From owner-svn-ports-all@freebsd.org Thu Aug 13 05:44:12 2020 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id CB3FA3B8309; Thu, 13 Aug 2020 05:44:12 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4BRwVh4kBTz3crb; Thu, 13 Aug 2020 05:44:12 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 8543D18471; Thu, 13 Aug 2020 05:44:12 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 07D5iCKq087090; Thu, 13 Aug 2020 05:44:12 GMT (envelope-from fernape@FreeBSD.org) Received: (from fernape@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 07D5iBEu087086; Thu, 13 Aug 2020 05:44:11 GMT (envelope-from fernape@FreeBSD.org) Message-Id: <202008130544.07D5iBEu087086@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: fernape set sender to fernape@FreeBSD.org using -f From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= Date: Thu, 13 Aug 2020 05:44:11 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r544785 - in head/science/afni: . files X-SVN-Group: ports-head X-SVN-Commit-Author: fernape X-SVN-Commit-Paths: in head/science/afni: . files X-SVN-Commit-Revision: 544785 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 13 Aug 2020 05:44:12 -0000 Author: fernape Date: Thu Aug 13 05:44:11 2020 New Revision: 544785 URL: https://svnweb.freebsd.org/changeset/ports/544785 Log: science/afni: update to 20.2.11 Reported by: portscout Deleted: head/science/afni/files/patch-netcdf-3.5.0_src_configure 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 Aug 13 05:26:15 2020 (r544784) +++ head/science/afni/Makefile Thu Aug 13 05:44:11 2020 (r544785) @@ -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 Modified: head/science/afni/distinfo ============================================================================== --- head/science/afni/distinfo Thu Aug 13 05:26:15 2020 (r544784) +++ head/science/afni/distinfo Thu Aug 13 05:44:11 2020 (r544785) @@ -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 Modified: head/science/afni/files/patch-Makefile.INCLUDE ============================================================================== --- head/science/afni/files/patch-Makefile.INCLUDE Thu Aug 13 05:26:15 2020 (r544784) +++ head/science/afni/files/patch-Makefile.INCLUDE Thu Aug 13 05:44:11 2020 (r544785) @@ -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 \ Modified: head/science/afni/pkg-plist ============================================================================== --- head/science/afni/pkg-plist Thu Aug 13 05:26:15 2020 (r544784) +++ head/science/afni/pkg-plist Thu Aug 13 05:44:11 2020 (r544785) @@ -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