5 files changed, 55 insertions, 6 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index 393a627ad67e..6ca7b0d85b90 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -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
 
diff --git a/science/afni/distinfo b/science/afni/distinfo
index ba5c91280c59..5b3bda489f59 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -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
diff --git a/science/afni/files/patch-SUMA_gts_examples_happrox.c b/science/afni/files/patch-SUMA_gts_examples_happrox.c
new file mode 100644
index 000000000000..c684d34fff06
--- /dev/null
+++ b/science/afni/files/patch-SUMA_gts_examples_happrox.c
@@ -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>
diff --git a/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE b/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE
new file mode 100644
index 000000000000..b3374412c7e3
--- /dev/null
+++ b/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE
@@ -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
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index efc23f03605e..fa3c1318d82c 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -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