Index: head/biology/crux/Makefile
===================================================================
--- head/biology/crux/Makefile	(revision 235515)
+++ head/biology/crux/Makefile	(revision 235516)
@@ -1,38 +1,41 @@
 # New ports collection makefile for:   crux
 # Date created:        8 June 2009
 # Whom:                jasone
 #
 # $FreeBSD$
 #
 
 PORTNAME=      crux
 PORTVERSION=   1.0.1
 CATEGORIES=    python biology
 MASTER_SITES=  http://www.canonware.com/download/Crux/
 
 MAINTAINER=    jasone@FreeBSD.org
 COMMENT=       Software toolkit for phylogenetic inference
 
 USE_BZIP2=     yes
 GNU_CONFIGURE= yes
 CONFIGURE_ARGS=--with-python=${PYTHON_CMD} --disable-mpi
-CONFIGURE_ENV+=EXTRA_CFLAGS="-std=gnu99"
+USE_CSTD=      gnu99
 USE_GMAKE=     yes
 USE_PYTHON=    2.5+
 
 OPTIONS=       SYS_LINALG "Enable system ATLAS/LAPACK" Off
 
 .include <bsd.port.pre.mk>
 
 .if defined(WITH_SYS_LINALG)
+CPPFLAGS+=      -I${LOCALBASE}/include
+LDFLAGS+=       -L${LOCALBASE}/lib
 CONFIGURE_ARGS+= --enable-sys-linalg
-RUN_DEPENDS+=  libatlas:${PORTSDIR}/math/atlas
+CONFIGURE_ENV+= CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}"
+LIB_DEPENDS+=   atlas.2:${PORTSDIR}/math/atlas
 .else
 CONFIGURE_ARGS+= --disable-sys-linalg
 USE_FORTRAN=   yes
 .endif
 
 post-install:
 	@${PREFIX}/bin/crux -b -q /dev/null
 
 .include <bsd.port.post.mk>

Property changes on: head/biology/crux/Makefile
___________________________________________________________________
Modified: cvs2svn:cvs-rev
## -1 +1 ##
-1.1
\ No newline at end of property
+1.2
\ No newline at end of property
Index: head/biology/crux/pkg-plist
===================================================================
--- head/biology/crux/pkg-plist	(revision 235515)
+++ head/biology/crux/pkg-plist	(revision 235516)
@@ -1,71 +1,72 @@
 @comment $FreeBSD$
 bin/crux
 bin/redpoint
 bin/MrRogers
 %%PYTHON_SITELIBDIR%%/Crux/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Character.so
 %%PYTHON_SITELIBDIR%%/Crux/Config.py
 %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
 %%PYTHON_SITELIBDIR%%/Crux/Copying.py
 %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
 %%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/Fasta.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
 %%PYTHON_SITELIBDIR%%/Crux/Newick.so
 %%PYTHON_SITELIBDIR%%/Crux/Taxa.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Cx.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMath.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMat.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxNewickLexer.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxRi.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/CxDistMatrixLexer.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/CxLik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
+%%PYTHON_SITELIBDIR%%/Parsing.so
 share/Crux/lib/libCx.so
 share/Crux/parsers/Fasta.log
 share/Crux/parsers/Fasta.pickle
 share/Crux/parsers/Newick.log
 share/Crux/parsers/Newick.pickle
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
 @dirrm %%PYTHON_SITELIBDIR%%/Crux
 @dirrm share/Crux/lib
 @dirrm share/Crux/parsers
 @dirrm share/Crux

Property changes on: head/biology/crux/pkg-plist
___________________________________________________________________
Modified: cvs2svn:cvs-rev
## -1 +1 ##
-1.1
\ No newline at end of property
+1.2
\ No newline at end of property