From 144c4feb7d4e63abb25955ab7ffa53ff9f8e7008 Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Sat, 1 Jun 2019 12:59:52 +0000 Subject: [PATCH] science/afni: Upgrade to 19.1.14 Minor bug fixes and enhancements, some FreeBSD patches upstreamed --- science/afni/Makefile | 2 +- science/afni/distinfo | 6 +-- science/afni/files/patch-Makefile.INCLUDE | 45 ++++------------------- science/afni/pkg-plist | 2 + 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