Date: Mon, 16 Jul 2012 23:42:57 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/169923: Maintainer update: science/afni Message-ID: <201207162342.q6GNgvKn092431@red.freebsd.org> Resent-Message-ID: <201207162350.q6GNoAkc003958@freefall.freebsd.org>
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>Number: 169923 >Category: ports >Synopsis: Maintainer update: science/afni >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Mon Jul 16 23:50:10 UTC 2012 >Closed-Date: >Last-Modified: >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: >Unformatted:
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