ports/113887: [maintainer update] science/afni
Jason Bacon
bacon at smithers.neuro.mcw.edu
Wed Jun 20 19:30:04 UTC 2007
>Number: 113887
>Category: ports
>Synopsis: [maintainer update] science/afni
>Confidential: no
>Severity: serious
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Wed Jun 20 19:30:03 GMT 2007
>Closed-Date:
>Last-Modified:
>Originator: Jason Bacon
>Release: FreeBSD 5.4-RELEASE i386
>Organization:
Medical College of Wisconsin
>Environment:
System: FreeBSD smithers.neuro.mcw.edu 5.4-RELEASE FreeBSD 5.4-RELEASE #2: Wed Aug 24 14:54:53 CDT 2005 bacon at clone.neuro.mcw.edu:/usr/obj/usr/src/sys/clone i386
>Description:
The current afni port does not compile under Xorg 7.2. This update
corrects the problem and installs a newer version of AFNI.
>How-To-Repeat:
>Fix:
diff -ruN /usr/ports/science/afni/Makefile afni/Makefile
--- /usr/ports/science/afni/Makefile Sat Jun 9 23:04:38 2007
+++ afni/Makefile Fri Jun 15 13:41:17 2007
@@ -1,9 +1,9 @@
############################################################################
# Ports collection Makefile for: afni
# Date created: 11 Jan 2005
-# Whom: bacon at smithers.neuro.mcw.edu
+# Whom: Jason W. Bacon <bacon at smithers.neuro.mcw.edu>
#
-# $FreeBSD: ports/science/afni/Makefile,v 1.12 2007/06/10 04:04:38 kris Exp $
+# $FreeBSD$
#
############################################################################
@@ -16,8 +16,7 @@
# Makefile.BSD, which is included in the source distribution.
PORTNAME= afni
-PORTVERSION= 2007.04.18.1830
-PORTREVISION= 1
+PORTVERSION= 2007.06.15.1339
CATEGORIES= science biology graphics
MASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/${PORTVERSION}/ \
http://afni.nimh.nih.gov/pub/dist/tgz/
@@ -35,15 +34,13 @@
ppmtogif:${PORTSDIR}/graphics/netpbm \
endian:${PORTSDIR}/sysutils/endian
-BROKEN= Does not compile
-
.include <bsd.port.pre.mk>
.if ${ARCH} == "sparc64"
BROKEN= Does not compile on sparc64: "undefined reference to '_mcount'"
.endif
-USE_GL= glw
+USE_GL= glw glu
USE_GETTEXT= yes
USE_GMAKE= yes
USE_ICONV= yes
@@ -80,6 +77,8 @@
.for f in ${X11R6_FILES}
@${REINPLACE_CMD} -e 's|/usr/X11R6|$${X11BASE}|g' ${WRKSRC}/${f}
.endfor
+ @${CP} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${WRKDIR}
+ @${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1
post-build:
${MKDIR} ${STAGE}/bin \
@@ -90,10 +89,6 @@
${STAGE}/doc \
${STAGE}/share
${MV} ${INSTALL_WRKSRC}/libf2c.a \
- ${INSTALL_WRKSRC}/cjpeg \
- ${INSTALL_WRKSRC}/djpeg \
- ${INSTALL_WRKSRC}/mpeg_encode \
- ${INSTALL_WRKSRC}/whirlgif \
${STAGE}/trash
${MV} ${INSTALL_WRKSRC}/*.a \
${INSTALL_WRKSRC}/*.so \
@@ -106,6 +101,7 @@
${STAGE}/include
${MV} ${INSTALL_WRKSRC}/README* \
${STAGE}/doc
+ ${MV} ${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
${MV} $${binary} ${STAGE}/bin ; \
done
@@ -121,7 +117,7 @@
${INSTALL_SCRIPT} ${STAGE}/scripts/* ${PREFIX}/bin
${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR}
${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.3c-May0806/* ${DATADIR}
- ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${PREFIX}/man/man1
+ ${INSTALL_MAN} ${WRKDIR}/afni.1 ${PREFIX}/man/man1
.if !defined(NOPORTDOCS)
${MKDIR} ${DOCSDIR}
${INSTALL_DATA} ${STAGE}/doc/* ${DOCSDIR}
diff -ruN /usr/ports/science/afni/distinfo afni/distinfo
--- /usr/ports/science/afni/distinfo Sat Apr 21 08:37:39 2007
+++ afni/distinfo Fri Jun 15 14:43:56 2007
@@ -1,15 +1,15 @@
-MD5 (AFNI-2007.04.18.1830/afni_src.tgz) = 90ecae8727cadc6172517bc7149be67e
-SHA256 (AFNI-2007.04.18.1830/afni_src.tgz) = 53796de972179f122ab7c557bf29d3511ed113119d04707e16b0766763f49c21
-SIZE (AFNI-2007.04.18.1830/afni_src.tgz) = 11283995
-MD5 (AFNI-2007.04.18.1830/afni.1) = 80cc1f1c6ca0ef59a3032ad63abfbdd5
-SHA256 (AFNI-2007.04.18.1830/afni.1) = 647815326aa676d005fa15de116a6f046b486530aa50a3100d8b29c11da8aaf7
-SIZE (AFNI-2007.04.18.1830/afni.1) = 1702
-MD5 (AFNI-2007.04.18.1830/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee
-SHA256 (AFNI-2007.04.18.1830/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd
-SIZE (AFNI-2007.04.18.1830/TTatlas+tlrc.BRIK.gz) = 159912
-MD5 (AFNI-2007.04.18.1830/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5
-SHA256 (AFNI-2007.04.18.1830/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919
-SIZE (AFNI-2007.04.18.1830/TTatlas+tlrc.HEAD) = 1750
-MD5 (AFNI-2007.04.18.1830/CA_EZ_v1.3c-May0806.tgz) = dbb2caab5c030c505b306e1526d19150
-SHA256 (AFNI-2007.04.18.1830/CA_EZ_v1.3c-May0806.tgz) = b4e9a6bbb2324c01f70d50e911793e637373040c8cca8e5f17882a146396bc31
-SIZE (AFNI-2007.04.18.1830/CA_EZ_v1.3c-May0806.tgz) = 2652278
+MD5 (AFNI-2007.06.15.1339/afni_src.tgz) = 19f4c9e5dac9459b14c40475879f1dda
+SHA256 (AFNI-2007.06.15.1339/afni_src.tgz) = b4778ada0afb603f4a104ee2448792d5f3b0eea844defda8dd9141002c98a433
+SIZE (AFNI-2007.06.15.1339/afni_src.tgz) = 11331933
+MD5 (AFNI-2007.06.15.1339/afni.1) = 02708ca46c60d6774af4796535e263ed
+SHA256 (AFNI-2007.06.15.1339/afni.1) = f134d1f869b1dfd618c61e58fd24b9c4dcfea9c25bc5b1c26dbbb141719cd6f8
+SIZE (AFNI-2007.06.15.1339/afni.1) = 1667
+MD5 (AFNI-2007.06.15.1339/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee
+SHA256 (AFNI-2007.06.15.1339/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd
+SIZE (AFNI-2007.06.15.1339/TTatlas+tlrc.BRIK.gz) = 159912
+MD5 (AFNI-2007.06.15.1339/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5
+SHA256 (AFNI-2007.06.15.1339/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919
+SIZE (AFNI-2007.06.15.1339/TTatlas+tlrc.HEAD) = 1750
+MD5 (AFNI-2007.06.15.1339/CA_EZ_v1.3c-May0806.tgz) = dbb2caab5c030c505b306e1526d19150
+SHA256 (AFNI-2007.06.15.1339/CA_EZ_v1.3c-May0806.tgz) = b4e9a6bbb2324c01f70d50e911793e637373040c8cca8e5f17882a146396bc31
+SIZE (AFNI-2007.06.15.1339/CA_EZ_v1.3c-May0806.tgz) = 2652278
diff -ruN /usr/ports/science/afni/files/Makefile.FreeBSD_PORT afni/files/Makefile.FreeBSD_PORT
--- /usr/ports/science/afni/files/Makefile.FreeBSD_PORT Sat Apr 21 08:37:39 2007
+++ afni/files/Makefile.FreeBSD_PORT Fri May 25 14:40:54 2007
@@ -45,7 +45,7 @@
LD? = ${CC}
CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG
-CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE
+CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA
ifeq (${ARCH}, amd64)
CEXTRA += -DPIC -fPIC
endif
diff -ruN /usr/ports/science/afni/files/patch-Makefile.INCLUDE afni/files/patch-Makefile.INCLUDE
--- /usr/ports/science/afni/files/patch-Makefile.INCLUDE Wed Dec 31 18:00:00 1969
+++ afni/files/patch-Makefile.INCLUDE Fri Apr 27 15:03:56 2007
@@ -0,0 +1,11 @@
+--- Makefile.INCLUDE.orig Fri Apr 27 15:03:08 2007
++++ Makefile.INCLUDE Fri Apr 27 15:03:29 2007
+@@ -41,7 +41,7 @@
+ ## AFNI package, but included because they are useful. Some of
+ ## them are Open Source programs, not from the AFNI group at all.
+
+-EXTRAS = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv $(EXPROGS)
++EXTRAS = myget Xphace rmz aiv $(EXPROGS)
+
+ # mpegtoppm in above list
+
diff -ruN /usr/ports/science/afni/files/patch-SUMA-SUMA_display.c afni/files/patch-SUMA-SUMA_display.c
--- /usr/ports/science/afni/files/patch-SUMA-SUMA_display.c Wed Dec 31 18:00:00 1969
+++ afni/files/patch-SUMA-SUMA_display.c Wed Jun 6 12:46:30 2007
@@ -0,0 +1,53 @@
+--- SUMA/SUMA_display.c.orig Wed Jun 6 12:42:06 2007
++++ SUMA/SUMA_display.c Wed Jun 6 12:45:54 2007
+@@ -1854,22 +1854,14 @@
+
+
+
+- #ifdef SUMA_MOTIF_GLXAREA
+- /* Step 4. */
+- SUMAg_SVv[ic].X->FORM = XmCreateForm(SUMAg_SVv[ic].X->TOPLEVEL, "form", NULL, 0);
+- XtManageChild(SUMAg_SVv[ic].X->FORM);
+- SUMAg_SVv[ic].X->FRAME = XmCreateFrame(SUMAg_SVv[ic].X->FORM, "frame", NULL, 0);
+- XtVaSetValues(SUMAg_SVv[ic].X->FRAME,
+- XmNbottomAttachment, XmATTACH_FORM,
+- XmNtopAttachment, XmATTACH_FORM,
+- XmNleftAttachment, XmATTACH_FORM,
+- XmNrightAttachment, XmATTACH_FORM,
+- NULL);
+- XtManageChild(SUMAg_SVv[ic].X->FRAME);
+-
+- /* Step 5. */
+ SUMAg_SVv[ic].X->CMAP = SUMA_getShareableColormap(&(SUMAg_SVv[ic]));
+
++ /* create a frame to put glxarea in */
++ SUMAg_SVv[ic].X->FRAME = XmCreateFrame (mainw, "frame", NULL, 0);
++ XtManageChild(SUMAg_SVv[ic].X->FRAME);
++
++ #ifdef SUMA_MOTIF_GLXAREA
++ SUMA_LH("MOTIF Drawing Area");
+ /* Step 6. */
+ /* glwMDrawingAreaWidgetClass requires libMesaGLwM.a */
+ SUMAg_SVv[ic].X->GLXAREA = XtVaCreateManagedWidget("glxarea",
+@@ -1878,20 +1870,13 @@
+ XtNcolormap, SUMAg_SVv[ic].X->CMAP,
+ NULL);
+ #else
+- /* Step 4-6. */
+- SUMAg_SVv[ic].X->CMAP = SUMA_getShareableColormap(&(SUMAg_SVv[ic]));
+-
+- /* create a frame to put glxarea in */
+- SUMAg_SVv[ic].X->FRAME = XmCreateFrame (mainw, "frame", NULL, 0);
+- XtManageChild(SUMAg_SVv[ic].X->FRAME);
+-
++ SUMA_LH("GL Drawing Area");
+ /* glwDrawingAreaWidgetClass requires libMesaGLw.a */
+ SUMAg_SVv[ic].X->GLXAREA = XtVaCreateManagedWidget("glxarea",
+ glwDrawingAreaWidgetClass, SUMAg_SVv[ic].X->FRAME,
+ GLwNvisualInfo, SUMAg_SVv[ic].X->VISINFO,
+ XtNcolormap, SUMAg_SVv[ic].X->CMAP,
+ NULL);
+-
+ #endif
+
+
diff -ruN /usr/ports/science/afni/files/patch-SUMA-SUMA_xColBar.c afni/files/patch-SUMA-SUMA_xColBar.c
--- /usr/ports/science/afni/files/patch-SUMA-SUMA_xColBar.c Wed Dec 31 18:00:00 1969
+++ afni/files/patch-SUMA-SUMA_xColBar.c Wed Jun 6 12:44:38 2007
@@ -0,0 +1,26 @@
+--- SUMA/SUMA_xColBar.c.orig Wed Jun 6 12:42:16 2007
++++ SUMA/SUMA_xColBar.c Wed Jun 6 12:43:42 2007
+@@ -4087,6 +4087,15 @@
+ NULL);
+
+ /* open me a glxarea */
++ #ifdef SUMA_MOTIF_GLXAREA
++ SO->SurfCont->cmp_ren->cmap_wid = XtVaCreateManagedWidget("glxarea",
++ glwMDrawingAreaWidgetClass, rcc2,
++ GLwNvisualInfo, SUMAg_SVv[0].X->VISINFO,
++ XtNcolormap, SUMAg_SVv[0].X->CMAP,
++ XmNwidth, SUMA_CMAP_WIDTH,
++ XmNheight, SUMA_CMAP_HEIGHT,
++ NULL);
++ #else
+ SO->SurfCont->cmp_ren->cmap_wid = XtVaCreateManagedWidget("glxarea",
+ glwDrawingAreaWidgetClass, rcc2,
+ GLwNvisualInfo, SUMAg_SVv[0].X->VISINFO,
+@@ -4094,6 +4103,7 @@
+ XmNwidth, SUMA_CMAP_WIDTH,
+ XmNheight, SUMA_CMAP_HEIGHT,
+ NULL);
++ #endif
+
+ XtManageChild (rcc2);
+
diff -ruN /usr/ports/science/afni/pkg-descr afni/pkg-descr
--- /usr/ports/science/afni/pkg-descr Sun Sep 24 13:24:08 2006
+++ afni/pkg-descr Wed Jun 20 14:13:51 2007
@@ -2,6 +2,6 @@
a tool for analyzing 3 dimensional images, especially functional MRI
images used in brain mapping research.
-WWW: http://afni.nimh.nih.gov/
+WWW: http://www.neuro.mcw.edu/~bacon/Ports
-- Jason W. Bacon <bacon at smithers.neuro.mcw.edu>
diff -ruN /usr/ports/science/afni/pkg-message afni/pkg-message
--- /usr/ports/science/afni/pkg-message Sat Apr 21 08:37:39 2007
+++ afni/pkg-message Wed May 23 09:13:42 2007
@@ -13,5 +13,8 @@
For large 3dDeconvolve analyses, you may need to increase the shared
memory limit on your system. For instructions, visit
-http://www.neuro.mcw.edu/~bacon/FreeBSD_MRI/
+http://www.neuro.mcw.edu/~bacon/Ports/FreeBSD/shared_mem.html
+
+The program "abut" has been renamed "afni_abut" to resolve a collision
+with the unixstat port.
=============================================================================
diff -ruN /usr/ports/science/afni/pkg-plist afni/pkg-plist
--- /usr/ports/science/afni/pkg-plist Sat Apr 21 08:37:39 2007
+++ afni/pkg-plist Tue Jun 5 13:43:41 2007
@@ -69,6 +69,7 @@
bin/3dNLfim
bin/3dNotes
bin/3dOverlap
+bin/3dPAR2AFNI.pl
bin/3dROIstats
bin/3dRegAna
bin/3dRowFillin
@@ -209,9 +210,9 @@
bin/SurfaceMetrics
bin/Vecwarp
bin/Xphace
-bin/abut
bin/adwarp
bin/afni
+bin/afni_abut
bin/afni_base.py
bin/afni_proc.py
bin/afni_util.py
@@ -281,7 +282,6 @@
include/afni/3ddata.h
include/afni/afni_environ.h
include/afni/afni_warp.h
-include/afni/cdflib.h
include/afni/coxplot.h
include/afni/cs.h
include/afni/cs_sort_template.h
@@ -406,6 +406,7 @@
%%DATADIR%%/face_asanders.jpg
%%DATADIR%%/face_ashackman.jpg
%%DATADIR%%/face_athomas.jpg
+%%DATADIR%%/face_aysesaygin.jpg
%%DATADIR%%/face_bandettini.jpg
%%DATADIR%%/face_barbaracd.jpg
%%DATADIR%%/face_bargall.jpg
@@ -422,6 +423,7 @@
%%DATADIR%%/face_claudio.jpg
%%DATADIR%%/face_cmoritz.jpg
%%DATADIR%%/face_cmyers.jpg
+%%DATADIR%%/face_craigstark.jpg
%%DATADIR%%/face_cscholl.jpg
%%DATADIR%%/face_csenior.jpg
%%DATADIR%%/face_cwettig.jpg
@@ -469,6 +471,7 @@
%%DATADIR%%/face_lincoln1.jpg
%%DATADIR%%/face_lincoln2.jpg
%%DATADIR%%/face_lindachao.jpg
+%%DATADIR%%/face_lindathede.jpg
%%DATADIR%%/face_lisaeyler.jpg
%%DATADIR%%/face_lizyoder.jpg
%%DATADIR%%/face_ljcox.jpg
>Release-Note:
>Audit-Trail:
>Unformatted:
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