Yes, Now it works! interesting.. Still no luck with the PDF_DISPLAY workflow though..
Jorge On 6/16/06, Dan Higgins <higgins at nceas.ucsb.edu> wrote: > > Hi Jorge, > > I have some more information on your problem. > > When I execute the Kepler-1.0.0beta1 application on a PPC Mac by > double clicking 'Kepler-1.0.0beta1', I can reproduce the problem that > you reported. However, there is also a script for launching Kepler in > the distribution called 'kepler.sh'. If I open kepler from the terminal > using with './kepler.sh' with X11 running and DISPLAY set, then there is > no error and the linear regression example works and displays a plot! I > do NOT understand why the behavior should depend on exactly how Kepler > is launched! (Perhaps something in how the ENV variables are passed to > the app.) > > In any case, you might want to try launching Kepler from Terminal > with the shell script and see if that works for you. > > Dan > > --- > > Dan Higgins wrote: > > Hello Jorge, > > > > Sorry that you are having a problem with Kepler, (but thanks for > > reporting the problem). I thought that having X11 open and setting the > > DISPLAY problem avoided this problem for Mac PPC machines. It seems to > > work on machines in use here, but obviously not for you. [Incidently, > > interfacing with X11 is a known problem for the new Mac Intel > > machines, although we are not sure why.] I'll have to dig into this to > > see if I can find the problem. What version of R is installed on you > > Mac? [Kepler launches R the same way as you would by entering 'R' on > > the command line.] > > > > The problem is related to the fact that R on the Mac uses some X11 > > code for the jpeg display device, and I picked that device for the > > Kepler RExpression actor because we could display jpegs easily in > > Kepler on Windows, Mac, and Linux. A better display device for the Mac > > would be a PDF device (since that is handled natively), and I have > > been looking at changing the default behavior in Kepler. [Note that > > RExpression actors work on the Mac if you disable the 'Graphics > > Output' parameter and just look at text output] > > Attached is an example Kepler workflow showing how to use a 'pdf' > > command within an R script to override the default setup and display > > the pdf file using an IJMacro actor. Note that this workflow will not > > execute with the Kepler beta1 release until you replace the ij.jar in > > the $KEPLER/lib/jar/ directory with an updated version of this ImageJ > > jar (see http://rsb.info.nih.gov/ij/download.html and get the 1.36 > > version). > > > > Dan Higgins > > > > > > > > Jorge A. Ahumada wrote: > >> Hello, > >> > >> I am interested in using Kepler for creating workflows with R. I have > >> a MAC > >> 10.4.6 PPC Dual G5 and downloaded the beta 6.1 of Kepler. When > >> attempting to > >> run the linear regression workflow I get this error: > >> > >> [R]> setwd('/Users/jorge') > >> [R]> jpeg(filename = '1150472825782.jpg',width = 480, height = 480, > >> pointsize = 12,quality = 75, bg = 'white') > >> > >> Erro en X11(paste(\"jpeg::\", quality, \":\", filename, sep = \"\"), > >> width, > >> : no fue posible iniciar el dispositivo JPEG > >> Adem?s: Warning message: > >> no fue posible abrir la conecci?n con el dispositivo X11 '' > >> Ejecuci?n interrumpida > >> > >> X11 is open and I typed setenv DISPLAY localhost:0.0 > >> > >> Seems that the X11 command has the wrong syntax for Mac or Linux: > >> X11(paste(/"jpeg::/". Etc..) > >> > >> How do I change it? Is this the problem..Any ideas? > >> > >> Thanks, > >> > >> Jorge > >> > > > > > > ------------------------------------------------------------------------ > > > > <?xml version="1.0" standalone="no"?> > > <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" > > "http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd";> > > <entity name="PDF_Display_Example" class=" > ptolemy.actor.TypedCompositeActor"> > > <property name="_createdBy" class=" > ptolemy.kernel.attributes.VersionAttribute" value="6.0-devel"> > > </property> > > <property name="SDF Director" class=" > ptolemy.domains.sdf.kernel.SDFDirector"> > > <property name="iterations" class="ptolemy.data.expr.Parameter" > value="1"> > > </property> > > <property name="timeResolution" class=" > ptolemy.moml.SharedParameter" value="1E-10"> > > </property> > > <property name="entityId" class="org.kepler.moml.NamedObjId" > value="urn:lsid:kepler-project.org:director:1:1"> > > </property> > > <property name="class" class=" > ptolemy.kernel.util.StringAttribute" value=" > ptolemy.domains.sdf.kernel.SDFDirector"> > > <property name="id" class=" > ptolemy.kernel.util.StringAttribute" value="urn:lsid: > kepler-project.org:directorclass:1:1"> > > </property> > > </property> > > <property name="semanticType000" class=" > org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director"> > > </property> > > <property name="semanticType111" class=" > org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director"> > > </property> > > <property name="_location" class="ptolemy.kernel.util.Location" > value="[70.0, 45.0]"> > > </property> > > </property> > > <property name="Annotation" class=" > ptolemy.vergil.kernel.attributes.TextAttribute"> > > <property name="text" class="ptolemy.kernel.util.StringAttribute" > value="PDF Display Example using the IJMacro. Dan Higgins - > NCEAS June 7, 2006"> > > </property> > > <property name="entityId" class="org.kepler.moml.NamedObjId" > value="urn:lsid:kepler-project.org:actor:436:1"> > > </property> > > <property name="class" class=" > ptolemy.kernel.util.StringAttribute" value=" > ptolemy.vergil.kernel.attributes.TextAttribute"> > > <property name="id" class=" > ptolemy.kernel.util.StringAttribute" value="urn:lsid: > kepler-project.org:class:1199:1"> > > </property> > > </property> > > <property name="semanticType000" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:1:1#DocumentationActor"> > > </property> > > <property name="semanticType111" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:2:1#WorkflowDocumentation"> > > </property> > > <property name="_location" class="ptolemy.kernel.util.Location" > value="[-10.0, 280.0]"> > > </property> > > </property> > > <property name="_windowProperties" class=" > ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={32, 15, 872, > 788}, maximized=false}"> > > </property> > > <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" > value="[600, 658]"> > > </property> > > <property name="_vergilZoomFactor" class=" > ptolemy.data.expr.ExpertParameter" value="1.0"> > > </property> > > <property name="_vergilCenter" class=" > ptolemy.data.expr.ExpertParameter" value="{225.0590717299578, > 329.6724466452619}"> > > </property> > > <entity name="IJMacro" class="util.IJMacro"> > > <property name="macroString" class=" > ptolemy.data.expr.StringParameter" > value="call("ij.IJ.runPlugIn","ij.plugin.BrowserLauncher","file://_FILE_");"> > > <property name="macro" class=" > ptolemy.actor.gui.style.TextStyle"> > > <property name="height" class=" > ptolemy.data.expr.Parameter" value="10"> > > </property> > > <property name="width" class=" > ptolemy.data.expr.Parameter" value="30"> > > </property> > > </property> > > </property> > > <property name="fileOrURL" class=" > ptolemy.data.expr.FileParameter"> > > </property> > > <property name="entityId" class="org.kepler.moml.NamedObjId" > value="urn:lsid:kepler-project.org:actor:271:1"> > > </property> > > <property name="class" class=" > ptolemy.kernel.util.StringAttribute" value="util.IJMacro"> > > <property name="id" class=" > ptolemy.kernel.util.StringAttribute" value="urn:lsid: > kepler-project.org:class:1096:1"> > > </property> > > </property> > > <property name="semanticType000" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:1:1#ImageManipulationActor"> > > </property> > > <property name="semanticType111" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:2:1#ImageOperation"> > > </property> > > <property name="_location" class="ptolemy.kernel.util.Location" > value="[390.0, 225.0]"> > > </property> > > </entity> > > <entity name="RExpression" class=" > org.ecoinformatics.seek.R.RExpression"> > > <property name="expression" class=" > ptolemy.kernel.util.StringAttribute" value="fn <- > pdf_file pdf(file=fn,width=6,height=6) plot(x <- sort(rnorm(47)), > type = "s", main = "plot(x, type = > \"s\")") dev.off()"> > > <property name="R Expression" class=" > ptolemy.actor.gui.style.TextStyle"> > > <property name="height" class=" > ptolemy.data.expr.Parameter" value="10"> > > </property> > > <property name="width" class=" > ptolemy.data.expr.Parameter" value="30"> > > </property> > > </property> > > </property> > > <property name="Rcwd" class="ptolemy.data.expr.StringParameter" > value="C:\Documents and Settings\Dan Higgins"> > > </property> > > <property name="save_nosave" class=" > ptolemy.data.expr.StringParameter" value="--no-save"> > > </property> > > <property name="graphicsOutput" class=" > ptolemy.data.expr.Parameter" value="false"> > > </property> > > <property name="numXPixels" class=" > ptolemy.data.expr.StringParameter" value="480"> > > </property> > > <property name="numYPixels" class=" > ptolemy.data.expr.StringParameter" value="480"> > > </property> > > <property name="entityId" class="org.kepler.moml.NamedObjId" > value="urn:lsid:kepler-project.org:actor:360:1"> > > </property> > > <property name="class" class=" > ptolemy.kernel.util.StringAttribute" value=" > org.ecoinformatics.seek.R.RExpression"> > > <property name="id" class=" > ptolemy.kernel.util.StringAttribute" value="urn:lsid: > kepler-project.org:class:1126:1"> > > </property> > > </property> > > <property name="semanticType000" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:1:1#MathOperationActor"> > > </property> > > <property name="semanticType111" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:2:1#GeneralPurpose"> > > </property> > > <property name="_location" class="ptolemy.kernel.util.Location" > value="[240.0, 175.0]"> > > </property> > > <port name="fn" class="ptolemy.actor.TypedIOPort"> > > <property name="output"/> > > <property name="_type" class="ptolemy.actor.TypeAttribute" > value="string"> > > </property> > > </port> > > <port name="pdf_file" class="ptolemy.actor.TypedIOPort"> > > <property name="input"/> > > </port> > > </entity> > > <entity name="Constant" class="ptolemy.actor.lib.Const"> > > <property name="value" class="ptolemy.data.expr.Parameter" > value="property("KEPLER")+"/RData.pdf""> > > </property> > > <property name="entityId" class="org.kepler.moml.NamedObjId" > value="urn:lsid:kepler-project.org:actor:1:1"> > > </property> > > <property name="class" class=" > ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Const"> > > <property name="id" class=" > ptolemy.kernel.util.StringAttribute" value="urn:lsid: > kepler-project.org:class:877:1"> > > </property> > > </property> > > <property name="semanticType000" class=" > org.kepler.sms.SemanticType" > value="urn:lsid:localhost:onto:1:1#ConstantActor"> > > </property> > > <property name="semanticType111" class=" > org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Constant"> > > </property> > > <property name="kar" class="ptolemy.kernel.util.StringAttribute" > value="urn:lsid:kepler-project.org:kar:57:1"> > > </property> > > <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon > "> > > <property name="attributeName" class=" > ptolemy.kernel.util.StringAttribute" value="value"> > > </property> > > <property name="displayWidth" class=" > ptolemy.data.expr.Parameter" value="40"> > > </property> > > </property> > > <property name="_location" class="ptolemy.kernel.util.Location" > value="[65.0, 195.0]"> > > </property> > > </entity> > > <relation name="relation" class="ptolemy.actor.TypedIORelation"> > > <property name="width" class="ptolemy.data.expr.Parameter" > value="1"> > > </property> > > </relation> > > <relation name="relation2" class="ptolemy.actor.TypedIORelation"> > > <property name="width" class="ptolemy.data.expr.Parameter" > value="1"> > > </property> > > </relation> > > <link port="IJMacro.input" relation="relation2"/> > > <link port="RExpression.fn" relation="relation2"/> > > <link port="RExpression.pdf_file" relation="relation"/> > > <link port="Constant.output" relation="relation"/> > > </entity> > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Kepler-users mailing list > > Kepler-users at ecoinformatics.org > > > http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users > > > > > -- > ******************************************************************* > Dan Higgins higgins at nceas.ucsb.edu > http://www.nceas.ucsb.edu/ Ph: 805-893-5127 > National Center for Ecological Analysis and Synthesis (NCEAS) Marine > Science Building - Room 3405 > Santa Barbara, CA 93195 > ******************************************************************* > > > _______________________________________________ > Kepler-users mailing list > Kepler-users at ecoinformatics.org 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