From owner-freebsd-ports-bugs@FreeBSD.ORG Wed May 17 16:00:59 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 4D48716A7DE for ; Wed, 17 May 2006 16:00:59 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 2DB6C43D9A for ; Wed, 17 May 2006 16:00:41 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k4HG0fF6002807 for ; Wed, 17 May 2006 16:00:41 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k4HG0fvJ002806; Wed, 17 May 2006 16:00:41 GMT (envelope-from gnats) Resent-Date: Wed, 17 May 2006 16:00:41 GMT Resent-Message-Id: <200605171600.k4HG0fvJ002806@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Jason Bacon Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 17CF316A84C for ; Wed, 17 May 2006 15:58:10 +0000 (UTC) (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 5FCE643D48 for ; Wed, 17 May 2006 15:58:07 +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 k4HFw6ag053543 for ; Wed, 17 May 2006 10:58:06 -0500 (CDT) (envelope-from bacon@smithers.neuro.mcw.edu) Received: (from bacon@localhost) by smithers.neuro.mcw.edu (8.13.3/8.13.3/Submit) id k4HFw6O9053542; Wed, 17 May 2006 10:58:06 -0500 (CDT) (envelope-from bacon) Message-Id: <200605171558.k4HFw6O9053542@smithers.neuro.mcw.edu> Date: Wed, 17 May 2006 10:58:06 -0500 (CDT) From: Jason Bacon To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/97404: [maintainer update] science/afni update X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Jason Bacon List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 17 May 2006 16:01:04 -0000 >Number: 97404 >Category: ports >Synopsis: [maintainer update] science/afni update >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Wed May 17 16:00:40 GMT 2006 >Closed-Date: >Last-Modified: >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: Update science/afni to new version of software. >How-To-Repeat: >Fix: diff -ruN /usr/ports/science/afni/Makefile afni/Makefile --- /usr/ports/science/afni/Makefile Sat Apr 15 13:24:01 2006 +++ afni/Makefile Thu May 4 12:16:03 2006 @@ -3,7 +3,7 @@ # Date created: 11 Jan 2005 # Whom: bacon@smithers.neuro.mcw.edu # -# $FreeBSD: ports/science/afni/Makefile,v 1.5 2006/04/15 18:24:01 arved Exp $ +# $FreeBSD: ports/science/afni/Makefile,v 1.4 2006/02/13 10:24:18 vd Exp $ # ############################################################################ @@ -16,13 +16,14 @@ # Makefile.BSD, which is included in the source distribution. PORTNAME= afni -PORTVERSION= 2005.12.30.0934.2 +PORTVERSION= 2006.03.21.1314 CATEGORIES= science biology graphics -MASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/${PORTVERSION}/ -DISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ - Makefile.FreeBSD_PORT TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD +MASTER_SITES= http://afni.nimh.nih.gov/pub/dist/tgz/ \ + http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/${PORTVERSION}/ +DISTFILES= afni_src.tgz afni_doc.tgz afni.1 Makefile.FreeBSD_PORT \ + TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD CA_EZ_v1.3b-Mar1506.tgz DIST_SUBDIR= AFNI-${PORTVERSION} -EXTRACT_ONLY= afni_src.tgz afni_doc.tgz +EXTRACT_ONLY= afni_src.tgz afni_doc.tgz CA_EZ_v1.3b-Mar1506.tgz MAINTAINER= bacon@smithers.neuro.mcw.edu COMMENT= Advanced Functional Neuro Imaging @@ -35,7 +36,8 @@ RUN_DEPENDS= cjpeg:${PORTSDIR}/graphics/jpeg \ mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \ - whirlgif:${PORTSDIR}/graphics/whirlgif + whirlgif:${PORTSDIR}/graphics/whirlgif \ + ppmtogif:${PORTSDIR}/graphics/netpbm USE_GETTEXT= yes USE_GMAKE= yes @@ -85,9 +87,11 @@ @clip_volume \ @fix_FSsphere \ @make_stim_file \ + @np \ @parse_afni_name \ @parse_name \ - suma_change_spec \ + 3dMax \ + suma_change_spec PLIST_FILES+= ${SCRIPTS:S|^|bin/|} @@ -122,6 +126,7 @@ .endfor ${INSTALL_PROGRAM} ${INSTALL_WRKSRC}/* ${PREFIX}/bin ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR} + ${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.3b-Mar1506/* ${DATADIR} ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${PREFIX}/man/man1 @${MV} ${INSTALL_TEMP}/* ${INSTALL_WRKSRC} .if !defined(NOPORTDOCS) diff -ruN /usr/ports/science/afni/distinfo afni/distinfo --- /usr/ports/science/afni/distinfo Sat Apr 15 13:24:01 2006 +++ afni/distinfo Wed May 17 10:42:08 2006 @@ -1,18 +1,21 @@ -MD5 (AFNI-2005.12.30.0934.2/afni_src.tgz) = 3c711d3ba5295953f0e8acbb3062ab65 -SHA256 (AFNI-2005.12.30.0934.2/afni_src.tgz) = a7341ffa0f8725cd0c7bc3bd9ccb097d05ec5d56b60f92037a5f8a5e0d0e6316 -SIZE (AFNI-2005.12.30.0934.2/afni_src.tgz) = 10863304 -MD5 (AFNI-2005.12.30.0934.2/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 -SHA256 (AFNI-2005.12.30.0934.2/afni_doc.tgz) = 28bfcb085d97f63a7e6b753d784908d7f90d9d3ba735d96b18c1e893af4d6cd1 -SIZE (AFNI-2005.12.30.0934.2/afni_doc.tgz) = 3267095 -MD5 (AFNI-2005.12.30.0934.2/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e -SHA256 (AFNI-2005.12.30.0934.2/afni.1) = f14991934a8b78f2497cd1d0f48b849c1a6debef01c666eafd70993ba63c99da -SIZE (AFNI-2005.12.30.0934.2/afni.1) = 1103 -MD5 (AFNI-2005.12.30.0934.2/Makefile.FreeBSD_PORT) = 77fd9306b8e5c73c555edcf04aeaf562 -SHA256 (AFNI-2005.12.30.0934.2/Makefile.FreeBSD_PORT) = f29118dbe49cc95de62a6b3ca2b31cfae0017247854d764dc5e0069ed58f589b -SIZE (AFNI-2005.12.30.0934.2/Makefile.FreeBSD_PORT) = 3101 -MD5 (AFNI-2005.12.30.0934.2/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee -SHA256 (AFNI-2005.12.30.0934.2/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd -SIZE (AFNI-2005.12.30.0934.2/TTatlas+tlrc.BRIK.gz) = 159912 -MD5 (AFNI-2005.12.30.0934.2/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 -SHA256 (AFNI-2005.12.30.0934.2/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919 -SIZE (AFNI-2005.12.30.0934.2/TTatlas+tlrc.HEAD) = 1750 +MD5 (AFNI-2006.03.21.1314/afni_src.tgz) = 8af3ae355ba30d802ebc60a826ee5f6c +SHA256 (AFNI-2006.03.21.1314/afni_src.tgz) = 74a991f8689d4e717956d292552cb300fa574e33819941b7719b3390f9c9bfc3 +SIZE (AFNI-2006.03.21.1314/afni_src.tgz) = 10931595 +MD5 (AFNI-2006.03.21.1314/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 +SHA256 (AFNI-2006.03.21.1314/afni_doc.tgz) = 28bfcb085d97f63a7e6b753d784908d7f90d9d3ba735d96b18c1e893af4d6cd1 +SIZE (AFNI-2006.03.21.1314/afni_doc.tgz) = 3267095 +MD5 (AFNI-2006.03.21.1314/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e +SHA256 (AFNI-2006.03.21.1314/afni.1) = f14991934a8b78f2497cd1d0f48b849c1a6debef01c666eafd70993ba63c99da +SIZE (AFNI-2006.03.21.1314/afni.1) = 1103 +MD5 (AFNI-2006.03.21.1314/Makefile.FreeBSD_PORT) = 77fd9306b8e5c73c555edcf04aeaf562 +SHA256 (AFNI-2006.03.21.1314/Makefile.FreeBSD_PORT) = f29118dbe49cc95de62a6b3ca2b31cfae0017247854d764dc5e0069ed58f589b +SIZE (AFNI-2006.03.21.1314/Makefile.FreeBSD_PORT) = 3101 +MD5 (AFNI-2006.03.21.1314/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee +SHA256 (AFNI-2006.03.21.1314/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd +SIZE (AFNI-2006.03.21.1314/TTatlas+tlrc.BRIK.gz) = 159912 +MD5 (AFNI-2006.03.21.1314/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 +SHA256 (AFNI-2006.03.21.1314/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919 +SIZE (AFNI-2006.03.21.1314/TTatlas+tlrc.HEAD) = 1750 +MD5 (AFNI-2006.03.21.1314/CA_EZ_v1.3b-Mar1506.tgz) = a66e4abb3385878a945351e761d12723 +SHA256 (AFNI-2006.03.21.1314/CA_EZ_v1.3b-Mar1506.tgz) = c9e884370a1580b1101c01f44cc76f81fc0fd64af7796b76762091ee9de4feed +SIZE (AFNI-2006.03.21.1314/CA_EZ_v1.3b-Mar1506.tgz) = 2645818 diff -ruN /usr/ports/science/afni/pkg-message afni/pkg-message --- /usr/ports/science/afni/pkg-message Wed Dec 31 18:00:00 1969 +++ afni/pkg-message Fri Jan 6 09:49:01 2006 @@ -0,0 +1,21 @@ +============================================================================= +Users must have ${PREFIX}/${AFNI}/bin in their PATH in order +to run programs in the AFNI distribution. + +Documentation can be found in ${PREFIX}/${AFNI}/afni_doc. + +The environment variable AFNI_PLUGIN_PATH must also be set to +${PREFIX}/${AFNI}/bin in order to run AFNI plugins. + +Each user is advised to create a .afnirc file in their home directory +to customize settings. + +For questions or comments regarding the FreeBSD port, please contact the +port maintainer: + +bacon@smithers.neuro.mcw.edu + +For AFNI configuration and usage, please visit the AFNI WEB site at + +http://afni.nimh.nih.gov. +============================================================================= diff -ruN /usr/ports/science/afni/pkg-plist afni/pkg-plist --- /usr/ports/science/afni/pkg-plist Sat Apr 15 13:24:01 2006 +++ afni/pkg-plist Thu May 4 12:24:31 2006 @@ -3,6 +3,7 @@ bin/1deval bin/1dfft bin/1dgrayplot +bin/1dmatcalc bin/1dnorm bin/1dplot bin/1dsum @@ -11,7 +12,6 @@ bin/24swap bin/2dImReg bin/2swap -bin/3T_toafni bin/3dAFNIto3D bin/3dAFNItoANALYZE bin/3dAFNItoMINC @@ -29,6 +29,7 @@ bin/3dAutobox bin/3dAutomask bin/3dBRAIN_VOYAGERtoAFNI +bin/3dBrickStat bin/3dCM bin/3dCRUISEtoAFNI bin/3dClipLevel @@ -47,12 +48,12 @@ bin/3dFriedman bin/3dGetrow bin/3dIntracranial +bin/3dInvFMRI bin/3dKruskalWallis bin/3dLRflip bin/3dLocalstat bin/3dMINCtoAFNI bin/3dMannWhitney -bin/3dMax bin/3dMean bin/3dMedianFilter bin/3dNLfim @@ -76,6 +77,7 @@ bin/3dTshift bin/3dTsmooth bin/3dTstat +bin/3dTwotoComplex bin/3dUndump bin/3dUniformize bin/3dVol2Surf @@ -106,6 +108,7 @@ bin/3dinfo bin/3dmaskave bin/3dmaskdump +bin/3dmatcalc bin/3dmaxima bin/3dmerge bin/3dnewid @@ -309,6 +312,18 @@ lib/plug_volreg.so lib/plug_wavelets.so lib/plug_zeropad.so +%%DATADIR%%/Dist_Stamp +%%DATADIR%%/Readme_dist +%%DATADIR%%/TT_N27+tlrc.BRIK.gz +%%DATADIR%%/TT_N27+tlrc.HEAD +%%DATADIR%%/TT_N27_CA_EZ_MPM+tlrc.BRIK.gz +%%DATADIR%%/TT_N27_CA_EZ_MPM+tlrc.HEAD +%%DATADIR%%/TT_N27_CA_EZ_PMaps+tlrc.BRIK.gz +%%DATADIR%%/TT_N27_CA_EZ_PMaps+tlrc.HEAD +%%DATADIR%%/TT_N27_EZ_LR+tlrc.BRIK.gz +%%DATADIR%%/TT_N27_EZ_LR+tlrc.HEAD +%%DATADIR%%/TT_N27_EZ_ML+tlrc.BRIK.gz +%%DATADIR%%/TT_N27_EZ_ML+tlrc.HEAD %%DATADIR%%/TTatlas+tlrc.BRIK.gz %%DATADIR%%/TTatlas+tlrc.HEAD %%DATADIR%%/face_JimEliassen.jpg @@ -341,6 +356,7 @@ %%DATADIR%%/face_claudio.jpg %%DATADIR%%/face_cmoritz.jpg %%DATADIR%%/face_cmyers.jpg +%%DATADIR%%/face_cscholl.jpg %%DATADIR%%/face_csenior.jpg %%DATADIR%%/face_cwettig.jpg %%DATADIR%%/face_dglen.jpg @@ -376,11 +392,13 @@ %%DATADIR%%/face_kropella.jpg %%DATADIR%%/face_kschreiber.jpg %%DATADIR%%/face_kuba.jpg +%%DATADIR%%/face_kylesimmons.jpg %%DATADIR%%/face_lask.jpg %%DATADIR%%/face_laura.jpg %%DATADIR%%/face_lincoln1.jpg %%DATADIR%%/face_lincoln2.jpg %%DATADIR%%/face_lindachao.jpg +%%DATADIR%%/face_lisaeyler.jpg %%DATADIR%%/face_lizyoder.jpg %%DATADIR%%/face_ljcox.jpg %%DATADIR%%/face_llatour.jpg >Release-Note: >Audit-Trail: >Unformatted: