ports/169923: Maintainer update: science/afni
Jason Bacon
jwbacon at tds.net
Mon Jul 16 23:50:11 UTC 2012
>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 at 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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