diff --git a/science/afni/Makefile b/science/afni/Makefile index 26484348b9f7..6ce45e6ef5dc 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -2,7 +2,7 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 20.2.08 +DISTVERSION= 20.2.11 CATEGORIES= science biology graphics perl5 python MAINTAINER= ports@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 3c6f9a635806..cc936a063049 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1596395346 -SHA256 (afni-afni-AFNI_20.2.08_GH0.tar.gz) = 509e841cb7d2832d6e86a426f0afd9846a9ea700f10294812b1e1d45b13b32ba -SIZE (afni-afni-AFNI_20.2.08_GH0.tar.gz) = 43387687 +TIMESTAMP = 1597164968 +SHA256 (afni-afni-AFNI_20.2.11_GH0.tar.gz) = b500c4a4612c54fa05281fe3af14717dc1c8b972eac4a4d44c49e19ff1bf2d4d +SIZE (afni-afni-AFNI_20.2.11_GH0.tar.gz) = 42708230 diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE index a43eb2e1a841..857b8d15f960 100644 --- a/science/afni/files/patch-Makefile.INCLUDE +++ b/science/afni/files/patch-Makefile.INCLUDE @@ -1,6 +1,6 @@ ---- Makefile.INCLUDE.orig 2020-07-21 18:06:10 UTC +--- Makefile.INCLUDE.orig 2020-08-10 17:42:08 UTC +++ Makefile.INCLUDE -@@ -92,7 +92,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a +@@ -90,7 +90,7 @@ 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 -@@ -105,7 +105,7 @@ EXTRAS = cjpeg djpeg whirlgif myget Xphace rmz aiv m +@@ -103,7 +103,7 @@ EXTRAS = cjpeg djpeg whirlgif myget Xphace rmz aiv m 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 \ @@ -18,16 +18,16 @@ waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ 3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ -@@ -118,7 +118,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn +@@ -116,7 +116,7 @@ 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 \ - 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \ + 3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \ - 3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval \ + 3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dCM fdrval \ 3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \ - 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat \ -@@ -141,7 +141,7 @@ PROGS_3 = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor + 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dBrickStat \ +@@ -139,7 +139,7 @@ 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 \ -@@ -167,7 +167,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4) +@@ -165,7 +165,7 @@ 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 \ -@@ -210,7 +210,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize +@@ -208,7 +208,7 @@ 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 \ @@ -54,7 +54,7 @@ waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ 3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ -@@ -4109,7 +4109,10 @@ R_Makevars_mod_linux: +@@ -4030,7 +4030,10 @@ R_Makevars_mod_linux: R_io.so: R_io.c $(LIBMRI_OBJ) $(R_MAKEVARS_DEP) ( if which R >/dev/null ; then \ diff --git a/science/afni/files/patch-netcdf-3.5.0_src_configure b/science/afni/files/patch-netcdf-3.5.0_src_configure deleted file mode 100644 index 2cea4c66380a..000000000000 --- a/science/afni/files/patch-netcdf-3.5.0_src_configure +++ /dev/null @@ -1,43 +0,0 @@ ---- netcdf-3.5.0/src/configure.orig 2019-05-10 21:23:56 UTC -+++ netcdf-3.5.0/src/configure -@@ -933,10 +933,10 @@ echo "configure:928: checking for top-level source-dir - - - -- echo "checking for m4 preprocessor" 1>&6 --echo "configure:938: checking for m4 preprocessor" >&5 -+ echo "checking for gm4 preprocessor" 1>&6 -+echo "configure:938: checking for gm4 preprocessor" >&5 - case "${M4-unset}" in -- unset) for ac_prog in m4 gm4 -+ unset) for ac_prog in gm4 - do - # Extract the first word of "$ac_prog", so it can be a program name with args. - set dummy $ac_prog; ac_word=$2 -@@ -969,9 +969,9 @@ fi - - test -n "$M4" && break - done --test -n "$M4" || M4="m4" -+test -n "$M4" || M4="gm4" - ;; -- *) for ac_prog in $M4 m4 gm4 -+ *) for ac_prog in $M4 gm4 - do - # Extract the first word of "$ac_prog", so it can be a program name with args. - set dummy $ac_prog; ac_word=$2 -@@ -1004,11 +1004,11 @@ fi - - test -n "$M4" && break - done --test -n "$M4" || M4="m4" -+test -n "$M4" || M4="gm4" - ;; - esac -- echo $ac_n "checking m4 flags""... $ac_c" 1>&6 --echo "configure:1012: checking m4 flags" >&5 -+ echo $ac_n "checking gm4 flags""... $ac_c" 1>&6 -+echo "configure:1012: checking gm4 flags" >&5 - case "${M4FLAGS-unset}" in - unset) M4FLAGS=-B10000 ;; - esac diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index ef741d270776..8d1cee6367b7 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -39,7 +39,6 @@ bin/2swap bin/3dABoverlap bin/3dAFNIto3D bin/3dAFNItoANALYZE -bin/3dAFNItoMINC bin/3dAFNItoNIFTI bin/3dAFNItoNIML bin/3dAFNItoRaw @@ -133,7 +132,6 @@ bin/3dMEMA bin/3dMEMA.R bin/3dMEPFM bin/3dMEPFM.R -bin/3dMINCtoAFNI bin/3dMSE bin/3dMVM bin/3dMVM.R @@ -338,6 +336,7 @@ bin/@NoisySkullStrip bin/@Purify_1D bin/@Quiet_Talkers bin/@ROI_Corr_Mat +bin/@ROI_decluster bin/@ROI_modal_grow bin/@R_funclist bin/@RenamePanga