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science/afni: Upgrade to 19.1.14

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Minor bug fixes and enhancements, some FreeBSD patches upstreamed
This commit is contained in:
Jason W. Bacon 2019-06-01 12:59:52 +00:00
parent 4ab8846ea8
commit 144c4feb7d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=503233
4 changed files with 14 additions and 41 deletions
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2
science/afni/Makefile
View File

@ -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

6
science/afni/distinfo
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@ -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

45
science/afni/files/patch-Makefile.INCLUDE
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@ -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 \

2
science/afni/pkg-plist
View File

@ -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