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Message-Id: <201207162342.q6GNgvKn092431@red.freebsd.org>
Date: Mon, 16 Jul 2012 23:42:57 GMT
From: Jason Bacon <jwbacon@tds.net>
To: freebsd-gnats-submit@FreeBSD.org
Subject: Maintainer update: science/afni
X-Send-Pr-Version: www-3.1
X-GNATS-Notify:

>Number:         169923
>Category:       ports
>Synopsis:       Maintainer update: science/afni
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    zeising
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jul 16 23:50:10 UTC 2012
>Closed-Date:    Sun Mar 23 16:49:08 UTC 2014
>Last-Modified:  Sun Mar 23 16:49:08 UTC 2014
>Originator:     Jason Bacon
>Release:        9.0-RELEASE
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan  3 07:46:30 UTC 2012     root@farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  amd64
>Description:
Improvements to resolve conflicts and reduce use of bundled dependencies.
>How-To-Repeat:

>Fix:
Attached.


Patch attached with submission follows:

===> Generating patch
===> Viewing diff with more
diff -ruN --exclude=CVS /usr/ports/science/afni/Makefile /home/bacon/Prog/Ports/ports/science/afni/Makefile
--- /usr/ports/science/afni/Makefile	2012-06-01 00:23:53.000000000 -0500
+++ /home/bacon/Prog/Ports/ports/science/afni/Makefile	2012-07-16 09:27:10.000000000 -0500
@@ -16,7 +16,7 @@
 
 PORTNAME=	afni
 PORTVERSION=	2012.04.17.2129
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science biology graphics
 MASTER_SITES=	http://personalpages.tds.net/~jwbacon/Ports/distfiles/AFNI/${PORTVERSION}/ \
 		http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/
@@ -30,12 +30,19 @@
 
 LIB_DEPENDS=	Xm:${PORTSDIR}/x11-toolkits/open-motif \
 		R:${PORTSDIR}/math/R \
-		gsl:${PORTSDIR}/math/gsl
+		gsl:${PORTSDIR}/math/gsl \
+		netcdf:${PORTSDIR}/science/netcdf-ftn
 RUN_DEPENDS=	cjpeg:${PORTSDIR}/graphics/jpeg \
 		mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \
 		whirlgif:${PORTSDIR}/graphics/whirlgif \
 		ppmtogif:${PORTSDIR}/graphics/netpbm \
-		endian:${PORTSDIR}/sysutils/endian
+		endian:${PORTSDIR}/sysutils/endian \
+		qhull:${PORTSDIR}/math/qhull
+
+CONFLICTS=	im-[0-9]* \
+		nifticlib-[0-9]* \
+		open-usp-tukubai-[0-9]*
+# qhull-[0-9]*
 
 .include <bsd.port.pre.mk>
 
@@ -109,7 +116,6 @@
 	${MV}	${INSTALL_WRKSRC}/README* \
 		${STAGE}/doc
 	${MV}	${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
-	${MV}	${INSTALL_WRKSRC}/qhull ${INSTALL_WRKSRC}/afni_qhull
 	for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
 		${MV} $${binary} ${STAGE}/bin ; \
 	done
diff -ruN --exclude=CVS /usr/ports/science/afni/files/patch-Makefile.INCLUDE /home/bacon/Prog/Ports/ports/science/afni/files/patch-Makefile.INCLUDE
--- /usr/ports/science/afni/files/patch-Makefile.INCLUDE	2012-05-11 12:05:09.000000000 -0500
+++ /home/bacon/Prog/Ports/ports/science/afni/files/patch-Makefile.INCLUDE	2012-07-16 07:38:06.000000000 -0500
@@ -1,5 +1,5 @@
 --- Makefile.INCLUDE.orig	2012-04-17 15:56:21.000000000 -0500
-+++ Makefile.INCLUDE	2012-04-18 13:39:29.000000000 -0500
++++ Makefile.INCLUDE	2012-07-16 07:37:32.000000000 -0500
 @@ -48,7 +48,7 @@
  ## AFNI package, but included because they are useful.  Some of
  ## them are Open Source programs, not from the AFNI group at all.
@@ -9,6 +9,51 @@
  
  # mpegtoppm in above list
  
+@@ -58,7 +58,7 @@
+ PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count   \
+            sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals          \
+            fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
+-               cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta   \
++               2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta       \
+            waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket         \
+            3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk       \
+            3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna         \
+@@ -70,7 +70,7 @@
+            3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign        \
+            3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid        \
+            3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum     \
+-           3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
++           3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow       \
+            3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval     \
+            3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI  \
+            3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat  \
+@@ -89,7 +89,7 @@
+            3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip         \
+            3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D      \
+            3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI           \
+-           niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply        \
++           niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply                       \
+            1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport   \
+            3dNormalityTest                                                      \
+            $(EXTRAS)
+@@ -97,7 +97,7 @@
+ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge      \
+                   sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
+                   fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
+-                      cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit    \
++                      2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit        \
+                   waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
+                   3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna      \
+                   imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot    \
+@@ -133,7 +133,7 @@
+ PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge   \
+                sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count  \
+                fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
+-                   cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
++                   2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta     \
+                waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
+                3dAFNItoNIML    AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk     \
+                3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
 @@ -282,6 +282,9 @@
  3dbuc2fim:3dbuc2fim.o
  	$(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
diff -ruN --exclude=CVS /usr/ports/science/afni/pkg-plist /home/bacon/Prog/Ports/ports/science/afni/pkg-plist
--- /usr/ports/science/afni/pkg-plist	2012-05-11 12:05:09.000000000 -0500
+++ /home/bacon/Prog/Ports/ports/science/afni/pkg-plist	2012-07-16 08:20:20.000000000 -0500
@@ -339,7 +339,6 @@
 bin/afni_base.py
 bin/afni_history
 bin/afni_proc.py
-bin/afni_qhull
 bin/afni_run_R
 bin/afni_util.py
 bin/afni_vcheck
@@ -351,7 +350,6 @@
 bin/byteorder
 bin/cat_matvec
 bin/ccalc
-bin/cdf
 bin/count
 bin/db_mod.py
 bin/demo.fixed.niml.do
@@ -427,10 +425,8 @@
 bin/plugout_tta
 bin/prompt_user
 bin/python_module_test.py
-bin/qdelaunay
 bin/quick.alpha.vals.py
 bin/quickspec
-bin/rbox
 bin/realtime_receiver.py
 bin/rmz
 bin/rotcom
===> Done


>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->zeising 
Responsible-Changed-By: zeising 
Responsible-Changed-When: Thu Jul 19 12:24:16 UTC 2012 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=169923 
State-Changed-From-To: open->closed 
State-Changed-By: linimon 
State-Changed-When: Sun Mar 23 16:48:46 UTC 2014 
State-Changed-Why:  
Superseded by ports/186988. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=169923 
>Unformatted:
