -L${LOCALBASE}/lib|' ${WRKSRC}/modules/elementary_functions/Makefile.in
-	${REINPLACE_CMD} -e 's|freebsd|__FreeBSD__|g' ${WRKSRC}/modules/sparse/includes/spConfig.h
-	${REINPLACE_CMD} -e 's|exp10(|pow(10., |g' ${WRKSRC}/modules/graphics/src/c/Format.c \
+
+post-patch:
+	@# Configure fixes
+	@${REINPLACE_CMD} -e 's|-ldl | |' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|-L$$with_umfpack_library|-L$$with_umfpack_library -lgfortran|' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|-lumfpack|-lumfpack -lamd -L$$with_umfpack_library -lgfortran|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|TCLTK_LIBS=" -ldl"|TCLTK_LIBS=" "|' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|"x=" ==|"x" =|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|"x" ==|"x" =|g' ${WRKSRC}/configure
+	@# Build fixes
+	@${REINPLACE_CMD} -e 's|$$(CFLAGS:-O%=)|-I${LOCALBASE}/include -L${LOCALBASE}/lib|' ${WRKSRC}/modules/elementary_functions/Makefile.in
+	@${REINPLACE_CMD} -e 's|freebsd|__FreeBSD__|g' ${WRKSRC}/modules/sparse/includes/spConfig.h
+	@${REINPLACE_CMD} -e 's|exp10(|pow(10., |g' ${WRKSRC}/modules/graphics/src/c/Format.c \
 		${WRKSRC}/modules/graphics/src/c/getHandleProperty/set_log_flags_property.c
 	@# malloc.h -> stdlib.h conversions
 	@${GREP} -lr "<malloc.h>" ${WRKSRC} \
 		| ${XARGS} ${REINPLACE_CMD} -e \
 		's/[<"]malloc.h[>"]/<stdlib.h>/'
-	#Install fixes
-	${MV} ${WRKSRC}/modules/call_scilab/examples/call_scilab/NET/VB.NET/My\ Project/ \
-		${WRKSRC}/modules/call_scilab/examples/call_scilab/NET/VB.NET/My_Project/
-	${REINPLACE_CMD} -e 's|My Project|My_Project|g' ${WRKSRC}/modules/call_scilab/examples/call_scilab/NET/VB.NET/VB.NET.vbproj
-	${REINPLACE_CMD} -e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|' ${WRKSRC}/Makefile.in
-	# Run fixes
-	${REINPLACE_CMD} -e 's|%%JAVALIBDIR%%|${JAVALIBDIR}|' ${WRKSRC}/etc/librarypath.xml
-	${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|' ${WRKSRC}/etc/librarypath.xml
-.if defined(NOPORTDOCS)
-	@${REINPLACE_CMD} -e '/%%PORTDOCS%%/d' ${WRKSRC}/Makefile.in
-.else
-	@${REINPLACE_CMD} -e 's/%%PORTDOCS%%//' ${WRKSRC}/Makefile.in
+	@# Install fixes
+	@${REINPLACE_CMD} -e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|' ${WRKSRC}/Makefile.in
+	@# Run fixes
+	@${REINPLACE_CMD} -e 's|%%JAVALIBDIR%%|${JAVALIBDIR}|' ${WRKSRC}/etc/librarypath.xml
+	@${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|' ${WRKSRC}/etc/librarypath.xml
+.if !defined(WITHOUT_GUI)
+	@# Configure fixes
+	@${REINPLACE_CMD} -e 's|/usr/lib/java|${JAVALIBDIR}|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|/usr/lib64/jni|${LOCALBASE}/lib/|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|$$jardir/batik-all.jar|${LOCALBASE}/share/java/batik/lib/batik-all.jar|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|$$jardir/fop.jar|${LOCALBASE}/share/java/fop/build/fop.jar|' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|$$jardir/jeuclid-core*.jar|${LOCALBASE}/share/java/jeuclid/repo/jeuclid-core*.jar|' ${WRKSRC}/configure
+	@${MKDIR} ${WRKSRC}/thirdparty
+	@${CP} ${DISTDIR}/${JGRAPHX_JAR} ${WRKSRC}/thirdparty/jgraphx.jar
+	@${REINPLACE_CMD} -e 's|@JGRAPHX@|${DATADIR}/modules/jgraphx.jar|g' ${WRKSRC}/etc/classpath.xml.in
+	@# Run fixes
+	@${REINPLACE_CMD} -e 's|%%JAVALIBDIR%%|${JAVALIBDIR}|' ${WRKSRC}/etc/librarypath.xml
+	@${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|' ${WRKSRC}/etc/librarypath.xml
+	@${REINPLACE_CMD} -e 's|%%JAVA_HOME%%|${JAVA_HOME}|' ${WRKSRC}/bin/scilab \
+		${WRKSRC}/bin/scilab-adv-cli ${WRKSRC}/bin/scilab-cli
 .endif

 pre-install:
-	@${FIND} ${WRKSRC} -name \*.orig -delete
-	@${FIND} ${WRKSRC} -name \*.bak -delete
-	@${FIND} ${WRKSRC} -name .cvsignore -delete
 .if !defined(WITHOUT_GUI)
 	@${MKDIR} ${DATADIR}/modules && ${INSTALL_DATA} ${DISTDIR}/${JGRAPHX_JAR} ${DATADIR}/modules/jgraphx.jar
+	@${MKDIR} ${DATADIR}/.atoms
 .endif

+post-install:
+	@# Remove empty dirs in DATDIR/modules - they will be removed by the
+	@# toolbox uninstaller otherwise if 3rd party toolboxes are used
+	@${FIND} ${DATADIR}/modules -type d -empty -delete
+	@# plist for include/scilab
+	@${FIND} -s ${PREFIX}/include/scilab -not -type d | ${SORT} | \
+		${SED} -e 's#^${PREFIX}/##' >> ${TMPPLIST}
+	@${FIND} ${PREFIX}/include/scilab -type d | ${SORT} -r | \
+		${SED} -e 's,^${PREFIX}/,@dirrm ,' >> ${TMPPLIST}
+	@# plist for lib/scilab
+	@${FIND} -s ${PREFIX}/lib/scilab -not -type d | ${SORT} | \
+		${SED} -e 's#^${PREFIX}/##' >> ${TMPPLIST}
+	@${FIND} ${PREFIX}/lib/scilab -type d | ${SORT} -r | \
+		${SED} -e 's,^${PREFIX}/,@dirrm ,' >> ${TMPPLIST}
+	@# plist for share/scilab EXCEPT:
+	@# contrib and .atoms (3rd party toolboxes)
+	@${FIND} -s ${DATADIR} -not -type d -not -path ${DATADIR}/contrib\* | \
+		${SORT} | ${SED} -e 's#^${PREFIX}/##' >> ${TMPPLIST}
+	@${FIND} ${DATADIR} -type d -not -path ${DATADIR}/contrib\* \
+		-not -path ${DATADIR}/.atoms\* -not -path ${DATADIR} | \
+		${SORT} -r | ${SED} -e 's,^${PREFIX}/,@dirrm ,' >> ${TMPPLIST}
+	@${ECHO_CMD} "@unexec rmdir %D/share/scilab 2>/dev/null || true" >> ${TMPPLIST}
+
 .include <bsd.port.mk>
--- a/math/scilab/distinfo
+++ b/math/scilab/distinfo
@ -1,6 +1,4 @@
-MD5 (scilab-5.2.2-src.tar.gz) = 35e8a22edb348f405360d3a07ed4faab
-SHA256 (scilab-5.2.2-src.tar.gz) = 6f8800bc8ac9128187d1f9a98a5e459bbfa2b66967caed8ab659ff2ba51f1cf2
-SIZE (scilab-5.2.2-src.tar.gz) = 54088580
-MD5 (jgraphx-1_3_0_0.jar) = b9e24f0b428c679697e763e9b0ba5671
-SHA256 (jgraphx-1_3_0_0.jar) = 0f3728b47c9fd3977a063212f68e43639c2283eb84fbce437275b679e6e4a6b2
-SIZE (jgraphx-1_3_0_0.jar) = 326596
+SHA256 (scilab-5.3.0-src.tar.gz) = fba11bb3c3598ff11dfed54fb576a53e6f3c1a418e0f1ddc9eadba82434ea635
+SIZE (scilab-5.3.0-src.tar.gz) = 55397003
+SHA256 (jgraphx-1_4_1_0.jar) = 8c4bd7e63a5149b67373857c2cc3d45015463a9075d7b6f078d7307f6d1038ec
+SIZE (jgraphx-1_4_1_0.jar) = 503319
--- a/math/scilab/files/extra-patch-NOPORTDOCS
+++ b/math/scilab/files/extra-patch-NOPORTDOCS
@ -0,0 +1,28 @@
+--- Makefile.in.orig	2010-12-16 22:07:06.000000000 -0800
+++ Makefile.in	2010-12-16 22:07:26.000000000 -0800
+@@ -618,24 +618,7 @@
+ $(top_builddir)/Version.incl
+ 
+ infofilesdir = $(pkgdatadir)/
+-infofiles_DATA = $(top_srcdir)/CHANGES_2.X \
+-$(top_srcdir)/CHANGES_3.X \
+-$(top_srcdir)/CHANGES_4.X \
+-$(top_srcdir)/CHANGES_5.0.X \
+-$(top_srcdir)/CHANGES_5.1.X \
+-$(top_srcdir)/CHANGES_5.2.X \
+-$(top_srcdir)/CHANGES_5.3.X \
+-$(top_srcdir)/ACKNOWLEDGEMENTS \
+-$(top_srcdir)/COPYING \
+-$(top_srcdir)/COPYING-BSD \
+-$(top_srcdir)/COPYING-FR \
+-$(top_srcdir)/README_Unix \
+-$(top_srcdir)/RELEASE_NOTES_5.0.X \
+-$(top_srcdir)/RELEASE_NOTES_5.1.X \
+-$(top_srcdir)/RELEASE_NOTES_5.2.X \
+-$(top_srcdir)/RELEASE_NOTES_5.3.X \
+-$(top_srcdir)/Readme_Visual.txt \
+-$(top_srcdir)/README_Windows.txt
+infofiles_DATA = 
+ 
+ iconsdir = $(pkgdatadir)/icons/
+ icons_DATA = $(top_srcdir)/icons/scilab.xpm \
--- a/math/scilab/files/extra-patch-bin-JAVA_HOME
+++ b/math/scilab/files/extra-patch-bin-JAVA_HOME
@ -0,0 +1,30 @@
+--- bin/scilab.orig	2010-09-01 19:31:19.000000000 -0700
+++ bin/scilab	2010-09-01 19:32:29.000000000 -0700
+@@ -1,4 +1,7 @@
+ #!/bin/sh
+
+export JAVA_HOME=%%JAVA_HOME%%
+
+ #
+ # Scilab ( http://www.scilab.org/ ) - This file is part of Scilab
+ # Copyright (C) INRIA - 2006-2008 - Sylvestre Ledru
+--- bin/scilab-adv-cli.orig	2010-09-01 19:31:28.000000000 -0700
+++ bin/scilab-adv-cli	2010-09-01 19:32:46.000000000 -0700
+@@ -1,4 +1,7 @@
+ #!/bin/sh
+
+export JAVA_HOME=%%JAVA_HOME%%
+
+ #
+ # Scilab ( http://www.scilab.org/ ) - This file is part of Scilab
+ # Copyright (C) INRIA - 2006-2008 - Sylvestre Ledru
+--- bin/scilab-cli.orig	2010-09-01 19:31:34.000000000 -0700
+++ bin/scilab-cli	2010-09-01 19:32:57.000000000 -0700
+@@ -1,4 +1,7 @@
+ #!/bin/sh
+
+export JAVA_HOME=%%JAVA_HOME%%
+
+ #
+ # Scilab ( http://www.scilab.org/ ) - This file is part of Scilab
+ # Copyright (C) INRIA - 2006-2008 - Sylvestre Ledru
--- a/math/scilab/files/patch-build.incl.xml
+++ b/math/scilab/files/patch-build.incl.xml
@ -1,11 +1,11 @@
--- build.incl.xml.orig	2010-10-18 22:52:49.000000000 -0700
-+++ build.incl.xml	2010-10-18 22:53:09.000000000 -0700
-@@ -86,6 +86,8 @@
+--- build.incl.xml.orig	2010-11-24 00:50:29.000000000 -0800
+++ build.incl.xml	2010-12-15 02:55:11.000000000 -0800
+@@ -116,6 +116,8 @@
 
- 		<pathelement location="${fop.jar}"/>
+     <pathelement location="${jlatexmath-fop.jar}"/>
 
-+		<pathelement location="${xmlgraphics-commons.jar}"/>
+    <pathelement location="${xmlgraphics-commons.jar}"/>
 +
- 		<pathelement location="${avalon-framework.jar}"/>
+     <pathelement location="${avalon-framework.jar}"/>
 
- 		<pathelement location="${avalon-framework-impl.jar}"/>
+     <pathelement location="${avalon-framework-impl.jar}"/>
--- a/math/scilab/files/patch-etc-librarypath.xml
+++ b/math/scilab/files/patch-etc-librarypath.xml
@ -1,11 +1,14 @@
--- etc/librarypath.xml.orig	2010-08-18 22:12:51.000000000 -0700
-+++ etc/librarypath.xml	2010-08-18 22:15:41.000000000 -0700
-@@ -29,16 +29,11 @@
- <path value="$SCILAB/modules/xpad/.libs"/>
+--- etc/librarypath.xml.orig	2010-08-29 23:41:41.000000000 -0700
+++ etc/librarypath.xml	2010-08-29 23:42:38.000000000 -0700
+@@ -29,19 +29,11 @@
+ <path value="$SCILAB/modules/scinotes/.libs"/>
 <path value="$SCILAB/.libs"/>
 
 -<!-- Default path to the JNI classes under some Linux (JoGL under Debian for example) -->
 -<path value="/usr/lib/jni/"/>
+-
+-<!-- Some distributions (like openSUSE) put gluegen-rt in /usr/lib instead pf /usr/lib/jni -->
+-<path value="/usr/lib" />
 -
 <!-- Make install with prefix -->
 <path value="$SCILAB/../../lib/scilab/"/>
@ -15,7 +18,7 @@
 -
 -<!-- Standard path for 64 bits -->
 -<path value="/usr/lib64/scilab/"/>
-+<path value="%%JAVALIBDIR%%/"/>
-+<path value="%%PREFIX%%/lib/"/>
+<path value="%%JAVALIBDIR%%"/>
+<path value="%%PREFIX%%/lib"/>
 
 </librarypaths>
--- a/math/scilab/files/patch-modules-atoms-macros-atoms_gui-atomsGui.sci
+++ b/math/scilab/files/patch-modules-atoms-macros-atoms_gui-atomsGui.sci
@ -0,0 +1,11 @@
+--- modules/atoms/macros/atoms_gui/atomsGui.sci.orig	2010-12-15 02:20:51.000000000 -0800
+++ modules/atoms/macros/atoms_gui/atomsGui.sci	2010-12-15 02:21:41.000000000 -0800
+@@ -20,7 +20,7 @@
+ 
+     if errStatus<>0 | size(allModules, "*") == 0 then
+         if size(atomsRepositoryList(),"*") > 0 then
+-            messagebox(gettext("No ATOMS module is available. Please, check your Internet connection."), gettext("ATOMS error"), "error");
+            messagebox(gettext("ATOMS is not available for FreeBSD at this time."), gettext("ATOMS error"), "error");
+         else
+             messagebox(gettext("No ATOMS module is available: your repository list is empty."), gettext("ATOMS error"), "error");
+         end
--- a/math/scilab/files/patch-modules-atoms-macros-atoms_internals-atomsAUWriteAccess.sci
+++ b/math/scilab/files/patch-modules-atoms-macros-atoms_internals-atomsAUWriteAccess.sci
@ -0,0 +1,32 @@
+--- modules/atoms/macros/atoms_internals/atomsAUWriteAccess.sci.orig	2010-12-16 23:18:06.000000000 -0800
+++ modules/atoms/macros/atoms_internals/atomsAUWriteAccess.sci	2010-12-16 23:21:49.000000000 -0800
+@@ -24,25 +24,11 @@
+     atoms_system_directory  = atomsPath("system" ,"allusers");
+     atoms_install_directory = atomsPath("install","allusers");
+ 
+-    // Physical test
+-
+-    if ~ isdir(atoms_system_directory) then
+-        if mkdir(atoms_system_directory) <> 1 then
+-            return;
+-        end
+-    end
+-
+-    if execstr("mputl(""dummy"",atoms_system_directory+""dummy"");","errcatch") == 0 then
+    // Just assume root should install to DATADIR and everyone else should
+    // use ~/.Scilab
+    rep = unix_g("whoami");
+    if rep == "root" then
+         res = %T;
+-        mdelete(atoms_system_directory+"dummy");
+-    else
+-        return;
+-    end
+-
+-    if execstr("mputl(""dummy"",atoms_install_directory+""dummy"");","errcatch") <> 0 then
+-        res = %F;
+-    else
+-        mdelete(atoms_install_directory+"dummy");
+     end
+ 
+ endfunction
--- a/math/scilab/files/patch-modules-atoms-macros-atoms_internals-atomsDownload.sci
+++ b/math/scilab/files/patch-modules-atoms-macros-atoms_internals-atomsDownload.sci
@ -0,0 +1,84 @@
+--- modules/atoms/macros/atoms_internals/atomsDownload.sci.orig	2010-12-16 23:27:03.000000000 -0800
+++ modules/atoms/macros/atoms_internals/atomsDownload.sci	2010-12-16 23:41:40.000000000 -0800
+@@ -71,6 +71,7 @@
+     CURL         = %F;
+     WGET         = %F;
+     HTTPDOWNLOAD = %F;
+    FETCH        = %F;
+ 
+     // Maybe the detection has already been done
+ 
+@@ -83,10 +84,16 @@
+     elseif atomsGetConfig("downloadTool") == "httpdownload" & getos() == 'Windows' then
+         HTTPDOWNLOAD=%T;
+ 
+    elseif atomsGetConfig("downloadTool") == "fetch" then
+        FETCH=%T;
+
+     else
+ 
+         // Default values according to platform
+-        if LINUX | SOLARIS | BSD then
+        if BSD then
+            FETCH = %T;
+
+        elseif LINUX | SOLARIS then
+ 
+             // Need to detect under Linux platforms
+             [rep,stat,err] = unix_g("wget --version");
+@@ -125,9 +132,12 @@
+         if CURL then
+             // Curl
+             timeout_arg = " --connect-timeout ";
+-        else
+        elseif WGET then
+             // wget
+             timeout_arg = " --timeout=";
+        else
+            // fetch
+            timeout_arg = " -T ";
+         end
+ 
+         timeout = string(strtod(atomsGetConfig("downloadTimeout")));
+@@ -141,6 +151,9 @@
+         timeout_arg = timeout_arg + " ";
+ 
+         // Proxy configuration
+        //
+        // fetch should set environment variables for proxy - see fetch(3)
+        //
+         if (atomsGetConfig("useProxy") == "True") & (atomsGetConfig("proxyHost") <> "") then
+ 
+             // Host
+@@ -155,7 +168,7 @@
+             if CURL then
+                 // Curl
+                 proxy_host_arg = " --proxy "+ proxy_host;
+-            else
+            elseif WGET then
+                 // wget
+                 proxy_host_arg = " http_proxy="""+proxy_host+""" ";
+             end
+@@ -165,7 +178,7 @@
+                 if CURL then
+                     // Curl
+                     proxy_user_arg = " --proxy-user "+atomsGetConfig("proxyUser")+":"+atomsGetConfig("proxyPassword");
+-                else
+                elseif WGET then
+                     // wget
+                     proxy_user_arg = " --proxy-user="""+atomsGetConfig("proxyUser")+""" --proxy-password="""+atomsGetConfig("proxyPassword")+"""";
+                 end
+@@ -179,9 +192,12 @@
+         elseif CURL then
+             // curl
+             download_cmd = "curl "+proxy_host_arg+proxy_user_arg+timeout_arg+" -s "+url_in + " -o " + file_out;
+-        else
+        elseif WGET
+             // wget
+             download_cmd = proxy_host_arg+"wget"+proxy_user_arg+timeout_arg+" "+url_in + " -O " + file_out;
+        else
+            // fetch
+            download_cmd = "fetch " + timeout_arg + "-o " + file_out + " " + url_in;
+         end
+ 
+         [rep,stat,err] = unix_g(download_cmd);
--- a/math/scilab/files/patch-modules-core-includes-Thread_Wrapper.h
+++ b/math/scilab/files/patch-modules-core-includes-Thread_Wrapper.h
@ -0,0 +1,16 @@
+--- modules/core/includes/Thread_Wrapper.h.orig	2010-09-01 02:34:21.000000000 -0700
+++ modules/core/includes/Thread_Wrapper.h	2010-09-01 02:34:47.000000000 -0700
+@@ -70,13 +70,6 @@
+ #define __Lock(lockName)			pthread_mutex_lock(lockName)
+ 
+ #define __UnLock(lockName)			pthread_mutex_unlock(lockName)
+-/* PTHREAD_MUTEX_ERRORCHECK needed for a safe release atexit when we try to release without knowing if we own the lock
+-PTHREAD_PROCESS_SHARED needed for interprocess synch (plus alloc in shared mem thread_mutexattr_settype
+-Linux uses PTHREAD_MUTEX_ERRORCHECK_NP other Posix use PTHREAD_MUTEX_ERRORCHECK
+-*/
+-#ifndef PTHREAD_MUTEX_ERRORCHECK
+-#define PTHREAD_MUTEX_ERRORCHECK PTHREAD_MUTEX_ERRORCHECK_NP
+-#endif
+ #define __InitSignalLock(lockName) \
+     do { \
+     pthread_mutexattr_t attr; \
--- a/math/scilab/files/patch-modules-core-src-c-getmemory.c
+++ b/math/scilab/files/patch-modules-core-src-c-getmemory.c
@ -1,28 +0,0 @@
--- modules/core/src/c/getmemory.c.orig	2009-12-16 07:24:40.000000000 +0000
-+++ modules/core/src/c/getmemory.c	2010-01-06 19:27:34.939739546 +0000
-@@ -25,8 +25,12 @@
- #include <sys/sysctl.h>
- #define ARRAY_SIZE(a) (sizeof (a) / sizeof ((a)[0]))
- #define PAGESHIFT_UNDEF -100
-+#elif defined(__FreeBSD__)
-+#include <sys/param.h>
-+#include <sys/sysctl.h>
- #endif
- 
-+
- #include <stdio.h>
- #define kooctet 1024
- int getfreememory(void)
-@@ -160,6 +164,12 @@
- 
-     return 0;
-   }
-+#elif defined(__FreeBSD__)
-+  int avphys_pages;
-+  size_t oldlenp = sizeof (avphys_pages);
-+  sysctlbyname("vm.stats.vm.v_free_count", &avphys_pages, &oldlenp, NULL, NULL);
-+  return (avphys_pages / kooctet) * sysconf(_SC_PAGESIZE); 
-+
- #else
-   /* Solaris and others assumed*/
-   return (sysconf(_SC_AVPHYS_PAGES)/kooctet)*sysconf(_SC_PAGESIZE);
--- a/math/scilab/files/patch-modules-dynamic_link-macros-ilib_gen_Make_unix.sci
+++ b/math/scilab/files/patch-modules-dynamic_link-macros-ilib_gen_Make_unix.sci
@ -0,0 +1,42 @@
+--- modules/dynamic_link/macros/ilib_gen_Make_unix.sci.orig	2010-11-24 00:50:36.000000000 -0800
+++ modules/dynamic_link/macros/ilib_gen_Make_unix.sci	2010-12-15 05:04:30.000000000 -0800
+@@ -64,22 +64,7 @@
+     originPath  = pwd();
+     linkBuildDir    = TMPDIR;
+     commandpath = SCI+"/modules/dynamic_link/src/scripts";
+-    [fd,ierr] = mopen(commandpath+"/write.test","w+");
+-
+-    if (ierr<>0) then
+-      writePerm=%F
+-    else
+-      writePerm=%T
+-      mclose(fd)
+-      mdelete(commandpath+"/write.test");
+-    end
+-
+-    if (writePerm == %T & ( fileinfo(commandpath+"/Makefile.orig") == [] | fileinfo(commandpath+"/libtool") == [] )) then
+-      // We have write permission on the scilab tree, then generate the stuff into the directory in order to avoid the configure each time.
+-        generateConfigure(commandpath);
+-    end
+-
+-
+    
+     // Copy files => linkBuildDir
+     chdir(linkBuildDir);
+ 
+@@ -178,7 +163,7 @@
+         end
+     end
+ 
+-    if ldflags <> '' | cflags <> '' | fflags <> '' | cc <> '' | fileinfo(commandpath+"/Makefile.orig") == [] | fileinfo(commandpath+"/libtool") == [] then
+    if %T then
+         // Makefile.orig doesn't exists or may be invalid regarding the flags
+         // run the ./configure with the flags
+ 
+@@ -274,4 +259,4 @@
+     end
+ 
+ endfunction
+-//=============================================================================
+\ No newline at end of file
+//=============================================================================
--- a/math/scilab/files/patch-modules-hdf5-src-java-org-scilab-modules-hdf5-read-H5Read.java
+++ b/math/scilab/files/patch-modules-hdf5-src-java-org-scilab-modules-hdf5-read-H5Read.java
@ -1,12 +0,0 @@
--- modules/hdf5/src/java/org/scilab/modules/hdf5/read/H5Read.java.orig	2010-03-01 00:10:54.000000000 -0800
-+++ modules/hdf5/src/java/org/scilab/modules/hdf5/read/H5Read.java	2010-03-01 00:11:38.000000000 -0800
-@@ -53,7 +53,8 @@
- 	int nb_objs = H5.H5Gn_members(fileId, groupName);
- 	String[] allObjectsName = new String[nb_objs];
- 	int[] allObjectsType = new int[nb_objs];
-	H5.H5Gget_obj_info_all(fileId, groupName, allObjectsName, allObjectsType); 
-+	long[] refs = new long[nb_objs];
-+	H5.H5Gget_obj_info_all(fileId, groupName, allObjectsName, allObjectsType, refs); 
- 
- 	for (int i = 0 ; i < nb_objs ; ++i) {
- 	    if (allObjectsType[i] == HDF5Constants.H5G_DATASET) {
--- a/math/scilab/files/patch-modules-xcos-src-java-org-scilab-modules-graph-ScilabCanvas.java
+++ b/math/scilab/files/patch-modules-xcos-src-java-org-scilab-modules-graph-ScilabCanvas.java
@ -1,11 +0,0 @@
--- modules/xcos/src/java/org/scilab/modules/graph/ScilabCanvas.java.orig	2010-04-21 20:20:59.000000000 -0700
-+++ modules/xcos/src/java/org/scilab/modules/graph/ScilabCanvas.java	2010-04-21 20:21:25.000000000 -0700
-@@ -265,7 +265,7 @@
- 				boolean dashed = mxUtils.isTrue(style,
- 						mxConstants.STYLE_DASHED, false);
- 				drawConnector(pts, penWidth, penColor, startMarker, startSize,
-						endMarker, endSize, dashed, rounded);
-+						endMarker, endSize, rounded, style);
- 				
- 				Object centerMarker = style.get(ScilabConstants.STYLE_CENTERARROW);
- 				if (centerMarker != null) {
--- a/math/scilab/pkg-plist
+++ b/math/scilab/pkg-plist