mirror of
https://git.FreeBSD.org/ports.git
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science/afni: update to 20.2.16
Many utilities are not provided anymore. Most of them are marked in src/Makefile.INCLUDE under the comment "not distributed 25 Aug 2020" Others are not marked like that, but they are not shipped anyway, like 3dAnatNudge which has a comment that explains why: "This program (3dAnatNudge) is old, obsolete, and not maintained!" Reported by: portscout
This commit is contained in:
Fernando Apesteguía
parent
84c8a297da
commit
931b35f008
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=547424
@ -2,7 +2,7 @@
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PORTNAME= afni
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DISTVERSIONPREFIX= AFNI_
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DISTVERSION= 20.2.14
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DISTVERSION= 20.2.16
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CATEGORIES= science biology graphics perl5 python
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MAINTAINER= ports@FreeBSD.org
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@ -1,3 +1,3 @@
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TIMESTAMP = 1598100733
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SHA256 (afni-afni-AFNI_20.2.14_GH0.tar.gz) = d374fcffd11af19e793fa54e1a0beea117989709ae1c86ac60bac633dd94ea78
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SIZE (afni-afni-AFNI_20.2.14_GH0.tar.gz) = 42723569
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TIMESTAMP = 1599046011
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SHA256 (afni-afni-AFNI_20.2.16_GH0.tar.gz) = fdbc1d5419348540bea16c95627c9a808aeb1a4c704cd79c69366b82ba53a448
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SIZE (afni-afni-AFNI_20.2.16_GH0.tar.gz) = 42680019
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@ -1,68 +1,56 @@
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--- Makefile.INCLUDE.orig 2020-08-10 17:42:08 UTC
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--- Makefile.INCLUDE.orig 2020-09-02 01:23:07 UTC
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+++ Makefile.INCLUDE
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@@ -90,7 +90,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
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@@ -94,7 +94,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
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## AFNI package, but included because they are useful. Some of
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## them are Open Source programs, not from the AFNI group at all.
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-EXTRAS = cjpeg djpeg whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
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-EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat quotize $(EXPROGS)
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+EXTRAS = whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
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# mpegtoppm in above list
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@@ -103,7 +103,7 @@ EXTRAS = cjpeg djpeg whirlgif myget Xphace rmz aiv m
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PROGS_1 = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals \
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fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
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- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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@@ -107,7 +107,7 @@ EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat qu
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PROGS_1 = afni to3d from3d 3dclust nsize 3dinfo 3dmerge count \
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sfim tfim imrotate imreg imstat 3dnvals \
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fim2 imand immask imdump imaver 3dhistog 3daxialize \
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- cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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+ 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
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3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
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3dNLfim 3dTSgen plugout_tt plugout_ijk \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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@@ -116,7 +116,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
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3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \
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@@ -120,7 +120,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
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3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \
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3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \
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3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \
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- 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
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+ 3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
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3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dCM fdrval \
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3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \
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3dEntropy 3ddelay 3dRowFillin 1dgrayplot 3dToutcount 1dsum \
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- 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual \
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+ 3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual \
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3dGetrow 3dTcorrelate 3dcopy Vecwarp 3dCM fdrval \
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3dAFNItoANALYZE 3dAFNItoNIFTI \
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3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dBrickStat \
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@@ -139,7 +139,7 @@ PROGS_3 = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor
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@@ -143,7 +143,7 @@ PROGS_3 = 3dAnhist 3dAFNIto3D 3dWarp nicat
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PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
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3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \
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3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \
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- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
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+ niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
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1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \
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3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \
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column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust \
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@@ -165,7 +165,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
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PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
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fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
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- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \
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waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \
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@@ -208,7 +208,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize
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PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count \
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fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
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- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
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3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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@@ -4030,7 +4030,10 @@ R_Makevars_mod_linux:
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R_io.so: R_io.c $(LIBMRI_OBJ) $(R_MAKEVARS_DEP)
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( if which R >/dev/null ; then \
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- R CMD SHLIB -o R_io.so R_io.c ; \
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+ echo PKG_CPPFLAGS = $(INFLAGS) -I${LOCALBASE}/lib/R/include > Makevars ;\
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+ echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
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+ # Fails because R uses 'make' instead of gmake: R CMD SHLIB -n R_io.c; \
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+ $(MAKE) -f 'Makevars' -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' SHLIB='R_io.so' OBJECTS='R_io.o';\
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else echo WARNING: Cannot build R_io.so because R is not installed;\
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fi ; )
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1dCorrelate 3dNwarpCalc dicom_hinfo apsearch 1dBport \
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3dNormalityTest 3dmask_tool FIRdesign help_format 2perm \
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3dClustCount column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog \
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@@ -170,7 +170,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
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PROGRAMS_NOPLUG = \
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afni to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \
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imreg imstat count fim2 imand immask imdump imaver 3dhistog imupsam \
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- cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 3drefit waver 3dnewid \
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+ 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 3drefit waver 3dnewid \
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3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval 3dMannWhitney \
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3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna imstack byteorder \
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3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot 24swap 3dTsmooth RSFgen \
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@@ -208,7 +208,7 @@ PROGRAMS_NOPLUG =
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PROGRAMS_EXE = \
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afni.exe to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \
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imreg imstat 3dnvals count fim2 imand immask imdump imaver 3dhistog \
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- 3dGetrow cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta waver \
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+ 3dGetrow 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta waver \
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3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket 3dAFNItoNIML \
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plugout_tt plugout_ijk 3dMannWhitney 3dWilcoxon 3dKruskalWallis \
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3dFriedman 3dRegAna 2dImReg 3dmaskave byteorder imstack 3dDeconvolve \
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@ -3,7 +3,6 @@ bin/1dAstrip
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bin/1dBandpass
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bin/1dBport
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bin/1dCorrelate
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bin/1dDW_Grad_o_Mat
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bin/1dDW_Grad_o_Mat++
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bin/1dFlagMotion
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bin/1dGC.R
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@ -42,15 +41,12 @@ bin/3dAFNItoANALYZE
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bin/3dAFNItoNIFTI
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bin/3dAFNItoNIML
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bin/3dAFNItoRaw
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bin/3dANALYZEtoAFNI
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bin/3dANOVA
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bin/3dANOVA2
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bin/3dANOVA3
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bin/3dAOV.R
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bin/3dAcost
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bin/3dAllineate
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bin/3dAmpToRSFC
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bin/3dAnatNudge
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bin/3dAnhist
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bin/3dAttribute
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bin/3dAutoTcorrelate
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@ -71,7 +67,6 @@ bin/3dClusterize
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bin/3dCompareAffine
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bin/3dConformist
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bin/3dConvolve
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bin/3dCountSpikes
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bin/3dDFT
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bin/3dDTeig
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bin/3dDTtoDWI
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@ -79,7 +74,6 @@ bin/3dDTtoNoisyDWI
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bin/3dDWItoDT
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bin/3dDWUncert
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bin/3dDeconvolve
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bin/3dDeconvolve_f
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bin/3dDegreeCentrality
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bin/3dDespike
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bin/3dDetrend
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@ -93,9 +87,7 @@ bin/3dExtractGroupInCorr
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bin/3dExtrema
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bin/3dFDR
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bin/3dFFT
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bin/3dFWHM
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bin/3dFWHMx
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bin/3dFourier
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bin/3dFriedman
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bin/3dGC.R
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bin/3dGenFeatureDist
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@ -107,7 +99,6 @@ bin/3dHist
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bin/3dICA.R
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bin/3dICC
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bin/3dICC.R
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bin/3dICC_REML.R
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bin/3dISC
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bin/3dISC.R
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bin/3dIntracranial
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@ -139,7 +130,6 @@ bin/3dMVM_validator
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bin/3dMannWhitney
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bin/3dMaskToASCII
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bin/3dMatch
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bin/3dMax
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bin/3dMean
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bin/3dMedianFilter
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bin/3dMultiThresh
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@ -160,7 +150,6 @@ bin/3dPFM.R
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bin/3dPVmap
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bin/3dPeriodogram
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bin/3dPolyfit
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bin/3dProbTrackID
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bin/3dPval
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bin/3dQwarp
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bin/3dREMLfit
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@ -214,13 +203,11 @@ bin/3dTto1D
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bin/3dTwotoComplex
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bin/3dUndump
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bin/3dUnifize
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bin/3dUniformize
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bin/3dUpsample
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bin/3dVecRGB_to_HSL
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bin/3dVol2Surf
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bin/3dWarp
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bin/3dWarpDrive
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bin/3dWavelets
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bin/3dWilcoxon
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bin/3dWinsor
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bin/3dXClustSim
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@ -232,7 +219,6 @@ bin/3dZipperZapper
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bin/3dZregrid
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bin/3danisosmooth
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bin/3daxialize
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bin/3dbuc2fim
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bin/3dbucket
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bin/3dcalc
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bin/3dclust
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@ -240,9 +226,7 @@ bin/3dcopy
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bin/3ddelay
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bin/3ddot
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bin/3ddot_beta
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bin/3ddup
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bin/3dedge3
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bin/3dfim
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bin/3dfim+
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bin/3dfractionize
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bin/3dhistog
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@ -258,10 +242,8 @@ bin/3dmatmult
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bin/3dmaxima
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bin/3dmerge
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bin/3dnewid
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bin/3dnoise
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bin/3dnvals
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bin/3dpc
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bin/3dproject
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bin/3drefit
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bin/3drename
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bin/3dresample
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@ -270,7 +252,6 @@ bin/3drotate
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bin/3dsvm
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bin/3dsvm_linpredict
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bin/3dtoXdataset
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bin/3dttest
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bin/3dttest++
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bin/3dvolreg
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bin/4swap
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@ -291,7 +272,6 @@ bin/@ClustExp_CatLab
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bin/@ClustExp_run_shiny
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bin/@CommandGlobb
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bin/@DO.examples
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bin/@DTI_studio_reposition
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bin/@DeblankFileNames
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bin/@DiceMetric
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bin/@DriveAfni
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@ -359,7 +339,6 @@ bin/@SurfSmooth.HEAT_07.examples
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bin/@T1scale
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bin/@TimeDiff
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bin/@ToRAI
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bin/@UpdateAfni
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bin/@VolCenter
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bin/@afni.run.me
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bin/@afni_R_package_install
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@ -369,7 +348,6 @@ bin/@afni_refacer_make_onebigA12
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bin/@afni_refacer_run
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bin/@align_partial_oblique
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bin/@animal_warper
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bin/@auto_align
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bin/@auto_tlrc
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bin/@build_afni_Xlib
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bin/@chauffeur_afni
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@ -404,7 +382,6 @@ bin/@grayplot
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bin/@help.AFNI
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bin/@isOblique
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bin/@make_plug_diff
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bin/@make_stim_file
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bin/@measure_bb_thick
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bin/@measure_erosion_thick
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bin/@measure_in2out
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@ -415,7 +392,6 @@ bin/@parse_name
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bin/@radial_correlate
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bin/@simulate_motion
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bin/@snapshot_volreg
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bin/@snapshot_volreg3
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bin/@statauxcode
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bin/@suma_acknowledge
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bin/@suma_reprefixize_spec
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@ -430,7 +406,6 @@ bin/AFNI_atlas_spaces.niml
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bin/AFNI_version.txt
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bin/AFNIio.R
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bin/AFNIplot.R
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bin/AlphaSim
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bin/AnalyzeTrace
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bin/BayesianGroupAna.R
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bin/BayesianGroupAna.py
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@ -445,18 +420,14 @@ bin/ConvexHull
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bin/CreateIcosahedron
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bin/DTIStudioFibertoSegments
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bin/Dimon
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bin/Dimon1
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bin/DoPerRoi.py
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bin/DriveSuma
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bin/ExamineXmat
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bin/ExamineXmat.R
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bin/FATCAT_matplot
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bin/FD2
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bin/FIRdesign
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bin/FSread_annot
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bin/GLTsymtest
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bin/HalloSuma
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bin/Ifile
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bin/InstaTract
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bin/IsoSurface
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bin/Level2.R
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@ -498,7 +469,6 @@ bin/Xphace
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bin/abids_json_info.py
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bin/abids_json_tool.py
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bin/abids_tool.py
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bin/abut
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bin/adjunct_aw_tableize_roi_info.py
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bin/adjunct_calc_mont_dims.py
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bin/adjunct_combine_str.py
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@ -515,7 +485,6 @@ bin/afni_history
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bin/afni_open
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bin/afni_proc.py
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bin/afni_python_wrapper.py
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bin/afni_restproc.py
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bin/afni_run_R
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bin/afni_seeds_per_space.txt
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bin/afni_skeleton.py
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@ -530,7 +499,6 @@ bin/auto_warp.py
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bin/byteorder
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bin/cat_matvec
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bin/ccalc
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bin/check_dset_for_fs.py
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bin/cifti_tool
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bin/column_cat
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bin/convert_cdiflist_to_grads.py
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@ -544,15 +512,12 @@ bin/dicom_hinfo
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bin/dicom_to_raw
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bin/dsetstat2p
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bin/eg_main_chrono.py
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bin/ent16
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bin/epi_b0_correct.py
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bin/fat_lat_csv.py
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bin/fat_mat2d_plot.py
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bin/fat_mat_sel.py
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bin/fat_mat_tableize.py
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bin/fat_mvm_gridconv.py
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bin/fat_mvm_prep.py
|
||||
bin/fat_mvm_review.py
|
||||
bin/fat_mvm_scripter.py
|
||||
bin/fat_proc_align_anat_pair
|
||||
bin/fat_proc_axialize_anat
|
||||
@ -562,7 +527,6 @@ bin/fat_proc_convert_dcm_dwis
|
||||
bin/fat_proc_decmap
|
||||
bin/fat_proc_dwi_to_dt
|
||||
bin/fat_proc_filter_dwis
|
||||
bin/fat_proc_grad_plot
|
||||
bin/fat_proc_imit2w_from_t1w
|
||||
bin/fat_proc_map_to_dti
|
||||
bin/fat_proc_select_vols
|
||||
@ -573,8 +537,6 @@ bin/file_tool
|
||||
bin/fim2
|
||||
bin/float_scan
|
||||
bin/from3d
|
||||
bin/ftosh
|
||||
bin/ge_header
|
||||
bin/gen_epi_review.py
|
||||
bin/gen_group_command.py
|
||||
bin/gen_ss_review_scripts.py
|
||||
@ -599,14 +561,11 @@ bin/imstack
|
||||
bin/imstat
|
||||
bin/imupsam
|
||||
bin/inspec
|
||||
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/mritopgm
|
||||
bin/mycat
|
||||
bin/myget
|
||||
bin/neuro_deconvolve.py
|
||||
@ -638,10 +597,8 @@ bin/rotcom
|
||||
bin/rtfeedme
|
||||
bin/serial_helper
|
||||
bin/sfim
|
||||
bin/siemens_vision
|
||||
bin/slow_surf_clustsim.py
|
||||
bin/smooth.R
|
||||
bin/sqwave
|
||||
bin/stimband
|
||||
bin/strblast
|
||||
bin/suma
|
||||
@ -690,6 +647,7 @@ include/afni/mri_warpfield.h
|
||||
include/afni/mrilib.h
|
||||
include/afni/multivector.h
|
||||
include/afni/nifti1.h
|
||||
include/afni/nifti2.h
|
||||
include/afni/nifti2_io.h
|
||||
include/afni/nifticdf.h
|
||||
include/afni/niml.h
|
||||
@ -745,7 +703,6 @@ lib/afni/model_trnglwave_apf.so
|
||||
lib/afni/model_zero.so
|
||||
lib/afni/plug_3Ddump_V2.so
|
||||
lib/afni/plug_3ddot.so
|
||||
lib/afni/plug_3ddup.so
|
||||
lib/afni/plug_3dsvm.so
|
||||
lib/afni/plug_4Ddump.so
|
||||
lib/afni/plug_L1fit.so
|
||||
@ -823,10 +780,8 @@ lib/afni/plug_zeropad.so
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_csv.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_decay_timing.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_dti_sundry.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_fat_Rfactor.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_fat_funcs.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_fat_plot_sel.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_fs.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_gershgorin.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_info_dict.py
|
||||
%%PYTHON_SITELIBDIR%%/afnipy/lib_mat2d_base.py
|
||||
|
||||
Loading…
Reference in New Issue
Block a user