Date: Thu, 3 Sep 2020 07:16:21 +0000 (UTC) From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= <fernape@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r547424 - in head/science/afni: . files Message-ID: <202009030716.0837GLBg088672@repo.freebsd.org>
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Author: fernape Date: Thu Sep 3 07:16:21 2020 New Revision: 547424 URL: https://svnweb.freebsd.org/changeset/ports/547424 Log: 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 Modified: head/science/afni/Makefile head/science/afni/distinfo head/science/afni/files/patch-Makefile.INCLUDE head/science/afni/pkg-plist Modified: head/science/afni/Makefile ============================================================================== --- head/science/afni/Makefile Thu Sep 3 06:59:21 2020 (r547423) +++ head/science/afni/Makefile Thu Sep 3 07:16:21 2020 (r547424) @@ -2,7 +2,7 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 20.2.14 +DISTVERSION= 20.2.16 CATEGORIES= science biology graphics perl5 python MAINTAINER= ports@FreeBSD.org Modified: head/science/afni/distinfo ============================================================================== --- head/science/afni/distinfo Thu Sep 3 06:59:21 2020 (r547423) +++ head/science/afni/distinfo Thu Sep 3 07:16:21 2020 (r547424) @@ -1,3 +1,3 @@ -TIMESTAMP = 1598100733 -SHA256 (afni-afni-AFNI_20.2.14_GH0.tar.gz) = d374fcffd11af19e793fa54e1a0beea117989709ae1c86ac60bac633dd94ea78 -SIZE (afni-afni-AFNI_20.2.14_GH0.tar.gz) = 42723569 +TIMESTAMP = 1599046011 +SHA256 (afni-afni-AFNI_20.2.16_GH0.tar.gz) = fdbc1d5419348540bea16c95627c9a808aeb1a4c704cd79c69366b82ba53a448 +SIZE (afni-afni-AFNI_20.2.16_GH0.tar.gz) = 42680019 Modified: head/science/afni/files/patch-Makefile.INCLUDE ============================================================================== --- head/science/afni/files/patch-Makefile.INCLUDE Thu Sep 3 06:59:21 2020 (r547423) +++ head/science/afni/files/patch-Makefile.INCLUDE Thu Sep 3 07:16:21 2020 (r547424) @@ -1,68 +1,56 @@ ---- Makefile.INCLUDE.orig 2020-08-10 17:42:08 UTC +--- Makefile.INCLUDE.orig 2020-09-02 01:23:07 UTC +++ Makefile.INCLUDE -@@ -90,7 +90,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a +@@ -94,7 +94,7 @@ 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. --EXTRAS = cjpeg djpeg whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS) +-EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat quotize $(EXPROGS) +EXTRAS = whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS) # mpegtoppm in above list -@@ -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 \ -- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ -+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ - waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ - 3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ - 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ -@@ -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 3dCM fdrval \ - 3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \ - 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 \ -- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \ -+ niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \ - 1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \ - 3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \ - column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust \ -@@ -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 \ -- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \ -+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \ - waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \ - 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ - imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \ -@@ -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 \ -- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ -+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ - waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ - 3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ - 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ -@@ -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 \ -- R CMD SHLIB -o R_io.so R_io.c ; \ -+ echo PKG_CPPFLAGS = $(INFLAGS) -I${LOCALBASE}/lib/R/include > Makevars ;\ -+ echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) -L${LOCALBASE}/lib/R/lib >> Makevars ;\ -+ # Fails because R uses 'make' instead of gmake: R CMD SHLIB -n R_io.c; \ -+ $(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';\ - else echo WARNING: Cannot build R_io.so because R is not installed;\ - fi ; ) - +@@ -107,7 +107,7 @@ EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat qu + PROGS_1 = afni to3d from3d 3dclust nsize 3dinfo 3dmerge count \ + sfim tfim imrotate imreg imstat 3dnvals \ + fim2 imand immask imdump imaver 3dhistog 3daxialize \ +- cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ ++ 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ + waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ + 3dNLfim 3dTSgen plugout_tt plugout_ijk \ + 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ +@@ -120,7 +120,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn + 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \ + 3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \ + 3dEntropy 3ddelay 3dRowFillin 1dgrayplot 3dToutcount 1dsum \ +- 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual \ ++ 3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual \ + 3dGetrow 3dTcorrelate 3dcopy Vecwarp 3dCM fdrval \ + 3dAFNItoANALYZE 3dAFNItoNIFTI \ + 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dBrickStat \ +@@ -143,7 +143,7 @@ PROGS_3 = 3dAnhist 3dAFNIto3D 3dWarp nicat + PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \ + 3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \ + 3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \ +- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \ ++ niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \ + 1dCorrelate 3dNwarpCalc dicom_hinfo apsearch 1dBport \ + 3dNormalityTest 3dmask_tool FIRdesign help_format 2perm \ + 3dClustCount column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog \ +@@ -170,7 +170,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4) + PROGRAMS_NOPLUG = \ + afni to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ + imreg imstat count fim2 imand immask imdump imaver 3dhistog imupsam \ +- cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 3drefit waver 3dnewid \ ++ 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 3drefit waver 3dnewid \ + 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval 3dMannWhitney \ + 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna imstack byteorder \ + 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot 24swap 3dTsmooth RSFgen \ +@@ -208,7 +208,7 @@ PROGRAMS_NOPLUG = + PROGRAMS_EXE = \ + afni.exe to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ + imreg imstat 3dnvals count fim2 imand immask imdump imaver 3dhistog \ +- 3dGetrow cdf 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta waver \ ++ 3dGetrow 2swap 4swap 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta waver \ + 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket 3dAFNItoNIML \ + plugout_tt plugout_ijk 3dMannWhitney 3dWilcoxon 3dKruskalWallis \ + 3dFriedman 3dRegAna 2dImReg 3dmaskave byteorder imstack 3dDeconvolve \ Modified: head/science/afni/pkg-plist ============================================================================== --- head/science/afni/pkg-plist Thu Sep 3 06:59:21 2020 (r547423) +++ head/science/afni/pkg-plist Thu Sep 3 07:16:21 2020 (r547424) @@ -3,7 +3,6 @@ bin/1dAstrip bin/1dBandpass bin/1dBport bin/1dCorrelate -bin/1dDW_Grad_o_Mat bin/1dDW_Grad_o_Mat++ bin/1dFlagMotion bin/1dGC.R @@ -42,15 +41,12 @@ bin/3dAFNItoANALYZE bin/3dAFNItoNIFTI bin/3dAFNItoNIML bin/3dAFNItoRaw -bin/3dANALYZEtoAFNI bin/3dANOVA bin/3dANOVA2 bin/3dANOVA3 -bin/3dAOV.R bin/3dAcost bin/3dAllineate bin/3dAmpToRSFC -bin/3dAnatNudge bin/3dAnhist bin/3dAttribute bin/3dAutoTcorrelate @@ -71,7 +67,6 @@ bin/3dClusterize bin/3dCompareAffine bin/3dConformist bin/3dConvolve -bin/3dCountSpikes bin/3dDFT bin/3dDTeig bin/3dDTtoDWI @@ -79,7 +74,6 @@ bin/3dDTtoNoisyDWI bin/3dDWItoDT bin/3dDWUncert bin/3dDeconvolve -bin/3dDeconvolve_f bin/3dDegreeCentrality bin/3dDespike bin/3dDetrend @@ -93,9 +87,7 @@ bin/3dExtractGroupInCorr bin/3dExtrema bin/3dFDR bin/3dFFT -bin/3dFWHM bin/3dFWHMx -bin/3dFourier bin/3dFriedman bin/3dGC.R bin/3dGenFeatureDist @@ -107,7 +99,6 @@ bin/3dHist bin/3dICA.R bin/3dICC bin/3dICC.R -bin/3dICC_REML.R bin/3dISC bin/3dISC.R bin/3dIntracranial @@ -139,7 +130,6 @@ bin/3dMVM_validator bin/3dMannWhitney bin/3dMaskToASCII bin/3dMatch -bin/3dMax bin/3dMean bin/3dMedianFilter bin/3dMultiThresh @@ -160,7 +150,6 @@ bin/3dPFM.R bin/3dPVmap bin/3dPeriodogram bin/3dPolyfit -bin/3dProbTrackID bin/3dPval bin/3dQwarp bin/3dREMLfit @@ -214,13 +203,11 @@ bin/3dTto1D bin/3dTwotoComplex bin/3dUndump bin/3dUnifize -bin/3dUniformize bin/3dUpsample bin/3dVecRGB_to_HSL bin/3dVol2Surf bin/3dWarp bin/3dWarpDrive -bin/3dWavelets bin/3dWilcoxon bin/3dWinsor bin/3dXClustSim @@ -232,7 +219,6 @@ bin/3dZipperZapper bin/3dZregrid bin/3danisosmooth bin/3daxialize -bin/3dbuc2fim bin/3dbucket bin/3dcalc bin/3dclust @@ -240,9 +226,7 @@ bin/3dcopy bin/3ddelay bin/3ddot bin/3ddot_beta -bin/3ddup bin/3dedge3 -bin/3dfim bin/3dfim+ bin/3dfractionize bin/3dhistog @@ -258,10 +242,8 @@ bin/3dmatmult bin/3dmaxima bin/3dmerge bin/3dnewid -bin/3dnoise bin/3dnvals bin/3dpc -bin/3dproject bin/3drefit bin/3drename bin/3dresample @@ -270,7 +252,6 @@ bin/3drotate bin/3dsvm bin/3dsvm_linpredict bin/3dtoXdataset -bin/3dttest bin/3dttest++ bin/3dvolreg bin/4swap @@ -291,7 +272,6 @@ bin/@ClustExp_CatLab bin/@ClustExp_run_shiny bin/@CommandGlobb bin/@DO.examples -bin/@DTI_studio_reposition bin/@DeblankFileNames bin/@DiceMetric bin/@DriveAfni @@ -359,7 +339,6 @@ bin/@SurfSmooth.HEAT_07.examples bin/@T1scale bin/@TimeDiff bin/@ToRAI -bin/@UpdateAfni bin/@VolCenter bin/@afni.run.me bin/@afni_R_package_install @@ -369,7 +348,6 @@ bin/@afni_refacer_make_onebigA12 bin/@afni_refacer_run bin/@align_partial_oblique bin/@animal_warper -bin/@auto_align bin/@auto_tlrc bin/@build_afni_Xlib bin/@chauffeur_afni @@ -404,7 +382,6 @@ bin/@grayplot bin/@help.AFNI bin/@isOblique bin/@make_plug_diff -bin/@make_stim_file bin/@measure_bb_thick bin/@measure_erosion_thick bin/@measure_in2out @@ -415,7 +392,6 @@ bin/@parse_name bin/@radial_correlate bin/@simulate_motion bin/@snapshot_volreg -bin/@snapshot_volreg3 bin/@statauxcode bin/@suma_acknowledge bin/@suma_reprefixize_spec @@ -430,7 +406,6 @@ bin/AFNI_atlas_spaces.niml bin/AFNI_version.txt bin/AFNIio.R bin/AFNIplot.R -bin/AlphaSim bin/AnalyzeTrace bin/BayesianGroupAna.R bin/BayesianGroupAna.py @@ -445,18 +420,14 @@ bin/ConvexHull bin/CreateIcosahedron bin/DTIStudioFibertoSegments bin/Dimon -bin/Dimon1 -bin/DoPerRoi.py bin/DriveSuma bin/ExamineXmat bin/ExamineXmat.R bin/FATCAT_matplot -bin/FD2 bin/FIRdesign bin/FSread_annot bin/GLTsymtest bin/HalloSuma -bin/Ifile bin/InstaTract bin/IsoSurface bin/Level2.R @@ -498,7 +469,6 @@ bin/Xphace bin/abids_json_info.py bin/abids_json_tool.py bin/abids_tool.py -bin/abut bin/adjunct_aw_tableize_roi_info.py bin/adjunct_calc_mont_dims.py bin/adjunct_combine_str.py @@ -515,7 +485,6 @@ bin/afni_history bin/afni_open bin/afni_proc.py bin/afni_python_wrapper.py -bin/afni_restproc.py bin/afni_run_R bin/afni_seeds_per_space.txt bin/afni_skeleton.py @@ -530,7 +499,6 @@ bin/auto_warp.py bin/byteorder bin/cat_matvec bin/ccalc -bin/check_dset_for_fs.py bin/cifti_tool bin/column_cat bin/convert_cdiflist_to_grads.py @@ -544,15 +512,12 @@ bin/dicom_hinfo bin/dicom_to_raw bin/dsetstat2p bin/eg_main_chrono.py -bin/ent16 bin/epi_b0_correct.py -bin/fat_lat_csv.py bin/fat_mat2d_plot.py bin/fat_mat_sel.py bin/fat_mat_tableize.py bin/fat_mvm_gridconv.py 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
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