clValid-Error on WinXP and Ubuntu 12.04 VMs

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daniel
2013-01-28
2013-05-20
  • daniel

    daniel - 2013-01-28

    Hello,
    I am trying to use the clValid-package. MEV 4.8.1 runs fine, but clValid package doesn't. I can't figure out how to get clValid to work. I tried on two different machines: WinXP and Ubuntu 12.04, both 32 bit, both are freshly prepared Virtual Boxes.
    My workflow:
    I use the TDMS_format_sample dataset from the data-subdirectory. I use the HCL option: Gene tree with euclidean distance. Then I use cluster validation: cluster genes with internal validation and HCL as algorithm.
    I would appreciate any help!

    On WinXP, I get the following error:
    "32 bit Win"
    C:\Program Files\MEV\MeV_4_8_1
    MultiExperimentViewer - version 4.8.1 - Windows XP
    Java Runtime Environment version: 1.6.0_38
    Java Runtime Environment vendor: Sun Microsystems Inc.
    Java Virtual Machine name: Java HotSpot(TM) Client VM
    Java Virtual Machine version: 20.13-b02
    Java Virtual Machine vendor: Sun Microsystems Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Sun Microsystems, Inc.
    Java 3D Runtime Environment version:1.2
    Operating System name: Windows XP
    Operating System version: 5.1
    Operating System architecture: x86
    MeV Build: 2727
    MeV Revision Date: 2011/12/15 12:26:53
    MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/trunk
    result node is null
    user.home C:\Documents and Settings\a
    user.dir C:\Program Files\MEV\MeV_4_8_1
    Checking for R_HOME : C:\Program Files\MEV\MeV_4_8_1\R-2.11.1
    Creating Rengine (with arguments)

    R version 2.11.1 (2010-05-31)

    Copyright (C) 2010 The R Foundation for Statistical Computing

    ISBN 3-900051-07-0

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under certain conditions.
    Type 'license()' or 'licence()' for distribution details.

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    Rengine created, waiting for R
    Biobase_2.8.0.zip Package Installed
    annotate_1.26.1.zip Package Installed
    GO.db_2.4.1.zip Package Installed
    xtable_1.5-6.zip Package Installed
    kohonen_2.0.7.zip Package Installed
    mclust_3.4.8.zip Package Installed
    clValid_0.6-2.zip Package Installed
    Loading required package: cluster

    Loading required package: class

    org.tigr.microarray.mev.cluster.algorithm.AbortException: abort
            at org.tigr.microarray.mev.cluster.algorithm.impl.CLVALID.runRAlg(CLVALID.java:256)
            at org.tigr.microarray.mev.cluster.algorithm.impl.CLVALID.execute(CLVALID.java:95)
            at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:54)
            at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.performValidation(CLVALIDGUI.java:127)
            at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:100)
            at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625)
            at java.lang.Thread.run(Unknown Source)
    Error running clValid
    org.tigr.microarray.mev.cluster.algorithm.AlgorithmException: Error running Cluster Validation
            at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.performValidation(CLVALIDGUI.java:131)
            at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:100)
            at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625)
            at java.lang.Thread.run(Unknown Source)

     
  • daniel

    daniel - 2013-01-28

    On Ubuntu 12.04, I get the following error message:
    /home/daniel/MEV/MeV_4_8_1
    /home/daniel/MEV/MeV_4_8_1/tmev.sh: 41: [: -a: unexpected operator
    Attempting to build jri Library
    >>>>>>>>>>>>>>  Running auto conf to check R_HOME, JAVA_HOME and other JRI setting compatibility
    checking build system type… i686-pc-linux-gnu
    checking host system type… i686-pc-linux-gnu
    checking for gcc… gcc -std=gnu99
    checking for C compiler default output file name… a.out
    checking whether the C compiler works… yes
    checking whether we are cross compiling… no
    checking for suffix of executables…
    checking for suffix of object files… o
    checking whether we are using the GNU C compiler… yes
    checking whether gcc -std=gnu99 accepts -g… yes
    checking for gcc -std=gnu99 option to accept ISO C89… none needed
    checking how to run the C preprocessor… gcc -std=gnu99 -E
    checking for grep that handles long lines and -e… /bin/grep
    checking for egrep… /bin/grep -E
    checking for ANSI C header files… yes
    checking for java… /usr/bin/java
    checking for javac… /usr/bin/javac
    checking for javah… /usr/bin/javah
    checking for jar… /usr/bin/jar
    checking whether Java interpreter works… yes
    checking for Java environment… in /usr/lib/jvm/java-6-openjdk-i386/jre
    checking for /usr/lib/jvm/java-6-openjdk-i386/jre/include/jni.h… no
    checking for /usr/lib/jvm/java-6-openjdk-i386/jre/jni.h… no
    checking for /usr/lib/jvm/java-6-openjdk-i386/jre/../include/jni.h… yes
    checking for /usr/lib/jvm/java-6-openjdk-i386/jre/../include/./jni_md.h… yes
    checking whether JNI programs can be compiled… yes
    checking whether JNI programs can be run… yes
    checking JNI data types… ok
    checking whether Rinterface.h exports R_CStackXXX variables… yes
    checking whether Rinterface.h exports R_SignalHandlers… yes
    configure: creating ./config.status
    config.status: creating src/Makefile
    config.status: creating Makefile
    config.status: creating run
    config.status: creating src/config.h
    config.status: src/config.h is unchanged
    >>>>>>>>>>>>>>  Compiling libjri.so & JRI.jar
    make -C src JRI.jar
    make: Entering directory `/home/daniel/MEV/MeV_4_8_1/jri/src'
    /usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
    /usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../package-info.java ../RBool.java ../RConsoleOutputStream.java ../Rengine.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java
    /usr/bin/jar fc JRI.jar org libjri.so
    make: Leaving directory `/home/daniel/MEV/MeV_4_8_1/jri/src'
    rm -f libjri.so
    cp src/libjri.so libjri.so
    /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest2.java
    Note: examples/rtest2.java uses or overrides a deprecated API.
    Note: Recompile with -Xlint:deprecation for details.
    /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest.java
    Note: examples/rtest.java uses or overrides a deprecated API.
    Note: Recompile with -Xlint:deprecation for details.
    -rwxrwxr-x 1 daniel daniel 143533 Jan 28 10:18 jri/libjri.so
    -rw-rw-r- 1 daniel daniel  67398 Jan 28 10:18 jri/src/JRI.jar
    >>>>>>>>>>>>>>  Copying files to MeV lib directory
    -rw-r-r- 1 daniel daniel  67398 Jan 28 10:18 lib/JRI.jar
    -rwxrwxr-x 1 daniel daniel 143533 Jan 28 10:18 lib/libjri.so
    >>>>>>>>>>>>>> Removing compiled files from jri folder
    >>>>>>>>>>>>>> DONE !!!
    MultiExperimentViewer - version 4.8.1 - Linux
    Java Runtime Environment version: 1.6.0_24
    Java Runtime Environment vendor: Sun Microsystems Inc.
    Java Virtual Machine name: OpenJDK Client VM
    Java Virtual Machine version: 20.0-b12
    Java Virtual Machine vendor: Sun Microsystems Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Sun Microsystems, Inc.
    Java 3D Runtime Environment version:1.2
    Operating System name: Linux
    Operating System version: 3.2.0-36-generic-pae
    Operating System architecture: i386
    MeV Build: 2727
    MeV Revision Date: 2011/12/16 11:21:19
    MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/trunk
    result node is null
    user.home /home/daniel
    user.dir /home/daniel/MEV/MeV_4_8_1
    Checking for R_HOME : /usr/lib/R
    Creating Rengine (with arguments)

    R version 2.14.1 (2011-12-22)
    Copyright (C) 2011 The R Foundation for Statistical Computing
    ISBN 3-900051-07-0
    Platform: i686-pc-linux-gnu (32-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under certain conditions.
    Type 'license()' or 'licence()' for distribution details.

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    Rengine created, waiting for R
    To Download: 1 packages
    First Pkg: NOT
    Last Pkg: NOT
    createPkgUrls: baseUrl ftp://occams.dfci.harvard.edu/pub/bio/MeV_Etc/R_MeV_Support_devel/R2.11/linux/clvalid
    added PkgUrls ftp://occams.dfci.harvard.edu/pub/bio/MeV_Etc/R_MeV_Support_devel/R2.11/linux/clvalid/NOT
    getFileNameFromURL NOT
    updateLibAndPackages remote PKG NOT
    To Download: /home/daniel/MEV/MeV_4_8_1/RPackages/NOT
    org.tigr.microarray.mev.cluster.algorithm.AbortException: abort
        at org.tigr.microarray.mev.cluster.algorithm.impl.CLVALID.runRAlg(CLVALID.java:256)
        at org.tigr.microarray.mev.cluster.algorithm.impl.CLVALID.execute(CLVALID.java:95)
        at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:54)
        at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.performValidation(CLVALIDGUI.java:127)
        at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:100)
        at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625)
        at java.lang.Thread.run(Thread.java:679)
    Error running clValid
    org.tigr.microarray.mev.cluster.algorithm.AlgorithmException: Error running Cluster Validation
        at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.performValidation(CLVALIDGUI.java:131)
        at org.tigr.microarray.mev.cluster.gui.impl.clvalid.CLVALIDGUI.execute(CLVALIDGUI.java:100)
        at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625)
        at java.lang.Thread.run(Thread.java:679)

     
  • daniel

    daniel - 2013-01-28

    The connection between MEV and R seems to work: MEV-function: Statistics -> Limma (also relying on R) is working. clValid seems to be the problem.

     

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