Attachment 79267 Details for Bug 113887 – file.diff

[patch] file.diff

file.diff (text/plain), 12.28 KB, created by Jason Bacon on 2007-06-20 20:30:03 UTC

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Creator: Jason Bacon

Created: 2007-06-20 20:30:03 UTC

Size: 12.28 KB

patch

obsolete

>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@smithers.neuro.mcw.edu
>+# Whom:                Jason W. Bacon <bacon@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@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

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Attachments on bug 113887: 79267