Date: Wed, 22 May 2019 12:44:17 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r502266 - in head/science/afni: . files Message-ID: <201905221244.x4MCiHN4024844@repo.freebsd.org>
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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@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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