science/afni: Upgrade to 19.1.14

Minor bug fixes and enhancements, some FreeBSD patches upstreamed

4 files changed, 14 insertions, 41 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index 6ca7b0d85b90..625b96c99c51 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=		afni
 DISTVERSIONPREFIX=	AFNI_
-DISTVERSION=		19.1.10
+DISTVERSION=		19.1.14
 CATEGORIES=		science biology graphics perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/science/afni/distinfo b/science/afni/distinfo
index 5b3bda489f59..d8d75e59c3d9 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1558474958
-SHA256 (afni-afni-AFNI_19.1.10_GH0.tar.gz) = 893b102fb2dbb38781ef1367c32e6f13c5ada7f2e70ea574dcd1973c755ee636
-SIZE (afni-afni-AFNI_19.1.10_GH0.tar.gz) = 38816633
+TIMESTAMP = 1559308771
+SHA256 (afni-afni-AFNI_19.1.14_GH0.tar.gz) = d7ea266aeb3b16ea0b683ca0bced146369e429d96237978fea6c132077bd0cb6
+SIZE (afni-afni-AFNI_19.1.14_GH0.tar.gz) = 38910318
diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index adbfdb0f19f6..1d506296283d 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -1,6 +1,6 @@
---- Makefile.INCLUDE.orig	2019-05-10 21:23:56 UTC
+--- Makefile.INCLUDE.orig	2019-05-23 14:10:15 UTC
 +++ Makefile.INCLUDE
-@@ -64,7 +64,7 @@ MISC    = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
+@@ -67,7 +67,7 @@ MISC    = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
  ## AFNI package, but included because they are useful.  Some of
  ## them are Open Source programs, not from the AFNI group at all.
  
@@ -9,7 +9,7 @@
  
  # mpegtoppm in above list
  
-@@ -77,7 +77,7 @@ EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xpha
+@@ -80,7 +80,7 @@ EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xpha
  PROGS_1  = 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 \
@@ -18,7 +18,7 @@
             waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket         \
             3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk       \
             3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna         \
-@@ -90,7 +90,7 @@ PROGS_2  = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
+@@ -93,7 +93,7 @@ PROGS_2  = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
             3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign        \
             3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid        \
             3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum     \
@@ -27,7 +27,7 @@
             3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval     \
             3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI  \
             3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat  \
-@@ -112,7 +112,7 @@ PROGS_3  = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor
+@@ -115,7 +115,7 @@ PROGS_3  = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor
  PROGS_4  = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip         \
             3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D      \
             3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI           \
@@ -36,7 +36,7 @@
             1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport   \
             3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \
             column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust  \
-@@ -138,7 +138,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
+@@ -141,7 +141,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
  PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge      \
                    sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
                    fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
@@ -45,7 +45,7 @@
                    waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
                    3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna      \
                    imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot    \
-@@ -181,7 +181,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 
+@@ -184,7 +184,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 
  PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge   \
                 sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count  \
                 fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
@@ -54,36 +54,7 @@
                 waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
                 3dAFNItoNIML    AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk     \
                 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
-@@ -303,7 +303,7 @@ echo_progs:
- prog_list_bin:
- 	echo "$(PROGRAMS) $(SUMA_PROGS) $(SUMA_GTS_PROGS)"      \
- 	        | tr ' ' '\n' > ___plist_bin.txt
--	make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs  \
-+	$(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs  \
- 	        | tr ' ' '\n' >> ___plist_bin.txt
- 	cat ___plist_bin.txt | LC_COLLATE=C sort | uniq > prog_list_bin.txt
- 	\rm -f ___plist_bin.txt
-@@ -2884,7 +2884,7 @@ r_misc.o: rickr/r_misc.c rickr/r_misc.h
- 
- dcm2niix_afni:
- 	( cd crorden/dcm2niix_console ;		\
--	  make ;				\
-+	  $(MAKE) ;				\
- 	  $(MV) dcm2niix ../../dcm2niix_afni ; 	\
- 	  cd ../../ ; )
- 
-@@ -3108,8 +3108,8 @@ libjpeg.a:
-           $(MAKE) clean ; $(RM) Makefile )
- 
- libXmHTML.a:
--	( cd XmHTML ; make lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
--		$(MV) lib/libXmHTML.a .. ; make clean   )
-+	( cd XmHTML ; $(MAKE) lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
-+		$(MV) lib/libXmHTML.a .. ; $(MAKE) clean   )
- 
- xutil_webber.o:xutil_webber.c
- 	$(CC) -c xutil_webber.c -I./XmHTML/include $(INFLAGS)
-@@ -3920,9 +3920,10 @@ toyR: toyR.c AFNI_embeddedRCall.o
+@@ -3927,9 +3927,10 @@ toyR: toyR.c AFNI_embeddedRCall.o
  ####
  R_io.so:R_io.c $(LIBMRI_OBJ)
  	( if which R >/dev/null ; then \
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index fa3c1318d82c..b9712842412c 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -375,6 +375,7 @@ bin/@djunct_combine_str.py
 bin/@djunct_dwi_selector.tcsh
 bin/@djunct_edgy_align_check
 bin/@djunct_is_label.py
+bin/@djunct_json_value.py
 bin/@djunct_montage_coordinator
 bin/@djunct_select_str.py
 bin/@djunct_slice_space
@@ -1329,6 +1330,7 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/funstuff/splash_3monkeys.jpg
 %%DATADIR%%/funstuff/splash_Bpark.jpg
 %%DATADIR%%/funstuff/splash_Feb2016.jpg
+%%DATADIR%%/funstuff/splash_KUMC.jpg
 %%DATADIR%%/funstuff/splash_NMcloud.jpg
 %%DATADIR%%/funstuff/splash_Utah_Dog.jpg
 %%DATADIR%%/funstuff/splash_Utah_Tree.jpg