From bacon@smithers.neuro.mcw.edu Wed Dec 21 17:50:22 2005 Return-Path: Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 1437316A41F for ; Wed, 21 Dec 2005 17:50:22 +0000 (GMT) (envelope-from bacon@smithers.neuro.mcw.edu) Received: from smithers.neuro.mcw.edu (smithers.neuro.mcw.edu [141.106.204.28]) by mx1.FreeBSD.org (Postfix) with ESMTP id 585CB43D8F for ; Wed, 21 Dec 2005 17:50:07 +0000 (GMT) (envelope-from bacon@smithers.neuro.mcw.edu) Received: from smithers.neuro.mcw.edu (localhost [127.0.0.1]) by smithers.neuro.mcw.edu (8.13.3/8.13.3) with ESMTP id jBLHo0qP013444 for ; Wed, 21 Dec 2005 11:50:00 -0600 (CST) (envelope-from bacon@smithers.neuro.mcw.edu) Received: (from bacon@localhost) by smithers.neuro.mcw.edu (8.13.3/8.13.3/Submit) id jBLHo0xL013440; Wed, 21 Dec 2005 11:50:00 -0600 (CST) (envelope-from bacon) Message-Id: <200512211750.jBLHo0xL013440@smithers.neuro.mcw.edu> Date: Wed, 21 Dec 2005 11:50:00 -0600 (CST) From: Jason Bacon Reply-To: Jason Bacon To: FreeBSD-gnats-submit@freebsd.org Cc: Subject: New port: science/afni Analysis of Fucntional NeuroImages X-Send-Pr-Version: 3.113 X-GNATS-Notify: >Number: 90752 >Category: ports >Synopsis: New port: science/afni Analysis of Fucntional NeuroImages >Confidential: no >Severity: non-critical >Priority: low >Responsible: vd >State: closed >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Dec 21 18:00:18 GMT 2005 >Closed-Date: Wed Jan 25 17:53:08 GMT 2006 >Last-Modified: Tue Feb 14 19:10:45 CET 2006 >Originator: Jason Bacon >Release: FreeBSD 5.4-RELEASE i386 >Organization: Medical College of Wisconsin >Environment: System: FreeBSD smithers.neuro.mcw.edu 5.4-RELEASE FreeBSD 5.4-RELEASE #2: Wed Aug 24 14:54:53 CDT 2005 bacon@clone.neuro.mcw.edu:/usr/obj/usr/src/sys/clone i386 >Description: AFNI (Analysis of Functional NeuroImages) is a large suite of tools for viewing and analyzing brain image data, especially from functional MRI scans. Due to the enormous size of AFNI, I have purposely strayed from convention and designated a private subdirectory for it and other MRI tools in /usr/local/mri, so that /usr/local/bin won't get completely clobbered. Ports of other MRI tools will follow, and will also be installed in /usr/local/mri. # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # science/afni/ # science/afni/Makefile # science/afni/pkg-descr # science/afni/distinfo # science/afni/pkg-message # science/afni/pkg-plist # echo c - science/afni/ mkdir -p science/afni/ > /dev/null 2>&1 echo x - science/afni/Makefile sed 's/^X//' >science/afni/Makefile << 'END-of-science/afni/Makefile' X############################################################################ X# New ports collection Makefile for: afni X# Date created: 11 Jan 2005 X# Whom: jbacon X# X# $FreeBSD$ X# X X############################################################################ X# www.neuro.mcw.edu has the latest source distribution from which this port X# is built. It will be updated as time permits and necessiaty requires. X# X# afni.nimh.nih.gov is the ultimate source for AFNI, and will always X# contain the latest source release. If this port is not up to date, X# you can download the latest sources and build manually using X# Makefile.BSD, which is included in the source distribution. If the X# Makefile.BSD in the afni source distribution is out of date, as X# occasionally happens, you can download the latest from www.neuro.mcw.edu. X# I regularly submit updates to NIH, but it sometimes takes a while for them X# to get into the distribution. X XPORTNAME= afni XPORTVERSION= 2005.11.18.1920 XCATEGORIES= science graphics biology XMASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/ \ X http://afni.nimh.nih.gov/pub/dist/tgz/ XDISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ X Makefile.BSD TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD XDIST_SUBDIR= AFNI XEXTRACT_ONLY= afni_src.tgz afni_doc.tgz X XMAINTAINER= jbacon@mcw.edu XCOMMENT= Advanced Functional Neuro Imaging X XLIB_DEPENDS= Xm.3:${PORTSDIR}/x11-toolkits/open-motif X XUSE_GMAKE= yes X X# Build parameters XWRKSRC= ${WRKDIR}/afni_src XMAKEFILE= Makefile.BSD XALL_TARGET= vastness suma X X# Install parameters XSTRIP= XPREFIX= ${LOCALBASE}/mri/afni XMANCOMPRESSED= yes XNO_MTREE= yes X Xpost-extract: X ${CP} -f ${DISTDIR}/${DIST_SUBDIR}/Makefile.BSD ${WRKSRC} X Xdo-install: X ${MKDIR} ${PREFIX}/bin ${PREFIX}/afni_doc X ${INSTALL_PROGRAM} ${WRKSRC}/BSD/* ${PREFIX}/bin X ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${PREFIX}/bin X ${INSTALL_MAN} ${WRKDIR}/afni_doc/* ${PREFIX}/afni_doc X ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${LOCALBASE}/man/man1 X ${GZIP_CMD} ${LOCALBASE}/man/man1/afni.1 X Xpost-install: X ${CAT} pkg-message X X.include END-of-science/afni/Makefile echo x - science/afni/pkg-descr sed 's/^X//' >science/afni/pkg-descr << 'END-of-science/afni/pkg-descr' XThis is a port of afni, Advanced Functional Neuro Imaging X XWWW: http://www.neuro.mcw.edu/~bacon X X- Jason Xjbacon@mcw.edu END-of-science/afni/pkg-descr echo x - science/afni/distinfo sed 's/^X//' >science/afni/distinfo << 'END-of-science/afni/distinfo' XMD5 (AFNI/afni_src.tgz) = 8f118f55721573feee6efa7bfff64456 XSIZE (AFNI/afni_src.tgz) = 10481603 XMD5 (AFNI/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 XSIZE (AFNI/afni_doc.tgz) = 3267095 XMD5 (AFNI/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e XSIZE (AFNI/afni.1) = 1103 XMD5 (AFNI/Makefile.BSD) = 340123182e9e7ed765c902506c35bea9 XSIZE (AFNI/Makefile.BSD) = 3670 XMD5 (AFNI/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee XSIZE (AFNI/TTatlas+tlrc.BRIK.gz) = 159912 XMD5 (AFNI/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 XSIZE (AFNI/TTatlas+tlrc.HEAD) = 1750 END-of-science/afni/distinfo echo x - science/afni/pkg-message sed 's/^X//' >science/afni/pkg-message << 'END-of-science/afni/pkg-message' X X============================================================================= XUsers will need to have /usr/local/mri/afni/bin in their PATH in order Xto run programs in the AFNI distribution. X XDocumentation can be found in /usr/local/mri/afni/afni_doc. X XThe environment AFNI_PLUGIN_PATH must also be set to the bin directory Xin order to run AFNI plugins. X XEach user is advised to create a .afnirc file in their home directory Xto customize settings. X XFor questions or comments regarding this port, please contact the Xport maintainer: jbacon@mcw.edu X XFor AFNI usage, please visit the AFNI WEB site at http://afni.nimh.nih.gov. X============================================================================= X END-of-science/afni/pkg-message echo x - science/afni/pkg-plist sed 's/^X//' >science/afni/pkg-plist << 'END-of-science/afni/pkg-plist' Xafni_doc/1dplot.ps Xafni_doc/24swap.ps Xafni_doc/2dImReg.ps Xafni_doc/2swap.ps Xafni_doc/3T_toafni.ps Xafni_doc/3dANOVA.ps Xafni_doc/3dANOVA2.ps Xafni_doc/3dANOVA3.ps Xafni_doc/3dDeconvolve.ps Xafni_doc/3dExtrema.ps Xafni_doc/3dFDR.ps Xafni_doc/3dFWHM.ps Xafni_doc/3dFriedman.ps Xafni_doc/3dIntracranial.ps Xafni_doc/3dKruskalWallis.ps Xafni_doc/3dMannWhitney.ps Xafni_doc/3dNLfim.ps Xafni_doc/3dRegAna.ps Xafni_doc/3dStatClust.ps Xafni_doc/3dTSgen.ps Xafni_doc/3dTcat.ps Xafni_doc/3dTsmooth.ps Xafni_doc/3dWavelets.ps Xafni_doc/3dWilcoxon.ps Xafni_doc/3daxialize.ps Xafni_doc/3dbuc2fim.ps Xafni_doc/3dbucket.ps Xafni_doc/3dcalc.ps Xafni_doc/3dclust.ps Xafni_doc/3dcolon.ps Xafni_doc/3ddup.ps Xafni_doc/3dfim+.ps Xafni_doc/3dfim.ps Xafni_doc/3dfractionize.ps Xafni_doc/3dhistog.ps Xafni_doc/3dinfo.ps Xafni_doc/3dmaskave.ps Xafni_doc/3dmerge.ps Xafni_doc/3dnewid.ps Xafni_doc/3dnoise.ps Xafni_doc/3dnvals.ps Xafni_doc/3dpc.ps Xafni_doc/3dproject.ps Xafni_doc/3drefit.ps Xafni_doc/3drotate.ps Xafni_doc/3dttest.ps Xafni_doc/3dvolreg.ps Xafni_doc/4swap.ps Xafni_doc/AFNI.changes.cox Xafni_doc/AFNI.changes.rhammett Xafni_doc/AFNI.changes.rickr Xafni_doc/AlphaSim.ps Xafni_doc/AlphaSim_fig.ps Xafni_doc/FD2.ps Xafni_doc/Nonparametric.ps Xafni_doc/README Xafni_doc/README.Ifile Xafni_doc/README.attributes Xafni_doc/README.bzip2 Xafni_doc/README.changes Xafni_doc/README.compression Xafni_doc/README.copyright Xafni_doc/README.driver Xafni_doc/README.environment Xafni_doc/README.func_types Xafni_doc/README.notes Xafni_doc/README.roi Xafni_doc/README.permtest Xafni_doc/README.plugouts Xafni_doc/README.realtime Xafni_doc/README.registration Xafni_doc/README.render_scripts Xafni_doc/README.setup Xafni_doc/README.volreg Xafni_doc/README.web Xafni_doc/README.ziad Xafni_doc/RSFgen.ps Xafni_doc/Table.ps Xafni_doc/abut.ps Xafni_doc/adwarp.ps Xafni_doc/afni200.ps Xafni_doc/afni_aux.ps Xafni_doc/afni_plugins.ps Xafni_doc/afni_register.ps Xafni_doc/buckets.ps Xafni_doc/byteorder.ps Xafni_doc/ccalc.ps Xafni_doc/cdf.ps Xafni_doc/count.ps Xafni_doc/fim2.ps Xafni_doc/float_scan.ps Xafni_doc/from3d.ps Xafni_doc/ftosh.ps Xafni_doc/imand.ps Xafni_doc/imaver.ps Xafni_doc/imcalc.ps Xafni_doc/imdump.ps Xafni_doc/immask.ps Xafni_doc/imreg.ps Xafni_doc/imrotate.ps Xafni_doc/imstack.ps Xafni_doc/imstat.ps Xafni_doc/imupsam.ps Xafni_doc/mritopgm.ps Xafni_doc/nsize.ps Xafni_doc/p2t.ps Xafni_doc/sfim.ps Xafni_doc/sqwave.ps Xafni_doc/tfim.ps Xafni_doc/to3d.ps Xafni_doc/waver.ps Xbin/1dcat Xbin/1ddot Xbin/1deval Xbin/1dfft Xbin/1dgrayplot Xbin/1dnorm Xbin/1dplot Xbin/1dsum Xbin/1dsvd Xbin/1dtranspose Xbin/24swap Xbin/2dImReg Xbin/2swap Xbin/3T_toafni Xbin/3dAFNIto3D Xbin/3dAFNItoANALYZE Xbin/3dAFNItoMINC Xbin/3dAFNItoNIFTI Xbin/3dAFNItoNIML Xbin/3dAFNItoRaw Xbin/3dANALYZEtoAFNI Xbin/3dANOVA Xbin/3dANOVA2 Xbin/3dANOVA3 Xbin/3dAnatNudge Xbin/3dCM Xbin/3dAnhist Xbin/3dAttribute Xbin/3dAutoTcorrelate Xbin/3dAutobox Xbin/3dAutomask Xbin/3dBRAIN_VOYAGERtoAFNI Xbin/3dCRUISEtoAFNI Xbin/3dClipLevel Xbin/3dConvolve Xbin/3dDTeig Xbin/3dDWItoDT Xbin/3dDeconvolve Xbin/3dDeconvolve_f Xbin/3dDespike Xbin/3dDetrend Xbin/3dEntropy Xbin/3dExtrema Xbin/3dFDR Xbin/3dFWHM Xbin/3dFourier Xbin/3dFriedman Xbin/3dIntracranial Xbin/3dKruskalWallis Xbin/3dLRflip Xbin/3dLocalstat Xbin/3dMINCtoAFNI Xbin/3dMannWhitney Xbin/3dMax Xbin/3dMean Xbin/3dMedianFilter Xbin/3dNLfim Xbin/3dNotes Xbin/3dOverlap Xbin/3dROIstats Xbin/3dRegAna Xbin/3dRowFillin Xbin/3dSkullStrip Xbin/3dSpatNorm Xbin/3dStatClust Xbin/3dSurf2Vol Xbin/3dSurfMask Xbin/3dTSgen Xbin/3dTagalign Xbin/3dTcat Xbin/3dTcorrelate Xbin/3dThreetoRGB Xbin/3dToutcount Xbin/3dTqual Xbin/3dTshift Xbin/3dTstat Xbin/3dTsmooth Xbin/3dUndump Xbin/3dUniformize Xbin/3dVol2Surf Xbin/3dWarp Xbin/3dWarpDrive Xbin/3dWavelets Xbin/3dWilcoxon Xbin/3dWinsor Xbin/3dZcat Xbin/3dZcutup Xbin/3dZeropad Xbin/3dZregrid Xbin/3danisosmooth Xbin/3daxialize Xbin/3dbuc2fim Xbin/3dbucket Xbin/3dcalc Xbin/3dclust Xbin/3dcopy Xbin/3ddata.h Xbin/3ddelay Xbin/3ddot Xbin/3ddup Xbin/3dedge3 Xbin/3dfim Xbin/3dfim+ Xbin/3dfractionize Xbin/3dhistog Xbin/3dinfo Xbin/3dmaskave Xbin/3dmaskdump Xbin/3dmaxima Xbin/3dmerge Xbin/3dnewid Xbin/3dnoise Xbin/3dnvals Xbin/3dpc Xbin/3dproject Xbin/3drefit Xbin/3drename Xbin/3dresample Xbin/3dretroicor Xbin/3drotate Xbin/3dttest Xbin/3dvolreg Xbin/4swap Xbin/@4Daverage Xbin/@AfniOrient2RAImap Xbin/@AfniOrientSign Xbin/@Align_Centers Xbin/@Center_Distance Xbin/@FromRAI Xbin/@CheckForAfniDset Xbin/@CommandGlobb Xbin/@DTI_studio_reposition Xbin/@GetAfniOrient Xbin/@GetAfniPrefix Xbin/@GetAfniView Xbin/@NoExt Xbin/@Purify_1D Xbin/@RenamePanga Xbin/@SUMA_AlignToExperiment Xbin/@SUMA_Make_Spec_FS Xbin/@SUMA_Make_Spec_SF Xbin/@ToRAI Xbin/@UpdateAfni Xbin/@VolCenter Xbin/@align_partial_oblique Xbin/@auto_align Xbin/@auto_tlrc Xbin/@clip_volume Xbin/@fix_FSsphere Xbin/@make_stim_file Xbin/@parse_afni_name Xbin/@parse_name Xbin/AlphaSim Xbin/CompareSurfaces Xbin/ConvertDset Xbin/ConvertSurface Xbin/ConvexHull Xbin/CreateIcosahedron Xbin/DTIStudioFibertoSegments Xbin/Dimon Xbin/FD2 Xbin/FSread_annot Xbin/Ifile Xbin/Imon Xbin/IsoSurface Xbin/MakeColorMap Xbin/MapIcosahedron Xbin/ROI2dataset Xbin/ROIgrow Xbin/RSFgen Xbin/SUMA_glxdino Xbin/SUMA_paperplane Xbin/SUMA_pixmap2eps Xbin/Vecwarp Xbin/SampBias Xbin/ScaleToMap Xbin/SurfClust Xbin/SurfMeasures Xbin/SurfPatch Xbin/SurfQual Xbin/SurfSmooth Xbin/SurfToSurf Xbin/SurfaceMetrics Xbin/Xphace Xbin/abut Xbin/adwarp Xbin/afni Xbin/afni_environ.h Xbin/afni_vcheck Xbin/afni_warp.h Xbin/aiv Xbin/byteorder Xbin/cat_matvec Xbin/ccalc Xbin/cdf Xbin/cdflib.h Xbin/cjpeg Xbin/count Xbin/coxplot.h Xbin/cs.h Xbin/cs_sort_template.h Xbin/dicom_hdr Xbin/dicom_to_raw Xbin/djpeg Xbin/editvol.h Xbin/eispack.h Xbin/ent16 Xbin/f2c.h Xbin/face_JimEliassen.jpg Xbin/face_JohannaBaas.jpg Xbin/face_SalloumJB.jpg Xbin/face_ZangYF.jpg Xbin/face_aclark.jpg Xbin/face_adij_mannheim.jpg Xbin/face_afniman.jpg Xbin/face_agoldman.jpg Xbin/face_ahammett.jpg Xbin/face_anewmanetal.jpg Xbin/face_anugent.jpg Xbin/face_asanders.jpg Xbin/face_ashackman.jpg Xbin/face_athomas.jpg Xbin/face_bandettini.jpg Xbin/face_barbaracd.jpg Xbin/face_bargall.jpg Xbin/face_bea.jpg Xbin/face_becky.jpg Xbin/face_bmcnamee.jpg Xbin/face_bodurka.jpg Xbin/face_bprogers.jpg Xbin/face_bridget.jpg Xbin/face_brodmann.jpg Xbin/face_browndyke.jpg Xbin/face_carol.jpg Xbin/face_cbikle.jpg Xbin/face_claudio.jpg Xbin/face_cmoritz.jpg Xbin/face_cmyers.jpg Xbin/face_csenior.jpg Xbin/face_cwettig.jpg Xbin/face_dglen.jpg Xbin/face_einstein.jpg Xbin/face_eli.jpg Xbin/face_ernv.jpg Xbin/face_eteoh.jpg Xbin/face_faustalui.jpg Xbin/face_ftam.jpg Xbin/face_gambero.jpg Xbin/face_gangchen.jpg Xbin/face_gganis.jpg Xbin/face_ggiulietti.jpg Xbin/face_glarkin.jpg Xbin/face_grant.jpg Xbin/face_hanlon.jpg Xbin/face_heekeren.jpg Xbin/face_hoffmangobbini.jpg Xbin/face_ibitter.jpg Xbin/face_ilevy.jpg Xbin/face_imukai.jpg Xbin/fftest Xbin/face_jbinder.jpg Xbin/face_jbjork.jpg Xbin/face_jchoi.jpg Xbin/face_jigokudani.jpg Xbin/face_jkurata.jpg Xbin/face_jskipper.jpg Xbin/face_jweisberg.jpg Xbin/face_kastnerlab.jpg Xbin/face_kebb.jpg Xbin/face_kkwong.jpg Xbin/face_kropella.jpg Xbin/face_kschreiber.jpg Xbin/face_kuba.jpg Xbin/face_lask.jpg Xbin/face_laura.jpg Xbin/face_lincoln1.jpg Xbin/face_lincoln2.jpg Xbin/face_lindachao.jpg Xbin/face_lizyoder.jpg Xbin/face_ljcox.jpg Xbin/face_llatour.jpg Xbin/face_lmccall.jpg Xbin/face_locikidsucsd.jpg Xbin/face_lukas.jpg Xbin/face_mamann.jpg Xbin/face_maxwell.jpg Xbin/face_mbeauchamp.jpg Xbin/face_mbelmonte.jpg Xbin/face_megcrew.jpg Xbin/face_mgarolera.jpg Xbin/face_mkenney.jpg Xbin/face_mmaieron.jpg Xbin/face_mmk.jpg Xbin/face_mpinsk.jpg Xbin/face_mruppe.jpg Xbin/face_mscohen.jpg Xbin/face_notspm.jpg Xbin/face_pchristidis.jpg Xbin/face_phoebechan.jpg Xbin/face_prowser.jpg Xbin/face_psfb.jpg Xbin/face_qiulin.jpg Xbin/face_rabeauchamp.jpg Xbin/face_rbirn.jpg Xbin/face_rhammett.jpg Xbin/face_rhenderson.jpg Xbin/face_rhoge.jpg Xbin/face_richd.jpg Xbin/face_rjsquirrel.jpg Xbin/face_rprost.jpg Xbin/face_rreynolds.jpg Xbin/face_rwcox.jpg Xbin/face_rwcox2.jpg Xbin/face_rwcox3.jpg Xbin/face_rwcox4.jpg Xbin/face_rwcox5.jpg Xbin/face_rwcox6.jpg Xbin/face_sjapee.jpg Xbin/face_saccanch.jpg Xbin/face_skammy.jpg Xbin/face_skapdoskar.jpg Xbin/face_smarrett.jpg Xbin/face_ssaad.jpg Xbin/face_ssmall.jpg Xbin/face_steverao.jpg Xbin/face_tolkien.jpg Xbin/face_vhradil.jpg Xbin/face_vincent1.jpg Xbin/face_vincent2.jpg Xbin/face_vincent3.jpg Xbin/face_vincent4.jpg Xbin/face_vnapadow.jpg Xbin/face_wapostman1.jpg Xbin/face_wapostman2.jpg Xbin/face_wmluh.jpg Xbin/face_wpostman.jpg Xbin/face_zsaad.jpg Xbin/face_zzzdini.jpg Xbin/face_zzzsunbrain.jpg Xbin/file_tool Xbin/fim2 Xbin/float_scan Xbin/from3d Xbin/ftosh Xbin/ge_header Xbin/im2niml Xbin/imand Xbin/imaver Xbin/imcalc Xbin/imcutup Xbin/imdump Xbin/immask Xbin/imreg Xbin/imrotate Xbin/imstack Xbin/imstat Xbin/imupsam Xbin/inspec Xbin/killer.h Xbin/libSUMA.a Xbin/libcoxplot.a Xbin/libf2c.a Xbin/libmri.a Xbin/libmrix.a Xbin/libvolpack.a Xbin/machdep.h Xbin/mayo_analyze Xbin/mcw_glob.h Xbin/mcw_malloc.h Xbin/model_beta.so Xbin/model_constant.so Xbin/model_convgamma.so Xbin/model_convgamma2a.so Xbin/model_diffexp.so Xbin/model_diffusion.so Xbin/model_gammavar.so Xbin/model_linear.so Xbin/model_null.so Xbin/model_quadratic.so Xbin/model_sinewave_ap.so Xbin/model_sinewave_apf.so Xbin/model_squarewave_ap.so Xbin/model_squarewave_apf.so Xbin/model_trnglwave_ap.so Xbin/model_trnglwave_apf.so Xbin/mpeg_encode Xbin/mpegtoppm Xbin/mrilib.h Xbin/mritopgm Xbin/multivector.h Xbin/myget Xbin/nicat Xbin/nifti1_test Xbin/nifti_stats Xbin/nifti_tool Xbin/niml.h Xbin/nsize Xbin/p2t Xbin/plug_3Ddump_V2.so Xbin/plug_3ddot.so Xbin/plug_3ddup.so Xbin/plug_4Ddump.so Xbin/plug_L1fit.so Xbin/plug_betafit.so Xbin/plug_clust.so Xbin/plug_compress.so Xbin/plug_coorder.so Xbin/plug_copy.so Xbin/plug_crender.so Xbin/plug_deconvolve.so Xbin/plug_delay_V2.so Xbin/plug_drawdset.so Xbin/plug_edit.so Xbin/plug_extract.so Xbin/plug_fourier.so Xbin/plug_hemisub.so Xbin/plug_histog.so Xbin/plug_imreg.so Xbin/plug_lsqfit.so Xbin/plug_maskave.so Xbin/plug_maskcalc.so Xbin/plug_maxima.so Xbin/plug_nlfit.so Xbin/plug_notes.so Xbin/plug_nth_dataset.so Xbin/plug_nudge.so Xbin/rmz Xbin/plug_permtest.so Xbin/plug_power.so Xbin/plug_realtime.so Xbin/plug_rename.so Xbin/plug_render.so Xbin/plug_reorder.so Xbin/plug_retroicor.so Xbin/plug_roiedit.so Xbin/plug_roiplot.so Xbin/plug_scatplot.so Xbin/plug_second_dataset.so Xbin/plug_stats.so Xbin/plug_stavg.so Xbin/plug_tag.so Xbin/plug_threshold.so Xbin/plug_ttget.so Xbin/plug_vol2surf.so Xbin/plug_volreg.so Xbin/plug_wavelets.so Xbin/plug_zeropad.so Xbin/plugout_drive Xbin/plugout_ijk Xbin/plugout_tt Xbin/plugout_tta Xbin/poem_bj1.txt Xbin/poem_eapoe1.txt Xbin/poem_em.txt Xbin/poem_ghm3.txt Xbin/poem_gmh1.txt Xbin/poem_gmh2.txt Xbin/poem_gmh3.txt Xbin/poem_jm1.txt Xbin/poem_pbs1.txt Xbin/poem_pbs2.txt Xbin/poem_rf1.txt Xbin/poem_rk1.txt Xbin/poem_rls1.txt Xbin/poem_ww1.txt Xbin/poem_ww2.txt Xbin/qhull Xbin/quickspec Xbin/rotcom Xbin/rtfeedme Xbin/serial_helper Xbin/sfim Xbin/siemens_vision Xbin/splash_bobkarl.jpg Xbin/splash_earth.jpg Xbin/splash_emars.jpg Xbin/splash_kebb.jpg Xbin/splash_marsalbor.jpg Xbin/splash_mcw03.jpg Xbin/splash_sscc03.jpg Xbin/splash_vincent.jpg Xbin/sqwave Xbin/strblast Xbin/suma Xbin/suma_change_spec Xbin/tagset.h Xbin/tfim Xbin/thd_compress.h Xbin/thd_iochan.h Xbin/thd_maker.h Xbin/to3d Xbin/vecmat.h Xbin/vol2surf.h Xbin/volpack.h Xbin/waver Xbin/whereami Xbin/whirlgif Xbin/TTatlas+tlrc.BRIK.gz Xbin/TTatlas+tlrc.HEAD X../../man/man1/afni.1.gz X@dirrm bin X@dirrm afni_doc END-of-science/afni/pkg-plist exit >How-To-Repeat: >Fix: >Release-Note: >Audit-Trail: Responsible-Changed-From-To: freebsd-ports-bugs->ehaupt Responsible-Changed-By: ehaupt Responsible-Changed-When: Fri Dec 23 10:53:21 CET 2005 Responsible-Changed-Why: Take. http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 From: Emanuel Haupt To: bug-followup@FreeBSD.org, bacon@smithers.neuro.mcw.edu Cc: Subject: Re: ports/90752: New port: science/afni Analysis of Fucntional NeuroImages Date: Fri, 23 Dec 2005 11:54:21 +0100 Hi Jason, Thanks for your submission. The port does not respect CC [1] and CFLAGS [2]. If your port needs gmake you need to pass CC to MAKE_ENV. distinfo should now also contain SHA256 checksums. You can use 'make makesum' to calculate them. Attention, using distfile names without a version in it are generally dangerous, once you re-roll the tarball or update them the port will fail due to a checksum mismatch. Finally please install portlint (devel/portlint) and run it with the '-A' option and eradicate the fatal warnings. [1] http://www.freebsd.org/doc/en_US.ISO8859-1/books/porters-handbook/dads-cc.html [2] http://www.freebsd.org/doc/en_US.ISO8859-1/books/porters-handbook/dads-cflags.html Thanks in advance, Emanuel -- GnuPG key id: 0x55E67774 Download: http://pgp.mit.edu:11371 Key fingerprint: 17B3 FD8F BA68 4AB4 10FD A9D1 AD52 6588 55E6 7774 State-Changed-From-To: open->feedback State-Changed-By: ehaupt State-Changed-When: Fri Dec 23 14:40:27 CET 2005 State-Changed-Why: Ask for maintainer fix. http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 From: Jason Bacon To: Emanuel Haupt Cc: bug-followup@FreeBSD.org Subject: Re: ports/90752: New port: science/afni Analysis of Fucntional NeuroImages Date: Sat, 24 Dec 2005 19:46:50 -0600 --Boundary-00=_LofrD7l6fjyx9TS Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Emanuel, Thanks for the quick feedback. Bear with me here - I'm just getting familiar with the internals of ports system, and this has proven to be a tricky port. The new shar is attached. Please see my responses below. > The port does not respect CC [1] and CFLAGS [2]. I assume you're referring to Makefile.BSD here, which I've updated to respect CC. This is the only thing in the AFNI distribution that I can tamper with, and it must be maintained in a format usable outside the FreeBSD ports system for those who choose to build manually. Note that most of the work in building AFNI is done by Makefile.INCLUDE, the universal portion of the AFNI make setup that Makefile.BSD, et. al. set the environment for. It ignores CFLAGS entirely, and suggesting any changes to it is not likely to be fruitful, so I had to tack flags directly onto CC in Makefile.BSD. This may seem a little kludgey, but I don't see a better solution at the moment. > If your port needs > gmake you need to pass CC to MAKE_ENV. Added this to the port Makefile. > distinfo should now also contain > SHA256 checksums. You can use 'make makesum' to calculate them. Had already done that. Did you run into checksum problems? > Attention, using distfile names without a version in it are generally > dangerous, once you re-roll the tarball or update them the port will > fail due to a checksum mismatch. I'd already thought of this, but I'm not sure what the best solution would be. I doubt the author of AFNI will want to start adding version numbers on his site. I *could* remove it from MASTER_SITES and list only my own copy, with version numbers added. Would it be acceptable not having the original download site in MASTER_SITES? > Finally please install portlint (devel/portlint) and run it with the > '-A' option and eradicate the fatal warnings. Done. Happy holidays, Jason -- Jason W. Bacon Systems Manager, fMRI Research Labs Medical College of Wisconsin 8701 Watertown Plank Rd Room MFRC 4037 Milwaukee, WI 53226 (414) 456-5881 (414) 456-6562 FAX --Boundary-00=_LofrD7l6fjyx9TS Content-Type: text/plain; charset="iso-8859-1"; name="afni.tree" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="afni.tree" # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # science/afni # science/afni/Makefile # science/afni/pkg-descr # science/afni/distinfo # science/afni/pkg-message # science/afni/pkg-plist # echo c - science/afni mkdir -p science/afni > /dev/null 2>&1 echo x - science/afni/Makefile sed 's/^X//' >science/afni/Makefile << 'END-of-science/afni/Makefile' X############################################################################ X# New ports collection Makefile for: afni X# Date created: 11 Jan 2005 X# Whom: jbacon X# X# $FreeBSD$ X# X X############################################################################ X# www.neuro.mcw.edu has the latest source distribution from which this port X# is built. It will be updated as time permits and necessiaty requires. X# X# afni.nimh.nih.gov is the ultimate source for AFNI, and will always X# contain the latest source release. If this port is not up to date, X# you can download the latest sources and build manually using X# Makefile.BSD, which is included in the source distribution. If the X# Makefile.BSD in the afni source distribution is out of date, as X# occasionally happens, you can download the latest from www.neuro.mcw.edu. X# I regularly submit updates to NIH, but it sometimes takes a while for them X# to get into the distribution. X XPORTNAME= afni XPORTVERSION= 2005.11.18.1920 XCATEGORIES= science graphics biology XMASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/ \ X http://afni.nimh.nih.gov/pub/dist/tgz/ XDISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ X Makefile.BSD TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD XDIST_SUBDIR= AFNI XEXTRACT_ONLY= afni_src.tgz afni_doc.tgz X XMAINTAINER= jbacon@mcw.edu XCOMMENT= Advanced Functional Neuro Imaging X XLIB_DEPENDS= Xm.3:${PORTSDIR}/x11-toolkits/open-motif X XUSE_GMAKE= yes XMAKE_ENV= CC="${CC}" XMAN1= afni.1 X X# Build parameters XWRKSRC= ${WRKDIR}/afni_src XMAKEFILE= Makefile.BSD XALL_TARGET= vastness suma X X# Install parameters XSTRIP= XPREFIX= ${LOCALBASE}/mri/afni XMANCOMPRESSED= yes XNO_MTREE= yes X Xpost-extract: X ${CP} -f ${DISTDIR}/${DIST_SUBDIR}/Makefile.BSD ${WRKSRC} X Xdo-install: X ${MKDIR} ${PREFIX}/bin ${PREFIX}/afni_doc X ${INSTALL_PROGRAM} ${WRKSRC}/BSD/* ${PREFIX}/bin X ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${PREFIX}/bin X ${INSTALL_MAN} ${WRKDIR}/afni_doc/* ${PREFIX}/afni_doc X ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${LOCALBASE}/man/man1 X ${GZIP_CMD} ${LOCALBASE}/man/man1/afni.1 X Xpost-install: X ${CAT} pkg-message X X.include END-of-science/afni/Makefile echo x - science/afni/pkg-descr sed 's/^X//' >science/afni/pkg-descr << 'END-of-science/afni/pkg-descr' XThis is a port of afni, Advanced Functional Neuro Imaging X XWWW: http://www.neuro.mcw.edu/~bacon X X- Jason Xjbacon@mcw.edu END-of-science/afni/pkg-descr echo x - science/afni/distinfo sed 's/^X//' >science/afni/distinfo << 'END-of-science/afni/distinfo' XMD5 (AFNI/afni_src.tgz) = 8f118f55721573feee6efa7bfff64456 XSIZE (AFNI/afni_src.tgz) = 10481603 XMD5 (AFNI/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 XSIZE (AFNI/afni_doc.tgz) = 3267095 XMD5 (AFNI/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e XSIZE (AFNI/afni.1) = 1103 XMD5 (AFNI/Makefile.BSD) = c18d1044cb32808dbf2274ef6ad5b567 XSIZE (AFNI/Makefile.BSD) = 3646 XMD5 (AFNI/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee XSIZE (AFNI/TTatlas+tlrc.BRIK.gz) = 159912 XMD5 (AFNI/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 XSIZE (AFNI/TTatlas+tlrc.HEAD) = 1750 END-of-science/afni/distinfo echo x - science/afni/pkg-message sed 's/^X//' >science/afni/pkg-message << 'END-of-science/afni/pkg-message' X X============================================================================= XUsers will need to have ${PREFIX}/bin in their PATH in order Xto run programs in the AFNI distribution. X XDocumentation can be found in ${PREFIX}/afni_doc. X XThe environment AFNI_PLUGIN_PATH must also be set to the bin directory Xin order to run AFNI plugins. X XEach user is advised to create a .afnirc file in their home directory Xto customize settings. X XFor questions or comments regarding this port, please contact the Xport maintainer: jbacon@mcw.edu X XFor AFNI usage, please visit the AFNI WEB site at http://afni.nimh.nih.gov. X============================================================================= END-of-science/afni/pkg-message echo x - science/afni/pkg-plist sed 's/^X//' >science/afni/pkg-plist << 'END-of-science/afni/pkg-plist' Xafni_doc/1dplot.ps Xafni_doc/24swap.ps Xafni_doc/2dImReg.ps Xafni_doc/2swap.ps Xafni_doc/3T_toafni.ps Xafni_doc/3dANOVA.ps Xafni_doc/3dANOVA2.ps Xafni_doc/3dANOVA3.ps Xafni_doc/3dDeconvolve.ps Xafni_doc/3dExtrema.ps Xafni_doc/3dFDR.ps Xafni_doc/3dFWHM.ps Xafni_doc/3dFriedman.ps Xafni_doc/3dIntracranial.ps Xafni_doc/3dKruskalWallis.ps Xafni_doc/3dMannWhitney.ps Xafni_doc/3dNLfim.ps Xafni_doc/3dRegAna.ps Xafni_doc/3dStatClust.ps Xafni_doc/3dTSgen.ps Xafni_doc/3dTcat.ps Xafni_doc/3dTsmooth.ps Xafni_doc/3dWavelets.ps Xafni_doc/3dWilcoxon.ps Xafni_doc/3daxialize.ps Xafni_doc/3dbuc2fim.ps Xafni_doc/3dbucket.ps Xafni_doc/3dcalc.ps Xafni_doc/3dclust.ps Xafni_doc/3dcolon.ps Xafni_doc/3ddup.ps Xafni_doc/3dfim+.ps Xafni_doc/3dfim.ps Xafni_doc/3dfractionize.ps Xafni_doc/3dhistog.ps Xafni_doc/3dinfo.ps Xafni_doc/3dmaskave.ps Xafni_doc/3dmerge.ps Xafni_doc/3dnewid.ps Xafni_doc/3dnoise.ps Xafni_doc/3dnvals.ps Xafni_doc/3dpc.ps Xafni_doc/3dproject.ps Xafni_doc/3drefit.ps Xafni_doc/3drotate.ps Xafni_doc/3dttest.ps Xafni_doc/3dvolreg.ps Xafni_doc/4swap.ps Xafni_doc/AFNI.changes.cox Xafni_doc/AFNI.changes.rhammett Xafni_doc/AFNI.changes.rickr Xafni_doc/AlphaSim.ps Xafni_doc/AlphaSim_fig.ps Xafni_doc/FD2.ps Xafni_doc/Nonparametric.ps Xafni_doc/README Xafni_doc/README.Ifile Xafni_doc/README.attributes Xafni_doc/README.bzip2 Xafni_doc/README.changes Xafni_doc/README.compression Xafni_doc/README.copyright Xafni_doc/README.driver Xafni_doc/README.environment Xafni_doc/README.func_types Xafni_doc/README.notes Xafni_doc/README.roi Xafni_doc/README.permtest Xafni_doc/README.plugouts Xafni_doc/README.realtime Xafni_doc/README.registration Xafni_doc/README.render_scripts Xafni_doc/README.setup Xafni_doc/README.volreg Xafni_doc/README.web Xafni_doc/README.ziad Xafni_doc/RSFgen.ps Xafni_doc/Table.ps Xafni_doc/abut.ps Xafni_doc/adwarp.ps Xafni_doc/afni200.ps Xafni_doc/afni_aux.ps Xafni_doc/afni_plugins.ps Xafni_doc/afni_register.ps Xafni_doc/buckets.ps Xafni_doc/byteorder.ps Xafni_doc/ccalc.ps Xafni_doc/cdf.ps Xafni_doc/count.ps Xafni_doc/fim2.ps Xafni_doc/float_scan.ps Xafni_doc/from3d.ps Xafni_doc/ftosh.ps Xafni_doc/imand.ps Xafni_doc/imaver.ps Xafni_doc/imcalc.ps Xafni_doc/imdump.ps Xafni_doc/immask.ps Xafni_doc/imreg.ps Xafni_doc/imrotate.ps Xafni_doc/imstack.ps Xafni_doc/imstat.ps Xafni_doc/imupsam.ps Xafni_doc/mritopgm.ps Xafni_doc/nsize.ps Xafni_doc/p2t.ps Xafni_doc/sfim.ps Xafni_doc/sqwave.ps Xafni_doc/tfim.ps Xafni_doc/to3d.ps Xafni_doc/waver.ps Xbin/1dcat Xbin/1ddot Xbin/1deval Xbin/1dfft Xbin/1dgrayplot Xbin/1dnorm Xbin/1dplot Xbin/1dsum Xbin/1dsvd Xbin/1dtranspose Xbin/24swap Xbin/2dImReg Xbin/2swap Xbin/3T_toafni Xbin/3dAFNIto3D Xbin/3dAFNItoANALYZE Xbin/3dAFNItoMINC Xbin/3dAFNItoNIFTI Xbin/3dAFNItoNIML Xbin/3dAFNItoRaw Xbin/3dANALYZEtoAFNI 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Xbin/3dWinsor Xbin/3dZcat Xbin/3dZcutup Xbin/3dZeropad Xbin/3dZregrid Xbin/3danisosmooth Xbin/3daxialize Xbin/3dbuc2fim Xbin/3dbucket Xbin/3dcalc Xbin/3dclust Xbin/3dcopy Xbin/3ddata.h Xbin/3ddelay Xbin/3ddot Xbin/3ddup Xbin/3dedge3 Xbin/3dfim Xbin/3dfim+ Xbin/3dfractionize Xbin/3dhistog Xbin/3dinfo Xbin/3dmaskave Xbin/3dmaskdump Xbin/3dmaxima Xbin/3dmerge Xbin/3dnewid Xbin/3dnoise Xbin/3dnvals Xbin/3dpc Xbin/3dproject Xbin/3drefit Xbin/3drename Xbin/3dresample Xbin/3dretroicor Xbin/3drotate Xbin/3dttest Xbin/3dvolreg Xbin/4swap Xbin/@4Daverage Xbin/@AfniOrient2RAImap Xbin/@AfniOrientSign Xbin/@Align_Centers Xbin/@Center_Distance Xbin/@FromRAI Xbin/@CheckForAfniDset Xbin/@CommandGlobb Xbin/@DTI_studio_reposition Xbin/@GetAfniOrient Xbin/@GetAfniPrefix Xbin/@GetAfniView Xbin/@NoExt Xbin/@Purify_1D Xbin/@RenamePanga Xbin/@SUMA_AlignToExperiment Xbin/@SUMA_Make_Spec_FS Xbin/@SUMA_Make_Spec_SF Xbin/@ToRAI Xbin/@UpdateAfni Xbin/@VolCenter Xbin/@align_partial_oblique Xbin/@auto_align 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Xbin/face_prowser.jpg Xbin/face_psfb.jpg Xbin/face_qiulin.jpg Xbin/face_rabeauchamp.jpg Xbin/face_rbirn.jpg Xbin/face_rhammett.jpg Xbin/face_rhenderson.jpg Xbin/face_rhoge.jpg Xbin/face_richd.jpg Xbin/face_rjsquirrel.jpg Xbin/face_rprost.jpg Xbin/face_rreynolds.jpg Xbin/face_rwcox.jpg Xbin/face_rwcox2.jpg Xbin/face_rwcox3.jpg Xbin/face_rwcox4.jpg Xbin/face_rwcox5.jpg Xbin/face_rwcox6.jpg Xbin/face_sjapee.jpg Xbin/face_saccanch.jpg Xbin/face_skammy.jpg Xbin/face_skapdoskar.jpg Xbin/face_smarrett.jpg Xbin/face_ssaad.jpg Xbin/face_ssmall.jpg Xbin/face_steverao.jpg Xbin/face_tolkien.jpg Xbin/face_vhradil.jpg Xbin/face_vincent1.jpg Xbin/face_vincent2.jpg Xbin/face_vincent3.jpg Xbin/face_vincent4.jpg Xbin/face_vnapadow.jpg Xbin/face_wapostman1.jpg Xbin/face_wapostman2.jpg Xbin/face_wmluh.jpg Xbin/face_wpostman.jpg Xbin/face_zsaad.jpg Xbin/face_zzzdini.jpg Xbin/face_zzzsunbrain.jpg Xbin/file_tool Xbin/fim2 Xbin/float_scan Xbin/from3d Xbin/ftosh Xbin/ge_header Xbin/im2niml Xbin/imand Xbin/imaver Xbin/imcalc Xbin/imcutup Xbin/imdump Xbin/immask Xbin/imreg Xbin/imrotate Xbin/imstack Xbin/imstat Xbin/imupsam Xbin/inspec Xbin/killer.h Xbin/libSUMA.a Xbin/libcoxplot.a Xbin/libf2c.a Xbin/libmri.a Xbin/libmrix.a Xbin/libvolpack.a Xbin/machdep.h Xbin/mayo_analyze Xbin/mcw_glob.h Xbin/mcw_malloc.h Xbin/model_beta.so Xbin/model_constant.so Xbin/model_convgamma.so Xbin/model_convgamma2a.so Xbin/model_diffexp.so Xbin/model_diffusion.so Xbin/model_gammavar.so Xbin/model_linear.so Xbin/model_null.so Xbin/model_quadratic.so Xbin/model_sinewave_ap.so Xbin/model_sinewave_apf.so Xbin/model_squarewave_ap.so Xbin/model_squarewave_apf.so Xbin/model_trnglwave_ap.so Xbin/model_trnglwave_apf.so Xbin/mpeg_encode Xbin/mpegtoppm Xbin/mrilib.h Xbin/mritopgm Xbin/multivector.h Xbin/myget Xbin/nicat Xbin/nifti1_test Xbin/nifti_stats Xbin/nifti_tool Xbin/niml.h Xbin/nsize Xbin/p2t Xbin/plug_3Ddump_V2.so Xbin/plug_3ddot.so Xbin/plug_3ddup.so Xbin/plug_4Ddump.so Xbin/plug_L1fit.so Xbin/plug_betafit.so Xbin/plug_clust.so Xbin/plug_compress.so Xbin/plug_coorder.so Xbin/plug_copy.so Xbin/plug_crender.so Xbin/plug_deconvolve.so Xbin/plug_delay_V2.so Xbin/plug_drawdset.so Xbin/plug_edit.so Xbin/plug_extract.so Xbin/plug_fourier.so Xbin/plug_hemisub.so Xbin/plug_histog.so Xbin/plug_imreg.so Xbin/plug_lsqfit.so Xbin/plug_maskave.so Xbin/plug_maskcalc.so Xbin/plug_maxima.so Xbin/plug_nlfit.so Xbin/plug_notes.so Xbin/plug_nth_dataset.so Xbin/plug_nudge.so Xbin/rmz Xbin/plug_permtest.so Xbin/plug_power.so Xbin/plug_realtime.so Xbin/plug_rename.so Xbin/plug_render.so Xbin/plug_reorder.so Xbin/plug_retroicor.so Xbin/plug_roiedit.so Xbin/plug_roiplot.so Xbin/plug_scatplot.so Xbin/plug_second_dataset.so Xbin/plug_stats.so Xbin/plug_stavg.so Xbin/plug_tag.so Xbin/plug_threshold.so Xbin/plug_ttget.so Xbin/plug_vol2surf.so Xbin/plug_volreg.so Xbin/plug_wavelets.so Xbin/plug_zeropad.so Xbin/plugout_drive Xbin/plugout_ijk Xbin/plugout_tt Xbin/plugout_tta Xbin/poem_bj1.txt Xbin/poem_eapoe1.txt Xbin/poem_em.txt Xbin/poem_ghm3.txt Xbin/poem_gmh1.txt Xbin/poem_gmh2.txt Xbin/poem_gmh3.txt Xbin/poem_jm1.txt Xbin/poem_pbs1.txt Xbin/poem_pbs2.txt Xbin/poem_rf1.txt Xbin/poem_rk1.txt Xbin/poem_rls1.txt Xbin/poem_ww1.txt Xbin/poem_ww2.txt Xbin/qhull Xbin/quickspec Xbin/rotcom Xbin/rtfeedme Xbin/serial_helper Xbin/sfim Xbin/siemens_vision Xbin/splash_bobkarl.jpg Xbin/splash_earth.jpg Xbin/splash_emars.jpg Xbin/splash_kebb.jpg Xbin/splash_marsalbor.jpg Xbin/splash_mcw03.jpg Xbin/splash_sscc03.jpg Xbin/splash_vincent.jpg Xbin/sqwave Xbin/strblast Xbin/suma Xbin/suma_change_spec Xbin/tagset.h Xbin/tfim Xbin/thd_compress.h Xbin/thd_iochan.h Xbin/thd_maker.h Xbin/to3d Xbin/vecmat.h Xbin/vol2surf.h Xbin/volpack.h Xbin/waver Xbin/whereami Xbin/whirlgif Xbin/TTatlas+tlrc.BRIK.gz Xbin/TTatlas+tlrc.HEAD X@dirrm bin X@dirrm afni_doc END-of-science/afni/pkg-plist exit --Boundary-00=_LofrD7l6fjyx9TS-- From: Jason Bacon To: Emanuel Haupt Cc: bug-followup@FreeBSD.org, bacon@smithers.neuro.mcw.edu Subject: Re: ports/90752: New port: science/afni Analysis of Fucntional NeuroImages Date: Sun, 25 Dec 2005 17:11:47 -0600 --Boundary-00=_0cyrD0ObHn8JQAP Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Sorry to inundate your inbox, but there was one more tweak necessary to complete the build. Please replace the previous shar file with this one. Cheers, Jason On Friday 23 December 2005 04:54, Emanuel Haupt wrote: > Hi Jason, > > Thanks for your submission. > > The port does not respect CC [1] and CFLAGS [2]. If your port needs > gmake you need to pass CC to MAKE_ENV. distinfo should now also contain > SHA256 checksums. You can use 'make makesum' to calculate them. > Attention, using distfile names without a version in it are generally > dangerous, once you re-roll the tarball or update them the port will > fail due to a checksum mismatch. > > Finally please install portlint (devel/portlint) and run it with the > '-A' option and eradicate the fatal warnings. > > [1] > http://www.freebsd.org/doc/en_US.ISO8859-1/books/porters-handbook/dads-cc.h >tml [2] > http://www.freebsd.org/doc/en_US.ISO8859-1/books/porters-handbook/dads-cfla >gs.html > > Thanks in advance, > Emanuel -- Jason W. Bacon Systems Manager, fMRI Research Labs Medical College of Wisconsin 8701 Watertown Plank Rd Room MFRC 4037 Milwaukee, WI 53226 (414) 456-5881 (414) 456-6562 FAX --Boundary-00=_0cyrD0ObHn8JQAP Content-Type: text/plain; charset="iso-8859-1"; name="afni.tree" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="afni.tree" # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # science/afni # science/afni/Makefile # science/afni/pkg-descr # science/afni/distinfo # science/afni/pkg-message # science/afni/pkg-plist # echo c - science/afni mkdir -p science/afni > /dev/null 2>&1 echo x - science/afni/Makefile sed 's/^X//' >science/afni/Makefile << 'END-of-science/afni/Makefile' X############################################################################ X# New ports collection Makefile for: afni X# Date created: 11 Jan 2005 X# Whom: jbacon X# X# $FreeBSD$ X# X X############################################################################ X# www.neuro.mcw.edu has the latest source distribution from which this port X# is built. It will be updated as time permits and necessiaty requires. X# X# afni.nimh.nih.gov is the ultimate source for AFNI, and will always X# contain the latest source release. If this port is not up to date, X# you can download the latest sources and build manually using X# Makefile.BSD, which is included in the source distribution. If the X# Makefile.BSD in the afni source distribution is out of date, as X# occasionally happens, you can download the latest from www.neuro.mcw.edu. X# I regularly submit updates to NIH, but it sometimes takes a while for them X# to get into the distribution. X XPORTNAME= afni XPORTVERSION= 2005.11.18.1920 XCATEGORIES= science graphics biology XMASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/ \ X http://afni.nimh.nih.gov/pub/dist/tgz/ XDISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ X Makefile.BSD TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD XDIST_SUBDIR= AFNI XEXTRACT_ONLY= afni_src.tgz afni_doc.tgz X XMAINTAINER= jbacon@mcw.edu XCOMMENT= Advanced Functional Neuro Imaging X XLIB_DEPENDS= Xm.3:${PORTSDIR}/x11-toolkits/open-motif X XUSE_GMAKE= yes XMAKE_ENV= CC="${CC}" XMAN1= afni.1 X X# Build parameters XWRKSRC= ${WRKDIR}/afni_src XMAKEFILE= Makefile.BSD XALL_TARGET= vastness suma X X# Install parameters XSTRIP= XPREFIX= ${LOCALBASE}/mri/afni XMANCOMPRESSED= yes XNO_MTREE= yes X Xpost-extract: X ${CP} -f ${DISTDIR}/${DIST_SUBDIR}/Makefile.BSD ${WRKSRC} X Xdo-install: X ${MKDIR} ${PREFIX}/bin ${PREFIX}/afni_doc X ${INSTALL_PROGRAM} ${WRKSRC}/BSD/* ${PREFIX}/bin X ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${PREFIX}/bin X ${INSTALL_MAN} ${WRKDIR}/afni_doc/* ${PREFIX}/afni_doc X ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${LOCALBASE}/man/man1 X ${GZIP_CMD} ${LOCALBASE}/man/man1/afni.1 X Xpost-install: X ${CAT} pkg-message X X.include END-of-science/afni/Makefile echo x - science/afni/pkg-descr sed 's/^X//' >science/afni/pkg-descr << 'END-of-science/afni/pkg-descr' XThis is a port of afni, Advanced Functional Neuro Imaging X XWWW: http://www.neuro.mcw.edu/~bacon X X- Jason Xjbacon@mcw.edu END-of-science/afni/pkg-descr echo x - science/afni/distinfo sed 's/^X//' >science/afni/distinfo << 'END-of-science/afni/distinfo' XMD5 (AFNI/afni_src.tgz) = 8f118f55721573feee6efa7bfff64456 XSIZE (AFNI/afni_src.tgz) = 10481603 XMD5 (AFNI/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 XSIZE (AFNI/afni_doc.tgz) = 3267095 XMD5 (AFNI/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e XSIZE (AFNI/afni.1) = 1103 XMD5 (AFNI/Makefile.BSD) = 765ec1dddb0063fbd5310214c065463e XSIZE (AFNI/Makefile.BSD) = 3625 XMD5 (AFNI/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee XSIZE (AFNI/TTatlas+tlrc.BRIK.gz) = 159912 XMD5 (AFNI/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 XSIZE (AFNI/TTatlas+tlrc.HEAD) = 1750 END-of-science/afni/distinfo echo x - science/afni/pkg-message sed 's/^X//' >science/afni/pkg-message << 'END-of-science/afni/pkg-message' X X============================================================================= XUsers will need to have ${PREFIX}/bin in their PATH in order Xto run programs in the AFNI distribution. X XDocumentation can be found in ${PREFIX}/afni_doc. X XThe environment AFNI_PLUGIN_PATH must also be set to the bin directory Xin order to run AFNI plugins. X XEach user is advised to create a .afnirc file in their home directory Xto customize settings. X XFor questions or comments regarding this port, please contact the Xport maintainer: jbacon@mcw.edu X XFor AFNI usage, please visit the AFNI WEB site at http://afni.nimh.nih.gov. X============================================================================= END-of-science/afni/pkg-message echo x - science/afni/pkg-plist sed 's/^X//' >science/afni/pkg-plist << 'END-of-science/afni/pkg-plist' Xafni_doc/1dplot.ps Xafni_doc/24swap.ps Xafni_doc/2dImReg.ps Xafni_doc/2swap.ps Xafni_doc/3T_toafni.ps Xafni_doc/3dANOVA.ps Xafni_doc/3dANOVA2.ps Xafni_doc/3dANOVA3.ps Xafni_doc/3dDeconvolve.ps Xafni_doc/3dExtrema.ps Xafni_doc/3dFDR.ps Xafni_doc/3dFWHM.ps Xafni_doc/3dFriedman.ps Xafni_doc/3dIntracranial.ps Xafni_doc/3dKruskalWallis.ps Xafni_doc/3dMannWhitney.ps Xafni_doc/3dNLfim.ps Xafni_doc/3dRegAna.ps Xafni_doc/3dStatClust.ps Xafni_doc/3dTSgen.ps Xafni_doc/3dTcat.ps Xafni_doc/3dTsmooth.ps Xafni_doc/3dWavelets.ps Xafni_doc/3dWilcoxon.ps Xafni_doc/3daxialize.ps Xafni_doc/3dbuc2fim.ps Xafni_doc/3dbucket.ps Xafni_doc/3dcalc.ps Xafni_doc/3dclust.ps Xafni_doc/3dcolon.ps Xafni_doc/3ddup.ps Xafni_doc/3dfim+.ps Xafni_doc/3dfim.ps Xafni_doc/3dfractionize.ps Xafni_doc/3dhistog.ps Xafni_doc/3dinfo.ps Xafni_doc/3dmaskave.ps Xafni_doc/3dmerge.ps Xafni_doc/3dnewid.ps Xafni_doc/3dnoise.ps Xafni_doc/3dnvals.ps Xafni_doc/3dpc.ps Xafni_doc/3dproject.ps Xafni_doc/3drefit.ps Xafni_doc/3drotate.ps Xafni_doc/3dttest.ps Xafni_doc/3dvolreg.ps Xafni_doc/4swap.ps Xafni_doc/AFNI.changes.cox Xafni_doc/AFNI.changes.rhammett Xafni_doc/AFNI.changes.rickr Xafni_doc/AlphaSim.ps Xafni_doc/AlphaSim_fig.ps Xafni_doc/FD2.ps Xafni_doc/Nonparametric.ps Xafni_doc/README Xafni_doc/README.Ifile Xafni_doc/README.attributes Xafni_doc/README.bzip2 Xafni_doc/README.changes Xafni_doc/README.compression Xafni_doc/README.copyright Xafni_doc/README.driver Xafni_doc/README.environment Xafni_doc/README.func_types Xafni_doc/README.notes Xafni_doc/README.roi Xafni_doc/README.permtest Xafni_doc/README.plugouts Xafni_doc/README.realtime Xafni_doc/README.registration Xafni_doc/README.render_scripts Xafni_doc/README.setup Xafni_doc/README.volreg Xafni_doc/README.web Xafni_doc/README.ziad Xafni_doc/RSFgen.ps Xafni_doc/Table.ps Xafni_doc/abut.ps Xafni_doc/adwarp.ps Xafni_doc/afni200.ps Xafni_doc/afni_aux.ps Xafni_doc/afni_plugins.ps Xafni_doc/afni_register.ps Xafni_doc/buckets.ps Xafni_doc/byteorder.ps Xafni_doc/ccalc.ps Xafni_doc/cdf.ps Xafni_doc/count.ps Xafni_doc/fim2.ps Xafni_doc/float_scan.ps Xafni_doc/from3d.ps Xafni_doc/ftosh.ps Xafni_doc/imand.ps Xafni_doc/imaver.ps Xafni_doc/imcalc.ps Xafni_doc/imdump.ps Xafni_doc/immask.ps Xafni_doc/imreg.ps Xafni_doc/imrotate.ps Xafni_doc/imstack.ps Xafni_doc/imstat.ps Xafni_doc/imupsam.ps Xafni_doc/mritopgm.ps Xafni_doc/nsize.ps Xafni_doc/p2t.ps Xafni_doc/sfim.ps Xafni_doc/sqwave.ps Xafni_doc/tfim.ps Xafni_doc/to3d.ps Xafni_doc/waver.ps Xbin/1dcat Xbin/1ddot Xbin/1deval Xbin/1dfft Xbin/1dgrayplot Xbin/1dnorm Xbin/1dplot Xbin/1dsum Xbin/1dsvd Xbin/1dtranspose Xbin/24swap Xbin/2dImReg Xbin/2swap Xbin/3T_toafni Xbin/3dAFNIto3D Xbin/3dAFNItoANALYZE Xbin/3dAFNItoMINC Xbin/3dAFNItoNIFTI Xbin/3dAFNItoNIML Xbin/3dAFNItoRaw Xbin/3dANALYZEtoAFNI Xbin/3dANOVA Xbin/3dANOVA2 Xbin/3dANOVA3 Xbin/3dAnatNudge Xbin/3dCM Xbin/3dAnhist Xbin/3dAttribute Xbin/3dAutoTcorrelate Xbin/3dAutobox Xbin/3dAutomask Xbin/3dBRAIN_VOYAGERtoAFNI Xbin/3dCRUISEtoAFNI Xbin/3dClipLevel Xbin/3dConvolve Xbin/3dDTeig Xbin/3dDWItoDT Xbin/3dDeconvolve Xbin/3dDeconvolve_f Xbin/3dDespike Xbin/3dDetrend Xbin/3dEntropy Xbin/3dExtrema Xbin/3dFDR Xbin/3dFWHM Xbin/3dFourier Xbin/3dFriedman Xbin/3dIntracranial Xbin/3dKruskalWallis Xbin/3dLRflip Xbin/3dLocalstat Xbin/3dMINCtoAFNI Xbin/3dMannWhitney Xbin/3dMax Xbin/3dMean Xbin/3dMedianFilter Xbin/3dNLfim Xbin/3dNotes Xbin/3dOverlap Xbin/3dROIstats Xbin/3dRegAna Xbin/3dRowFillin Xbin/3dSkullStrip Xbin/3dSpatNorm Xbin/3dStatClust Xbin/3dSurf2Vol Xbin/3dSurfMask Xbin/3dTSgen Xbin/3dTagalign Xbin/3dTcat Xbin/3dTcorrelate Xbin/3dThreetoRGB Xbin/3dToutcount Xbin/3dTqual Xbin/3dTshift Xbin/3dTstat Xbin/3dTsmooth Xbin/3dUndump Xbin/3dUniformize Xbin/3dVol2Surf Xbin/3dWarp Xbin/3dWarpDrive Xbin/3dWavelets Xbin/3dWilcoxon Xbin/3dWinsor Xbin/3dZcat Xbin/3dZcutup Xbin/3dZeropad Xbin/3dZregrid Xbin/3danisosmooth Xbin/3daxialize Xbin/3dbuc2fim Xbin/3dbucket Xbin/3dcalc Xbin/3dclust Xbin/3dcopy Xbin/3ddata.h Xbin/3ddelay Xbin/3ddot Xbin/3ddup Xbin/3dedge3 Xbin/3dfim Xbin/3dfim+ Xbin/3dfractionize Xbin/3dhistog Xbin/3dinfo Xbin/3dmaskave Xbin/3dmaskdump Xbin/3dmaxima Xbin/3dmerge Xbin/3dnewid Xbin/3dnoise Xbin/3dnvals Xbin/3dpc Xbin/3dproject Xbin/3drefit Xbin/3drename Xbin/3dresample Xbin/3dretroicor Xbin/3drotate Xbin/3dttest Xbin/3dvolreg Xbin/4swap Xbin/@4Daverage Xbin/@AfniOrient2RAImap Xbin/@AfniOrientSign Xbin/@Align_Centers Xbin/@Center_Distance Xbin/@FromRAI Xbin/@CheckForAfniDset Xbin/@CommandGlobb Xbin/@DTI_studio_reposition Xbin/@GetAfniOrient Xbin/@GetAfniPrefix Xbin/@GetAfniView Xbin/@NoExt Xbin/@Purify_1D Xbin/@RenamePanga Xbin/@SUMA_AlignToExperiment Xbin/@SUMA_Make_Spec_FS Xbin/@SUMA_Make_Spec_SF Xbin/@ToRAI Xbin/@UpdateAfni Xbin/@VolCenter Xbin/@align_partial_oblique Xbin/@auto_align Xbin/@auto_tlrc Xbin/@clip_volume Xbin/@fix_FSsphere Xbin/@make_stim_file Xbin/@parse_afni_name Xbin/@parse_name Xbin/AlphaSim Xbin/CompareSurfaces Xbin/ConvertDset Xbin/ConvertSurface Xbin/ConvexHull Xbin/CreateIcosahedron Xbin/DTIStudioFibertoSegments Xbin/Dimon Xbin/FD2 Xbin/FSread_annot Xbin/Ifile Xbin/Imon Xbin/IsoSurface Xbin/MakeColorMap Xbin/MapIcosahedron Xbin/ROI2dataset Xbin/ROIgrow Xbin/RSFgen Xbin/SUMA_glxdino Xbin/SUMA_paperplane Xbin/SUMA_pixmap2eps Xbin/Vecwarp Xbin/SampBias Xbin/ScaleToMap Xbin/SurfClust Xbin/SurfMeasures Xbin/SurfPatch Xbin/SurfQual Xbin/SurfSmooth Xbin/SurfToSurf Xbin/SurfaceMetrics Xbin/Xphace Xbin/abut Xbin/adwarp Xbin/afni Xbin/afni_environ.h Xbin/afni_vcheck Xbin/afni_warp.h Xbin/aiv Xbin/byteorder Xbin/cat_matvec Xbin/ccalc Xbin/cdf Xbin/cdflib.h Xbin/cjpeg Xbin/count Xbin/coxplot.h Xbin/cs.h Xbin/cs_sort_template.h Xbin/dicom_hdr Xbin/dicom_to_raw Xbin/djpeg Xbin/editvol.h Xbin/eispack.h Xbin/ent16 Xbin/f2c.h Xbin/face_JimEliassen.jpg Xbin/face_JohannaBaas.jpg Xbin/face_SalloumJB.jpg Xbin/face_ZangYF.jpg Xbin/face_aclark.jpg Xbin/face_adij_mannheim.jpg Xbin/face_afniman.jpg Xbin/face_agoldman.jpg Xbin/face_ahammett.jpg Xbin/face_anewmanetal.jpg Xbin/face_anugent.jpg Xbin/face_asanders.jpg Xbin/face_ashackman.jpg Xbin/face_athomas.jpg Xbin/face_bandettini.jpg Xbin/face_barbaracd.jpg Xbin/face_bargall.jpg Xbin/face_bea.jpg Xbin/face_becky.jpg Xbin/face_bmcnamee.jpg Xbin/face_bodurka.jpg Xbin/face_bprogers.jpg Xbin/face_bridget.jpg Xbin/face_brodmann.jpg Xbin/face_browndyke.jpg Xbin/face_carol.jpg Xbin/face_cbikle.jpg Xbin/face_claudio.jpg Xbin/face_cmoritz.jpg Xbin/face_cmyers.jpg Xbin/face_csenior.jpg Xbin/face_cwettig.jpg Xbin/face_dglen.jpg Xbin/face_einstein.jpg Xbin/face_eli.jpg Xbin/face_ernv.jpg Xbin/face_eteoh.jpg Xbin/face_faustalui.jpg Xbin/face_ftam.jpg Xbin/face_gambero.jpg Xbin/face_gangchen.jpg Xbin/face_gganis.jpg Xbin/face_ggiulietti.jpg Xbin/face_glarkin.jpg Xbin/face_grant.jpg Xbin/face_hanlon.jpg Xbin/face_heekeren.jpg Xbin/face_hoffmangobbini.jpg Xbin/face_ibitter.jpg Xbin/face_ilevy.jpg Xbin/face_imukai.jpg Xbin/fftest Xbin/face_jbinder.jpg Xbin/face_jbjork.jpg Xbin/face_jchoi.jpg Xbin/face_jigokudani.jpg Xbin/face_jkurata.jpg Xbin/face_jskipper.jpg Xbin/face_jweisberg.jpg Xbin/face_kastnerlab.jpg Xbin/face_kebb.jpg Xbin/face_kkwong.jpg Xbin/face_kropella.jpg Xbin/face_kschreiber.jpg Xbin/face_kuba.jpg Xbin/face_lask.jpg Xbin/face_laura.jpg Xbin/face_lincoln1.jpg Xbin/face_lincoln2.jpg Xbin/face_lindachao.jpg Xbin/face_lizyoder.jpg Xbin/face_ljcox.jpg Xbin/face_llatour.jpg Xbin/face_lmccall.jpg Xbin/face_locikidsucsd.jpg Xbin/face_lukas.jpg Xbin/face_mamann.jpg Xbin/face_maxwell.jpg Xbin/face_mbeauchamp.jpg Xbin/face_mbelmonte.jpg Xbin/face_megcrew.jpg Xbin/face_mgarolera.jpg Xbin/face_mkenney.jpg Xbin/face_mmaieron.jpg Xbin/face_mmk.jpg Xbin/face_mpinsk.jpg Xbin/face_mruppe.jpg Xbin/face_mscohen.jpg Xbin/face_notspm.jpg Xbin/face_pchristidis.jpg Xbin/face_phoebechan.jpg Xbin/face_prowser.jpg Xbin/face_psfb.jpg Xbin/face_qiulin.jpg Xbin/face_rabeauchamp.jpg Xbin/face_rbirn.jpg Xbin/face_rhammett.jpg Xbin/face_rhenderson.jpg Xbin/face_rhoge.jpg Xbin/face_richd.jpg Xbin/face_rjsquirrel.jpg Xbin/face_rprost.jpg Xbin/face_rreynolds.jpg Xbin/face_rwcox.jpg Xbin/face_rwcox2.jpg Xbin/face_rwcox3.jpg Xbin/face_rwcox4.jpg Xbin/face_rwcox5.jpg Xbin/face_rwcox6.jpg Xbin/face_sjapee.jpg Xbin/face_saccanch.jpg Xbin/face_skammy.jpg Xbin/face_skapdoskar.jpg Xbin/face_smarrett.jpg Xbin/face_ssaad.jpg Xbin/face_ssmall.jpg Xbin/face_steverao.jpg Xbin/face_tolkien.jpg Xbin/face_vhradil.jpg Xbin/face_vincent1.jpg Xbin/face_vincent2.jpg Xbin/face_vincent3.jpg Xbin/face_vincent4.jpg Xbin/face_vnapadow.jpg Xbin/face_wapostman1.jpg Xbin/face_wapostman2.jpg Xbin/face_wmluh.jpg Xbin/face_wpostman.jpg Xbin/face_zsaad.jpg Xbin/face_zzzdini.jpg Xbin/face_zzzsunbrain.jpg Xbin/file_tool Xbin/fim2 Xbin/float_scan Xbin/from3d Xbin/ftosh Xbin/ge_header Xbin/im2niml Xbin/imand Xbin/imaver Xbin/imcalc Xbin/imcutup Xbin/imdump Xbin/immask Xbin/imreg Xbin/imrotate Xbin/imstack Xbin/imstat Xbin/imupsam Xbin/inspec Xbin/killer.h Xbin/libSUMA.a Xbin/libcoxplot.a Xbin/libf2c.a Xbin/libmri.a Xbin/libmrix.a Xbin/libvolpack.a Xbin/machdep.h Xbin/mayo_analyze Xbin/mcw_glob.h Xbin/mcw_malloc.h Xbin/model_beta.so Xbin/model_constant.so Xbin/model_convgamma.so Xbin/model_convgamma2a.so Xbin/model_diffexp.so Xbin/model_diffusion.so Xbin/model_gammavar.so Xbin/model_linear.so Xbin/model_null.so Xbin/model_quadratic.so Xbin/model_sinewave_ap.so Xbin/model_sinewave_apf.so Xbin/model_squarewave_ap.so Xbin/model_squarewave_apf.so Xbin/model_trnglwave_ap.so Xbin/model_trnglwave_apf.so Xbin/mpeg_encode Xbin/mpegtoppm Xbin/mrilib.h Xbin/mritopgm Xbin/multivector.h Xbin/myget Xbin/nicat Xbin/nifti1_test Xbin/nifti_stats Xbin/nifti_tool Xbin/niml.h Xbin/nsize Xbin/p2t Xbin/plug_3Ddump_V2.so Xbin/plug_3ddot.so Xbin/plug_3ddup.so Xbin/plug_4Ddump.so Xbin/plug_L1fit.so Xbin/plug_betafit.so Xbin/plug_clust.so Xbin/plug_compress.so Xbin/plug_coorder.so Xbin/plug_copy.so Xbin/plug_crender.so Xbin/plug_deconvolve.so Xbin/plug_delay_V2.so Xbin/plug_drawdset.so Xbin/plug_edit.so Xbin/plug_extract.so Xbin/plug_fourier.so Xbin/plug_hemisub.so Xbin/plug_histog.so Xbin/plug_imreg.so Xbin/plug_lsqfit.so Xbin/plug_maskave.so Xbin/plug_maskcalc.so Xbin/plug_maxima.so Xbin/plug_nlfit.so Xbin/plug_notes.so Xbin/plug_nth_dataset.so Xbin/plug_nudge.so Xbin/rmz Xbin/plug_permtest.so Xbin/plug_power.so Xbin/plug_realtime.so Xbin/plug_rename.so Xbin/plug_render.so Xbin/plug_reorder.so Xbin/plug_retroicor.so Xbin/plug_roiedit.so Xbin/plug_roiplot.so Xbin/plug_scatplot.so Xbin/plug_second_dataset.so Xbin/plug_stats.so Xbin/plug_stavg.so Xbin/plug_tag.so Xbin/plug_threshold.so Xbin/plug_ttget.so Xbin/plug_vol2surf.so Xbin/plug_volreg.so Xbin/plug_wavelets.so Xbin/plug_zeropad.so Xbin/plugout_drive Xbin/plugout_ijk Xbin/plugout_tt Xbin/plugout_tta Xbin/poem_bj1.txt Xbin/poem_eapoe1.txt Xbin/poem_em.txt Xbin/poem_ghm3.txt Xbin/poem_gmh1.txt Xbin/poem_gmh2.txt Xbin/poem_gmh3.txt Xbin/poem_jm1.txt Xbin/poem_pbs1.txt Xbin/poem_pbs2.txt Xbin/poem_rf1.txt Xbin/poem_rk1.txt Xbin/poem_rls1.txt Xbin/poem_ww1.txt Xbin/poem_ww2.txt Xbin/qhull Xbin/quickspec Xbin/rotcom Xbin/rtfeedme Xbin/serial_helper Xbin/sfim Xbin/siemens_vision Xbin/splash_bobkarl.jpg Xbin/splash_earth.jpg Xbin/splash_emars.jpg Xbin/splash_kebb.jpg Xbin/splash_marsalbor.jpg Xbin/splash_mcw03.jpg Xbin/splash_sscc03.jpg Xbin/splash_vincent.jpg Xbin/sqwave Xbin/strblast Xbin/suma Xbin/suma_change_spec Xbin/tagset.h Xbin/tfim Xbin/thd_compress.h Xbin/thd_iochan.h Xbin/thd_maker.h Xbin/to3d Xbin/vecmat.h Xbin/vol2surf.h Xbin/volpack.h Xbin/waver Xbin/whereami Xbin/whirlgif Xbin/TTatlas+tlrc.BRIK.gz Xbin/TTatlas+tlrc.HEAD X@dirrm bin X@dirrm afni_doc END-of-science/afni/pkg-plist exit --Boundary-00=_0cyrD0ObHn8JQAP-- From: Emanuel Haupt To: Jason Bacon Cc: bug-followup@FreeBSD.org Subject: Re: ports/90752: New port: science/afni Analysis of Fucntional NeuroImages Date: Mon, 26 Dec 2005 16:19:50 +0100 --Signature=_Mon__26_Dec_2005_16_19_50_+0100_9dX33hb7_xL7wsGi Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi Jason > [snip] > > > The port does not respect CC [1] and CFLAGS [2].=20 >=20 > I assume you're referring to Makefile.BSD here, which I've updated to > respect CC. This is the only thing in the AFNI distribution that I > can tamper with, and it must be maintained in a format usable outside > the FreeBSD ports system for those who choose to build manually.=20 > Note that most of the work in building AFNI is done by > Makefile.INCLUDE, the universal portion of the AFNI make setup that > Makefile.BSD, et. al. set the environment for. It ignores CFLAGS > entirely, and suggesting any changes to it is not likely to be=20 > fruitful, so I had to tack flags directly onto CC in Makefile.BSD.=20 > This may seem a little kludgey, but I don't see a better solution at > the moment. You can either modify 'Makefile.INCLUDE' with a REINPLACE_CMD statement in the post-patch section or if the modifications are more complex with a unified patch (diff -uN) in 'files/'. If standard CFLAGS should fail for any reason try to figure out if you maybe can fix the problem otherwise (or ask me) if not, try to figure out if it fails to build on 4.x/5.x/6.x and add non-standard CFLAGS for the according version only. A good way to test this is adding something like -DYEAHWERESPECTCFLAGS to CFLAGS in /etc/make.conf. > > If your port needs=20 > > gmake you need to pass CC to MAKE_ENV.=20 >=20 > Added this to the port Makefile. This alone does not solve the CC ignorance (see [1] -> 'VAR=3Dfoo' vs 'VAR+=3Dfoo'). > > distinfo should now also contain=20 > > SHA256 checksums. You can use 'make makesum' to calculate them. >=20 > Had already done that. Did you run into checksum problems? No, your distinfo file only contains MD5 checksum, new ports also need SHA256 hashes. > > Attention, using distfile names without a version in it are > > generally dangerous, once you re-roll the tarball or update them the > > port will fail due to a checksum mismatch. >=20 > I'd already thought of this, but I'm not sure what the best solution > would be. =20 >=20 > I doubt the author of AFNI will want to start adding version numbers > on his site. I *could* remove it from MASTER_SITES and list only my > own copy, with version numbers added. Would it be acceptable not > having the original download site in MASTER_SITES? This would be acceptable. Another solution would be mirroring the files without renaming them and add your mirror as second master site. That way modifications on the authors mastersite will cause the port to try the second mastersite. Some of our distfile furies or fenners distfile survey [2] will then notify you in case you don't notice it first :-) > > Finally please install portlint (devel/portlint) and run it with the > > '-A' option and eradicate the fatal warnings. >=20 > Done. Thanks in advance for a new shell archive. Happy holidays to you too, Emanuel References: [1] http://www.freebsd.org/doc/en_US.ISO8859-1/books/porters-handbook/dads-= cc.html [2] http://people.freebsd.org/~fenner/portsurvey/ --=20 GnuPG key id: 0x55E67774 Download: http://pgp.mit.edu:11371 Key fingerprint: 17B3 FD8F BA68 4AB4 10FD A9D1 AD52 6588 55E6 7774 --Signature=_Mon__26_Dec_2005_16_19_50_+0100_9dX33hb7_xL7wsGi Content-Type: application/pgp-signature -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (FreeBSD) iD8DBQFDsAoarVJliFXmd3QRAt5PAJ0ZWXNyjyX1UmwdqK3ZAbSCwPGuIQCgqp9v T1MnVIf4McUSY0f/RC0Oo9A= =aWh+ -----END PGP SIGNATURE----- --Signature=_Mon__26_Dec_2005_16_19_50_+0100_9dX33hb7_xL7wsGi-- State-Changed-From-To: feedback->open State-Changed-By: ehaupt State-Changed-When: Fri Jan 6 20:16:15 CET 2006 State-Changed-Why: Feedback received. http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 State-Changed-From-To: open->feedback State-Changed-By: ehaupt State-Changed-When: Sun Jan 8 01:44:00 CET 2006 State-Changed-Why: Awaiting maintainer feedback. http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 Responsible-Changed-From-To: ehaupt->freebsd-ports-bugs Responsible-Changed-By: ehaupt Responsible-Changed-When: Sat Jan 14 15:09:55 CET 2006 Responsible-Changed-Why: Back to the queue, I will be away for the next 3 weeks. http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 From: Jason Bacon To: Emanuel Haupt Cc: bug-followup@FreeBSD.org Subject: Re: ports/90752: New port: science/afni Analysis of Fucntional NeuroImages Date: Mon, 23 Jan 2006 23:19:52 -0600 --Boundary-00=_5jb1DZHX13yoXJe Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Alrightythen... The attached shar file should be pretty close, if not there. It comes up clean with portlint -A, and I tested it on 4.11, 5.4, and 6.0, and made sure deinstall cleans up completely. I still use a ${PREFIX} of ${LOCALBASE}/mri/afni, since the MRI research community is accustomed to software installations having their own directories. If you think it's more important to follow ports convention and have it default to ${LOCALBASE}, it should be OK. I've done my best to eliminate any potential collisions in bin and lib. Thanks, Jason -- Jason W. Bacon Systems Manager, fMRI Research Labs Medical College of Wisconsin 8701 Watertown Plank Rd Room MFRC 4037 Milwaukee, WI 53226 (414) 456-5881 (414) 456-6562 FAX --Boundary-00=_5jb1DZHX13yoXJe Content-Type: text/plain; charset="iso-8859-1"; name="afni.shar" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="afni.shar" # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # afni # afni/Makefile # afni/distinfo # afni/pkg-descr # afni/pkg-message # afni/pkg-plist # echo c - afni mkdir -p afni > /dev/null 2>&1 echo x - afni/Makefile sed 's/^X//' >afni/Makefile << 'END-of-afni/Makefile' X############################################################################ X# Ports collection Makefile for: afni X# Date created: 11 Jan 2005 X# Whom: bacon@smithers.neuro.mcw.edu X# X# $FreeBSD$ X# X X############################################################################ X# www.neuro.mcw.edu has the latest source distribution from which this port X# is built. It will be updated as time permits. X# X# afni.nimh.nih.gov is the ultimate source for AFNI, and will always X# contain the latest source release. If this port is not up to date, X# you can download the latest sources and build manually using X# Makefile.BSD, which is included in the source distribution. X XPORTNAME= afni XPORTVERSION= 2005.12.30.0934 XCATEGORIES= science biology graphics XMASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/ XDISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ X Makefile.FreeBSD_PORT TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD XDIST_SUBDIR= AFNI XEXTRACT_ONLY= afni_src.tgz afni_doc.tgz X XMAINTAINER= bacon@smithers.neuro.mcw.edu XCOMMENT= Advanced Functional Neuro Imaging X XBUILD_DEPENDS= gettext:${PORTSDIR}/devel/gettext XRUN_DEPENDS= cjpeg:${PORTSDIR}/graphics/jpeg \ X mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \ X whirlgif:${PORTSDIR}/graphics/whirlgif X XUSE_GMAKE= yes XUSE_ICONV= yes XUSE_MOTIF= yes XMAKE_ENV= CC="${CC}" X XWRKSRC= ${WRKDIR}/afni_src XMAKEFILE= Makefile.FreeBSD_PORT XALL_TARGET= vastness suma X X########################################################################### X# Install parameters X X# Stop INSTALL_PROGRAM from stripping debug info from binaries. XSTRIP= XPREFIX= ${LOCALBASE}/mri/afni XMANCOMPRESSED= no XMAN1= afni.1 X XINSTALL_WRKSRC= ${WRKSRC}/BSD XINSTALL_TEMP= ${WRKSRC}/Backup.BSD XNO_MTREE= yes X Xpost-extract: X ${CP} -f ${DISTDIR}/${DIST_SUBDIR}/Makefile.FreeBSD_PORT ${WRKSRC} X Xdo-install: X ${MKDIR} ${PREFIX}/bin ${PREFIX}/man/man1 ${PREFIX}/lib \ X ${PREFIX}/include ${DATADIR} ${DOCSDIR} ${INSTALL_TEMP} X ${MV} ${INSTALL_WRKSRC}/libf2c.a ${INSTALL_TEMP} X ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.so ${INSTALL_WRKSRC}/*.a \ X ${PREFIX}/lib X ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.h ${PREFIX}/include X ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.jpg ${INSTALL_WRKSRC}/*.txt \ X ${DATADIR} X ${MV} ${INSTALL_WRKSRC}/*.so \ X ${INSTALL_WRKSRC}/*.a \ X ${INSTALL_WRKSRC}/*.h \ X ${INSTALL_WRKSRC}/*.jpg \ X ${INSTALL_WRKSRC}/*.txt \ X ${INSTALL_WRKSRC}/cjpeg \ X ${INSTALL_WRKSRC}/djpeg \ X ${INSTALL_WRKSRC}/mpeg_encode \ X ${INSTALL_WRKSRC}/whirlgif \ X ${INSTALL_TEMP} X ${INSTALL_PROGRAM} ${INSTALL_WRKSRC}/* ${PREFIX}/bin X ${MV} ${INSTALL_TEMP}/* ${INSTALL_WRKSRC} X ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR} X ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${PREFIX}/man/man1 X.if !defined(NOPORTDOCS) X ${INSTALL_DATA} ${WRKDIR}/afni_doc/* ${DOCSDIR} X.endif X Xpost-install: X ${CAT} pkg-message X X.include END-of-afni/Makefile echo x - afni/distinfo sed 's/^X//' >afni/distinfo << 'END-of-afni/distinfo' XMD5 (AFNI/afni_src.tgz) = e6daf296ad9c5dd0284239e934ea701e XSHA256 (AFNI/afni_src.tgz) = 949a6960e89f2b140207e61fd45b265b03232c4956aaa57271779dcd492aff89 XSIZE (AFNI/afni_src.tgz) = 10512539 XMD5 (AFNI/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 XSHA256 (AFNI/afni_doc.tgz) = 28bfcb085d97f63a7e6b753d784908d7f90d9d3ba735d96b18c1e893af4d6cd1 XSIZE (AFNI/afni_doc.tgz) = 3267095 XMD5 (AFNI/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e XSHA256 (AFNI/afni.1) = f14991934a8b78f2497cd1d0f48b849c1a6debef01c666eafd70993ba63c99da XSIZE (AFNI/afni.1) = 1103 XMD5 (AFNI/Makefile.FreeBSD_PORT) = 5a22ac13683686b6919415bef3784af1 XSHA256 (AFNI/Makefile.FreeBSD_PORT) = 0adbd36cedfc2dac76535fe621349a45e9812709eb5b2768427fffda9b42c628 XSIZE (AFNI/Makefile.FreeBSD_PORT) = 3002 XMD5 (AFNI/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee XSHA256 (AFNI/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd XSIZE (AFNI/TTatlas+tlrc.BRIK.gz) = 159912 XMD5 (AFNI/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 XSHA256 (AFNI/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919 XSIZE (AFNI/TTatlas+tlrc.HEAD) = 1750 END-of-afni/distinfo echo x - afni/pkg-descr sed 's/^X//' >afni/pkg-descr << 'END-of-afni/pkg-descr' XThis is a port of AFNI, Advanced Functional Neuro Imaging. AFNI is Xa tool for analyzing 3 dimensional images, especially functional MRI Ximages used in brain mapping research. X XWWW: http://afni.nimh.nih.gov/ X XPort maintainer: X Jason W. Bacon X bacon@smithers.neuro.mcw.edu END-of-afni/pkg-descr echo x - afni/pkg-message sed 's/^X//' >afni/pkg-message << 'END-of-afni/pkg-message' X============================================================================= XUsers must have ${PREFIX}/bin in their PATH in order Xto run programs in the AFNI distribution. X X${PREFIX}/man must be in MANPATH for the afni man page to be viewable. X XPostscript documentation and READMEs can be found in ${DOCSDIR}. X XThe environment variable AFNI_PLUGIN_PATH must contain X"${PREFIX}/lib:${PREFIX}/share/afni" in order to run AFNI plugins Xand view splash images. X XFor questions or comments regarding the FreeBSD port, please contact the Xport maintainer: X Xbacon@smithers.neuro.mcw.edu X XFor AFNI configuration and usage, please visit the AFNI WEB site at X Xhttp://afni.nimh.nih.gov. X============================================================================= END-of-afni/pkg-message echo x - afni/pkg-plist sed 's/^X//' >afni/pkg-plist << 'END-of-afni/pkg-plist' Xbin/1dcat Xbin/1ddot Xbin/1deval Xbin/1dfft Xbin/1dgrayplot Xbin/1dnorm Xbin/1dplot Xbin/1dsum Xbin/1dsvd Xbin/1dtranspose Xbin/24swap Xbin/2dImReg Xbin/2swap Xbin/3T_toafni Xbin/3dAFNIto3D Xbin/3dAFNItoANALYZE Xbin/3dAFNItoMINC Xbin/3dAFNItoNIFTI Xbin/3dAFNItoNIML Xbin/3dAFNItoRaw Xbin/3dANALYZEtoAFNI Xbin/3dANOVA Xbin/3dANOVA2 Xbin/3dANOVA3 Xbin/3dAnatNudge Xbin/3dAnhist Xbin/3dAttribute Xbin/3dAutoTcorrelate Xbin/3dAutobox Xbin/3dAutomask Xbin/3dBRAIN_VOYAGERtoAFNI Xbin/3dCM Xbin/3dCRUISEtoAFNI Xbin/3dClipLevel Xbin/3dConvolve Xbin/3dDTeig Xbin/3dDWItoDT Xbin/3dDeconvolve Xbin/3dDeconvolve_f Xbin/3dDespike Xbin/3dDetrend Xbin/3dEntropy Xbin/3dExtrema Xbin/3dFDR Xbin/3dFWHM Xbin/3dFourier Xbin/3dFriedman Xbin/3dIntracranial Xbin/3dKruskalWallis Xbin/3dLRflip Xbin/3dLocalstat Xbin/3dMINCtoAFNI Xbin/3dMannWhitney Xbin/3dMax Xbin/3dMean Xbin/3dMedianFilter Xbin/3dNLfim Xbin/3dNotes Xbin/3dOverlap Xbin/3dROIstats Xbin/3dRegAna Xbin/3dRowFillin Xbin/3dSkullStrip Xbin/3dSpatNorm Xbin/3dStatClust Xbin/3dSurf2Vol Xbin/3dSurfMask Xbin/3dTSgen Xbin/3dTagalign Xbin/3dTcat Xbin/3dTcorrelate Xbin/3dThreetoRGB Xbin/3dToutcount Xbin/3dTqual Xbin/3dTshift Xbin/3dTsmooth Xbin/3dTstat Xbin/3dUndump Xbin/3dUniformize Xbin/3dVol2Surf Xbin/3dWarp Xbin/3dWarpDrive Xbin/3dWavelets Xbin/3dWilcoxon Xbin/3dWinsor Xbin/3dZcat Xbin/3dZcutup Xbin/3dZeropad Xbin/3dZregrid Xbin/3danisosmooth Xbin/3daxialize Xbin/3dbuc2fim Xbin/3dbucket Xbin/3dcalc Xbin/3dclust Xbin/3dcopy Xbin/3ddelay Xbin/3ddot Xbin/3ddup Xbin/3dedge3 Xbin/3dfim Xbin/3dfim+ Xbin/3dfractionize Xbin/3dhistog Xbin/3dinfo Xbin/3dmaskave Xbin/3dmaskdump Xbin/3dmaxima Xbin/3dmerge Xbin/3dnewid Xbin/3dnoise Xbin/3dnvals Xbin/3dpc Xbin/3dproject Xbin/3drefit Xbin/3drename Xbin/3dresample Xbin/3dretroicor Xbin/3drotate Xbin/3dttest Xbin/3dvolreg 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http://www.freebsd.org/cgi/query-pr.cgi?pr=90752 >Unformatted: