[kepler-users] Question about R workflow in Mac OS X
Jorge A. Ahumada
ahumadameister at gmail.com
Fri Jun 16 11:41:31 PDT 2006
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 conecciÛn con el dispositivo X11 ''
> >> EjecuciÛn 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
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users
>
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