svn commit: r502266 - in head/science/afni: . files
Jason W. Bacon
jwb at FreeBSD.org
Wed May 22 12:44:19 UTC 2019
Author: jwb
Date: Wed May 22 12:44:17 2019
New Revision: 502266
URL: https://svnweb.freebsd.org/changeset/ports/502266
Log:
science/afni: Upgrade to 19.1.10
Rapid response from upstream on reported issue. Additional patches to be
upstreamed in next release.
Added:
head/science/afni/files/patch-SUMA_gts_examples_happrox.c (contents, props changed)
head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE (contents, props changed)
Modified:
head/science/afni/Makefile
head/science/afni/distinfo
head/science/afni/pkg-plist
Modified: head/science/afni/Makefile
==============================================================================
--- head/science/afni/Makefile Wed May 22 12:31:26 2019 (r502265)
+++ head/science/afni/Makefile Wed May 22 12:44:17 2019 (r502266)
@@ -2,7 +2,7 @@
PORTNAME= afni
DISTVERSIONPREFIX= AFNI_
-DISTVERSION= 19.1.08
+DISTVERSION= 19.1.10
CATEGORIES= science biology graphics perl5 python
MAINTAINER= jwb at FreeBSD.org
@@ -19,10 +19,10 @@ LIB_DEPENDS= libexpat.so:textproc/expat2 \
libgsl.so:math/gsl \
libnetcdff.so:science/netcdf-fortran \
libxml2.so:textproc/libxml2 \
- libXm.so:x11-toolkits/open-motif
+ libXm.so:x11-toolkits/open-motif \
+ libnetpbm.so:graphics/netpbm
RUN_DEPENDS= endian:sysutils/endian \
mpeg_encode:multimedia/mpeg_encode \
- ppmtogif:graphics/netpbm \
qhull:math/qhull5 \
R:math/R
Modified: head/science/afni/distinfo
==============================================================================
--- head/science/afni/distinfo Wed May 22 12:31:26 2019 (r502265)
+++ head/science/afni/distinfo Wed May 22 12:44:17 2019 (r502266)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557698397
-SHA256 (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 15dcb04412c68e3ca2673eaf90cdd9bb26c1d23c09ed3346bf330ecbf18c4269
-SIZE (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 38767080
+TIMESTAMP = 1558474958
+SHA256 (afni-afni-AFNI_19.1.10_GH0.tar.gz) = 893b102fb2dbb38781ef1367c32e6f13c5ada7f2e70ea574dcd1973c755ee636
+SIZE (afni-afni-AFNI_19.1.10_GH0.tar.gz) = 38816633
Added: head/science/afni/files/patch-SUMA_gts_examples_happrox.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/afni/files/patch-SUMA_gts_examples_happrox.c Wed May 22 12:44:17 2019 (r502266)
@@ -0,0 +1,11 @@
+--- SUMA/gts/examples/happrox.c.orig 2019-05-21 18:01:41 UTC
++++ SUMA/gts/examples/happrox.c
+@@ -20,7 +20,7 @@
+ #include <math.h>
+ #include <stdlib.h>
+ #include <string.h>
+-#include <pgm.h>
++#include <netpbm/pgm.h>
+ #include "config.h"
+ #ifdef HAVE_GETOPT_H
+ # include <getopt.h>
Added: head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE Wed May 22 12:44:17 2019 (r502266)
@@ -0,0 +1,16 @@
+--- ptaylor/Makefile.ptaylor.INCLUDE.orig 2019-05-21 17:27:32 UTC
++++ ptaylor/Makefile.ptaylor.INCLUDE
+@@ -228,11 +228,11 @@ map_TrackID:map_TrackID.o ${AFNI_3dOBJS} ${PTAYLORLIB}
+
+ 3dDWUncert.o: 3dDWUncert.c
+ $(RM) $@
+- $(CCOMP_PT) -c 3dDWUncert.c $(PTAYLOR_INCLUDE_PATH)
++ $(CCOMP_PT) -c -fopenmp 3dDWUncert.c $(PTAYLOR_INCLUDE_PATH)
+
+ 3dDWUncert:3dDWUncert.o ${AFNI_3dOBJS} ${PTAYLORLIB}
+ $(RM) $@
+- $(CCOMP_PT) -o 3dDWUncert 3dDWUncert.o ${AFNI_3dOBJS} \
++ $(CCOMP_PT) -fopenmp -o 3dDWUncert 3dDWUncert.o ${AFNI_3dOBJS} \
+ ${PTAYLOR_INCLUDE_PATH} ${PTAYLOR_LINK_PATH} \
+ $(LFLAGS) ${PTAYLORLIB} $(LLIBS) \
+ -lgsl -lgslcblas -lm
Modified: head/science/afni/pkg-plist
==============================================================================
--- head/science/afni/pkg-plist Wed May 22 12:31:26 2019 (r502265)
+++ head/science/afni/pkg-plist Wed May 22 12:44:17 2019 (r502266)
@@ -3,6 +3,8 @@ bin/1dAstrip
bin/1dBandpass
bin/1dBport
bin/1dCorrelate
+bin/1dDW_Grad_o_Mat
+bin/1dDW_Grad_o_Mat++
bin/1dFlagMotion
bin/1dGC.R
bin/1dMarry
@@ -47,6 +49,7 @@ bin/3dANOVA3
bin/3dAOV.R
bin/3dAcost
bin/3dAllineate
+bin/3dAmpToRSFC
bin/3dAnatNudge
bin/3dAnhist
bin/3dAttribute
@@ -64,22 +67,27 @@ bin/3dCRUISEtoAFNI
bin/3dClipLevel
bin/3dClustCount
bin/3dClustSim
+bin/3dClusterize
bin/3dConformist
bin/3dConvolve
bin/3dCountSpikes
bin/3dDFT
bin/3dDTeig
bin/3dDTtoDWI
+bin/3dDTtoNoisyDWI
bin/3dDWItoDT
+bin/3dDWUncert
bin/3dDeconvolve
bin/3dDeconvolve_f
bin/3dDegreeCentrality
bin/3dDespike
bin/3dDetrend
bin/3dECM
+bin/3dEigsToDT
bin/3dEmpty
bin/3dEntropy
bin/3dErrtsCormat
+bin/3dExchange
bin/3dExtractGroupInCorr
bin/3dExtrema
bin/3dFDR
@@ -113,6 +121,7 @@ bin/3dLocalHistog
bin/3dLocalPV
bin/3dLocalSVD
bin/3dLocalstat
+bin/3dLombScargle
bin/3dMEMA
bin/3dMEMA.R
bin/3dMEPFM
@@ -124,11 +133,13 @@ bin/3dMVM.R
bin/3dMVM_validator
bin/3dMannWhitney
bin/3dMaskToASCII
+bin/3dMatch
bin/3dMax
bin/3dMean
bin/3dMedianFilter
bin/3dMultiThresh
bin/3dNLfim
+bin/3dNetCorr
bin/3dNormalityTest
bin/3dNotes
bin/3dNwarpAdjust
@@ -148,9 +159,12 @@ bin/3dProbTrackID
bin/3dPval
bin/3dQwarp
bin/3dREMLfit
+bin/3dROIMaker
bin/3dROIstats
+bin/3dRSFC
bin/3dRank
bin/3dRankizer
+bin/3dReHo
bin/3dRegAna
bin/3dRetinoPhase
bin/3dRowFillin
@@ -162,11 +176,14 @@ bin/3dSharpen
bin/3dSignatures
bin/3dSignatures.R
bin/3dSkullStrip
+bin/3dSliceNDice
+bin/3dSpaceTimeCorr
bin/3dSpatNorm
bin/3dStatClust
bin/3dSurf2Vol
bin/3dSurfMask
bin/3dSynthesize
+bin/3dTORTOISEtoHere
bin/3dTRfix
bin/3dTSgen
bin/3dTagalign
@@ -194,6 +211,7 @@ bin/3dUndump
bin/3dUnifize
bin/3dUniformize
bin/3dUpsample
+bin/3dVecRGB_to_HSL
bin/3dVol2Surf
bin/3dWarp
bin/3dWarpDrive
@@ -205,6 +223,7 @@ bin/3dXYZcat
bin/3dZcat
bin/3dZcutup
bin/3dZeropad
+bin/3dZipperZapper
bin/3dZregrid
bin/3danisosmooth
bin/3daxialize
@@ -215,6 +234,7 @@ bin/3dclust
bin/3dcopy
bin/3ddelay
bin/3ddot
+bin/3ddot_beta
bin/3ddup
bin/3dedge3
bin/3dfim
@@ -592,6 +612,7 @@ bin/lpc_align.py
bin/make_pq_script.py
bin/make_random_timing.py
bin/make_stim_times.py
+bin/map_TrackID
bin/mayo_analyze
bin/meica.py
bin/module_test_lib.py
@@ -1416,6 +1437,7 @@ lib/afni/plug_zeropad.so
%%DATADIR%%/funstuff/splash_laworder.jpg
%%DATADIR%%/funstuff/splash_leaves2018.jpg
%%DATADIR%%/funstuff/splash_lightsaber.jpg
+%%DATADIR%%/funstuff/splash_lionsrock.jpg
%%DATADIR%%/funstuff/splash_listerhill2017.jpg
%%DATADIR%%/funstuff/splash_littlepetra.jpg
%%DATADIR%%/funstuff/splash_lunchtime.jpg
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