remove science/bblimage; attach science/pyvox to build;

add an entry to MOVED

PR:		158562

8 files changed, 1 insertions, 216 deletions

diff --git a/science/Makefile b/science/Makefile
index 1ec98d7aee02..aebd2f2f3f53 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -12,7 +12,6 @@
     SUBDIR += afni
     SUBDIR += at
     SUBDIR += avogadro
-    SUBDIR += bblimage
     SUBDIR += bddsolve
     SUBDIR += bft
     SUBDIR += bodr
@@ -167,6 +166,7 @@
     SUBDIR += pybrain
     SUBDIR += pycdf
     SUBDIR += pynn
+    SUBDIR += pyvox
     SUBDIR += qcl
     SUBDIR += qtresistors
     SUBDIR += ruby-dcl
diff --git a/science/bblimage/Makefile b/science/bblimage/Makefile
deleted file mode 100644
index 221a9bf84d7a..000000000000
--- a/science/bblimage/Makefile
+++ /dev/null
@@ -1,66 +0,0 @@
-# ex:ts=8
-# Ports collection Makefile for:	bblimage
-# Date created:			Jul 22, 2002
-# Whom:				ijliao
-#
-# $FreeBSD$
-#
-
-PORTNAME=	pyvox
-PORTVERSION=	0.72
-CATEGORIES=	science
-MASTER_SITES=	http://www.med.upenn.edu/bbl/downloads/pyvox/
-EXTRACT_SUFX=	.src.tgz
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A set of software tools for medical image processing
-
-LICENSE=	MIT
-
-LIB_DEPENDS=	lapack.4:${PORTSDIR}/math/lapack
-
-GNU_CONFIGURE=		yes
-LAPACK?=		-llapack -lblas
-CONFIGURE_ARGS =	--with-lapack="${LAPACK}" --with-python="${PYTHON_CMD}"
-CONFIGURE_ENV=		ac_cv_header_tgmath_h=no
-USE_GMAKE=		yes
-USE_LDCONFIG=		yes
-USE_PYTHON=		2.5+
-
-.if defined(WITHOUT_X11)
-CONFIGURE_ARGS+=--without-x
-PLIST_SUB+=	X11="@comment "
-.else
-CONFIGURE_ARGS+=--with-x
-BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
-RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/Pmw/__init__.py:${PORTSDIR}/x11-toolkits/py-Pmw
-USE_MOTIF=	yes
-USE_TK =	82+
-CFLAGS+=	-DUSE_COMPOSITELESS_PHOTO_PUT_BLOCK -I${LOCALBASE}/include \
-		-I${TCL_INCLUDEDIR} -I${TK_INCLUDEDIR}
-PLIST_SUB+=	X11=""
-.endif
-
-MAN1=	affreg.1 anonavw.1 bredit.1 decomment.1 dumpavw.1 editavw.1 makeavw.1 pyvox.1 \
-	reged.1 regedit.1 qdv.1
-MAN5=	cdata.5 param.5
-
-.include <bsd.port.pre.mk>
-
-post-patch:
-.if defined(WITHOUT_X11)
-	@${REINPLACE_CMD} -e '\|pmw=yes|s|yes|no|' -e '\|tkinter=yes|s|yes|no|' \
-		${WRKSRC}/configure
-	@${REINPLACE_CMD} -e '\|#include "tk.h"|d' ${WRKSRC}/include/pyvox.h
-.else
-	@${REINPLACE_CMD} -e 's|-ltk|&${USE_TK}|' \
-		${WRKSRC}/Makefile.in
-.endif
-
-.if defined(MAINTAINER_MODE)
-check regress regression-test test: build
-	 @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} \
-	 ${MAKEFILE} ${_MAKE_JOBS} ${MAKE_ARGS} regress)
-.endif
-
-.include <bsd.port.post.mk>
diff --git a/science/bblimage/distinfo b/science/bblimage/distinfo
deleted file mode 100644
index 62547d6b3ece..000000000000
--- a/science/bblimage/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (pyvox-0.72.src.tgz) = d7a733faa323d8cdca51e8244e9c50c91bccbb77543e546125f7b251a3c75a61
-SIZE (pyvox-0.72.src.tgz) = 1501027
diff --git a/science/bblimage/files/patch-src__parray.c b/science/bblimage/files/patch-src__parray.c
deleted file mode 100644
index a84acca50fdd..000000000000
--- a/science/bblimage/files/patch-src__parray.c
+++ /dev/null
@@ -1,76 +0,0 @@
---- ./src/parray.c.orig	2006-02-24 12:18:51.000000000 -0500
-+++ ./src/parray.c	2011-07-01 02:32:12.000000000 -0400
-@@ -991,7 +991,7 @@
-     if (DEBUG_ALLOC) {
- 	fprintf(stderr, "parray create:  %p\n", self);
- 	if (0) 
--	    fprintf(stderr, "...reference count = %d\n",
-+	    fprintf(stderr, "...reference count = %zd\n",
- 		    ((PyObject *)self)->ob_refcnt); 
-     }
- 
-@@ -1171,7 +1171,7 @@
-     if (DEBUG_ALLOC) {
- 	fprintf(stderr, "parray alloc:   %p\n", self);
- 	if (0) 
--	    fprintf(stderr, "...reference count = %d\n",
-+	    fprintf(stderr, "...reference count = %zd\n",
- 		    ((PyObject *)self)->ob_refcnt); 
-     }
- 
-@@ -2074,7 +2074,7 @@
- 
- static PyMappingMethods
- parray_as_mapping = {
--    (inquiry)       parray_length,    /* mp_length:        len(x)   */
-+    (lenfunc)       parray_length,    /* mp_length:        len(x)   */
-     (binaryfunc)    parray_getitem,   /* mp_subscript:     x[y]     */
-     (objobjargproc) parray_setitem,   /* mp_ass_subscript: x[y] = v */
- };
-@@ -2204,13 +2204,13 @@
- 
- static PySequenceMethods 
- parray_as_sequence = {
--    (inquiry)          0,                  /* sq_length:     len(x)     */
-+    (lenfunc)          0,                  /* sq_length:     len(x)     */
-     (binaryfunc)       0,                  /* sq_concat:     x + y      */
--    (intargfunc)       0,                  /* sq_repeat:     n * x      */
--    (intargfunc)       0,                  /* sq_item:       x[i]       */
--    (intintargfunc)    parray_getslice,    /* sq_slice:      x[i:j]     */
--    (intobjargproc)    0,                  /* sq_ass_item:   x[i] = v   */
--    (intintobjargproc) parray_setslice,    /* sq_ass_slice:  x[i:j] = v */
-+    (ssizeargfunc)       0,                  /* sq_repeat:     n * x      */
-+    (ssizeargfunc)       0,                  /* sq_item:       x[i]       */
-+    (ssizessizeargfunc)    parray_getslice,    /* sq_slice:      x[i:j]     */
-+    (ssizeobjargproc)    0,                  /* sq_ass_item:   x[i] = v   */
-+    (ssizessizeobjargproc) parray_setslice,    /* sq_ass_slice:  x[i:j] = v */
- };
- 
- 
-@@ -7386,7 +7386,7 @@
- 
-     /* DEBUG: Print ref counts of arguments */
-     if (0) {
--      printf("Refcnts 1: %d, %d\n", self->ob_refcnt, filename->ob_refcnt);
-+      printf("Refcnts 1: %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt);
-     }
- 
-     /* Paste self onto front of argument tuple.  FIXME: This is really
-@@ -7400,7 +7400,7 @@
- 
-     /* DEBUG: Print ref counts of arguments */
-     if (0) {
--      printf("Refcnts 2: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
-+      printf("Refcnts 2: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
- 	     newargs->ob_refcnt);
-     }
- 
-@@ -7418,7 +7418,7 @@
- 
-     /* DEBUG: Print ref counts of arguments */
-     if (0) {
--      printf("Refcnts 3: %d, %d, %d\n", self->ob_refcnt, filename->ob_refcnt,
-+      printf("Refcnts 3: %zd, %zd, %zd\n", self->ob_refcnt, filename->ob_refcnt,
- 	     newargs->ob_refcnt);
-     }
- 
diff --git a/science/bblimage/files/patch-src__pyvox.c b/science/bblimage/files/patch-src__pyvox.c
deleted file mode 100644
index 07f056943e7d..000000000000
--- a/science/bblimage/files/patch-src__pyvox.c
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./src/pyvox.c.orig	2006-02-24 16:33:41.000000000 -0500
-+++ ./src/pyvox.c	2011-07-01 02:29:06.000000000 -0400
-@@ -1850,7 +1850,7 @@
-     if (0) {
- 	fprintf(stderr, "Created new kernel object at %p\n", self);
- 	if (0) 
--	    fprintf(stderr, "...reference count = %d\n",
-+	    fprintf(stderr, "...reference count = %zd\n",
- 		    ((PyObject *)self)->ob_refcnt); 
-     }
- 
-@@ -2273,7 +2273,7 @@
- 
- static PyMappingMethods
- kernel_as_mapping = {
--    (inquiry)       kernel_length,    /* mp_length:        len(x)   */
-+    (lenfunc)       kernel_length,    /* mp_length:        len(x)   */
-     (binaryfunc)    kernel_getitem,   /* mp_subscript:     x[y]     */
-     (objobjargproc) kernel_setitem,   /* mp_ass_subscript: x[y] = v */
- };
diff --git a/science/bblimage/files/patch-src__tkphoto.c b/science/bblimage/files/patch-src__tkphoto.c
deleted file mode 100644
index 9be4a5503b5f..000000000000
--- a/science/bblimage/files/patch-src__tkphoto.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/tkphoto.c.orig	2005-12-29 13:33:15.000000000 -0500
-+++ ./src/tkphoto.c	2011-07-01 02:28:06.000000000 -0400
-@@ -632,7 +632,7 @@
-     if (0) {
- 	fprintf(stderr, "Created new tkphoto object at %p\n", self);
- 	if (0) 
--	    fprintf(stderr, "...reference count = %d\n",
-+	    fprintf(stderr, "...reference count = %zd\n",
- 		    ((PyObject *)pytk)->ob_refcnt); 
-     }
- 
diff --git a/science/bblimage/pkg-descr b/science/bblimage/pkg-descr
deleted file mode 100644
index 6daca94b72f2..000000000000
--- a/science/bblimage/pkg-descr
+++ /dev/null
@@ -1,14 +0,0 @@
-Pyvox (formerly known as BBLimage) is a set of software tools for medical
-image processing, particularly skull stripping and segmentation of MR brain
-images (tools to support other applications may be added later). These tools
-are intended to support researchers who need to prototype new image analysis
-algorithms or to develop automated image analysis tools for specific image
-analysis applications. The sequence of processing operations is specified
-through the scripting language Python, which can be used interactively or in
-command files.
-
-Pyvox scripts and date files are portable, easily extensible, and suitable
-both for rapid prototyping of new algorithms and analysis protocols, and also
-for efficient, automated processing of the finished analysis protocols.
-
-WWW: http://www.med.upenn.edu/bbl/downloads/pyvox/index.shtml
diff --git a/science/bblimage/pkg-plist b/science/bblimage/pkg-plist
deleted file mode 100644
index 2d3ecb6c87dd..000000000000
--- a/science/bblimage/pkg-plist
+++ /dev/null
@@ -1,26 +0,0 @@
-bin/affreg
-bin/anonavw
-bin/bredit
-bin/decomment
-bin/dumpavw
-bin/editavw
-bin/makeavw
-%%X11%%bin/qdv
-bin/regedit
-include/errm.h
-include/exim.h
-include/memm.h
-include/voxel.h
-lib/libpyvox.so
-lib/libvoxkit.so
-%%PYTHON_SITELIBDIR%%/exim.so
-%%PYTHON_SITELIBDIR%%/optim.py
-%%PYTHON_SITELIBDIR%%/optim.pyc
-%%PYTHON_SITELIBDIR%%/pyvox.py
-%%PYTHON_SITELIBDIR%%/pyvox.pyc
-%%PYTHON_SITELIBDIR%%/pyvoxC.so
-%%PYTHON_SITELIBDIR%%/reged.py
-%%PYTHON_SITELIBDIR%%/reged.pyc
-%%PYTHON_SITELIBDIR%%/regis.py
-%%PYTHON_SITELIBDIR%%/regis.pyc
-%%X11%%%%PYTHON_SITELIBDIR%%/tkphoto.so