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| Solved: Launch Biocep-core.jar with ant [ Reply ] By: Tully Yates on 2009-08-17 15:31 | [forum:1832] |
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For the benefit of anyone following this... The trick was to use -Duse.default.libs=true. Here is the target excerpt from my build file. <!-- Runs biocep core with an R server --> <target name="run_server" depends="initialise"> <java fork="true" spawn="false" classname="org.kchine.r.server.CoreMain"> <classpath> <path location="${biocep.core.jar}" /> </classpath> <env key="R_HOME" path="${r.home}" /> <env key="R_LIBS" path="${r.libs}:${bioc.libs}:${bioc.data}" /> <env key="LD_LIBRARY_PATH" path="${r.ld.libs}:${local.libs}:${gnu.libs}:${graphviz.libs}:${root.libs}:${java.libs}:${java.server.libs}" /> <jvmarg value="-Duse.default.libs=${default.libs.boolean}" /> <jvmarg value="-Dname=${r.server.name}" /> <jvmarg value="-Dlog.file=${r.server.log}" /> <jvmarg value="-Xmx512m" /> </java> </target> It will start and I can launch a virtual workbench and connect to the R server spawned by the above ant task. I still see the IO.Exception for main.log |
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| RE: Trying to launch Biocep-core.jar with ant [ Reply ] By: Tully Yates on 2009-08-07 09:40 | [forum:1803] |
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Thanks for quick response. Your assumption is correct, I would like to set up an R server listening for connections over RMI. I followed the biocep-core subsection in the Project Deliverables & Howtos section. http://biocep-distrib.r-forge.r-project.org/doc.html # run an R server →from your command line: rmiregistry & (on windows: start rmiregistry) →from your command line: java -Dname=toto -jar biocep-core.jar (replace toto with any other name, repeat the command with different server names to run several R servers) →connect to the server : open the workbench, choose "Connect to R via RMI", choose "Use:" → "Rmi Registry", click on "Refresh", choose your R Server name (toto, ..), OK There is no mention of having to provide the other jars you list on the classpath and I haven't tried. There are much stranger things happening that I would like to get to the bottom of first: 1. java.io.FileNotFoundException: main.log (No such file or directory) There is a main.log in my home directory which has been created by biocep-core.jar but it's empty. 2. I provide on the R_LIBS path the home of bioconductor2.4 and R2.9.1 where rJava, iplots, JavaGD are all installed. So why am I seeing: >>Installing missing packages [rJava, JavaGD, iplots].. Especially as a couple of lines before I see the message: +rjavapath:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64/rJava I mean, if the libraries are there and successfully installed (I have run the test code @http://www.rforge.net/rJava/), why does biocep try and get new copies? 3. The following message is reported: R_HOME is set to :/nfs/compdiag/package/R/2.9.1/x86_64/ then the somewhat contradictory: WARNING: ignoring environment value of R_HOME I have sent you a copy of my ant build.xml which I am using to launch biocep-core.jar [R server] and the biocep.jar [virtual workbench] Thank you for your time, I really appreciate it! |
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| RE: Trying to launch Biocep-core.jar with ant [ Reply ] By: Ian Long on 2009-08-06 16:44 | [forum:1801] |
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Which aspects of Biocep are you trying to use? i.e. what environment are you trying to set up? I presume an R server listening for connections over RMI? It is possible to set up an Ant task by running org.kchine.r.server.CoreMain and providing command line arguments detailing the path to your Biocep libraries: file:/D:/eclipse/stoat_biocep/biocep-core.jar file:/D:/eclipse/stoat_biocep/biocep.jar file:/D:/eclipse/stoat_biocep/derby.jar file:/D:/eclipse/stoat_biocep/derbynet.jar The only JVM environment variable I normally give to my Biocep server is: -Dlog.file="RServer.log" It appears as though your process is falling over relatively early in the start up process which trying to configure the Log4J logging system - looking for a file main.log. I haven't come across any references to main.log within my environment (but haven't looked for them either). Be aware that Biocep starts an instance of a Jetty HTTP server on the launch machine to enable the remote RMI processes to download the classes they need. If you wish to run with a firewall between the client and the server you will probably have to set the port used by Jetty. This can be done by setting the system property -Dlocaltomcat.port=3170 Ian. ================================================================ Statistical Software Developer ilong@stoatsoftware.com +44 117 3390048 |
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| Trying to launch Biocep-core.jar with ant [ Reply ] By: Tully Yates on 2009-08-06 14:50 | [forum:1800] |
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What do I need to provide in the way of environment variables to the Biocep-core.jar? I have written an ant script to simplfy this as there are several versions of R and bioconductor on the machine. The default locations are out of date versions of R and bioconductor. So far the jar lauchers then spews the following and hangs in (what I beleive is) an unsuccessful start-up. I can't connect to my R server using the RMI and the name I chose (probably a whole other issue.). The messages for biocep-core follow maybe you are able to tell me what is going wrong? Thanks for your help in advance! run_server: [java] log4j:ERROR setFile(null,true) call failed. [java] java.io.FileNotFoundException: main.log (No such file or directory) [java] at java.io.FileOutputStream.openAppend(Native Method) [java] at java.io.FileOutputStream.<init>(FileOutputStream.java:177) [java] at java.io.FileOutputStream.<init>(FileOutputStream.java:102) [java] at org.apache.log4j.FileAppender.setFile(FileAppender.java:290) [java] at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:164) [java] at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:257) [java] at org.apache.log4j.xml.DOMConfigurator.parseAppender(DOMConfigurator.java:285) [java] at org.apache.log4j.xml.DOMConfigurator.findAppenderByName(DOMConfigurator.java:171) [java] at org.apache.log4j.xml.DOMConfigurator.findAppenderByReference(DOMConfigurator.java:184) [java] at org.apache.log4j.xml.DOMConfigurator.parseChildrenOfLoggerElement(DOMConfigurator.java:502) [java] at org.apache.log4j.xml.DOMConfigurator.parseCategory(DOMConfigurator.java:415) [java] at org.apache.log4j.xml.DOMConfigurator.parse(DOMConfigurator.java:919) [java] at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:790) [java] at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:696) [java] at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:471) [java] at org.apache.log4j.LogManager.<clinit>(LogManager.java:125) [java] at org.apache.log4j.Logger.getLogger(Logger.java:105) [java] at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:289) [java] at org.apache.commons.logging.impl.Log4JLogger.<init>(Log4JLogger.java:109) [java] at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) [java] at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) [java] at java.lang.reflect.Constructor.newInstance(Constructor.java:494) [java] at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1116) [java] at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:914) [java] at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:604) [java] at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:336) [java] at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:310) [java] at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:685) [java] at org.kchine.r.server.CoreMain.<clinit>(CoreMain.java:34) [java] ----> naming mode :registry [java] $$$ HOST IP:132.199.249.2 [java] 2009-08-06 15:38:23.313::INFO: Logging to STDERR via org.mortbay.log.StdErrLog [java] 2009-08-06 15:38:23.362::INFO: jetty-6.1.x [java] 2009-08-06 15:38:23.433::INFO: Started SocketConnector@0.0.0.0:58485 [java] @@INSTALL_DIR=/home/yat60124/RWorkbench/ [java] SCI:null [java] application type : standard [java] !! use class path : true [java] java.class.path : /nfs/compdiag/user/yat60124/applications/biocep-core.jar [java] >>Inspecting R installation.. [java] R_HOME is set to :/nfs/compdiag/package/R/2.9.1/x86_64/ [java] r options:[--no-save] [java] trying to execute :/nfs/compdiag/package/R/2.9.1/x86_64/bin/R [java] exec->[/nfs/compdiag/package/R/2.9.1/x86_64/bin/R, CMD, BATCH, --no-save, /home/yat60124/RWorkbench/getInfo.R, /home/yat60124/RWorkbench/getInfo.Rout] [java] [XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt, R_HOME=/nfs/compdiag/package/R/2.9.1/x86_64, LANG=en_US.ISO-8859-15, DISPLAY=localhost:16.0, PWD=/home/yat60124, NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat, VENDOR=unknown, USER=yat60124, HOME=/nfs/compdiag/user/yat60124, LD_LIBRARY_PATH=/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/jre/lib/amd64/server:/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/jre/../lib/amd64:/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/jre/lib/amd64/server:/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun-1.5.0.17/lib/amd64:/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/usr/lib/graphviz, SSH_CONNECTION=132.199.132.238 51985 132.199.249.2 22, REMOTEHOST=pc56270.klinik.uni-regensburg.de, MACHTYPE=x86_64, LOGNAME=yat60124, SHELL=/bin/bash, SYSTEM_PATH=/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/nfs/compdiag/bin:/usr/lib/jvm/java-1.5.0-sun/bin:/nfs/compdiag/user/yat60124/applications/apache-ant-1.7.1/bin:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/nfs/compdiag/package/R/2.9.1/x86_64, OSTYPE=linux, PERL5LIB=/nfs/compdiag/user/thm09830/perl, SSH_TTY=/dev/pts/7, SHLVL=2, HOSTTYPE=x86_64-linux, GROUP=genomik, SSH_CLIENT=132.199.132.238 51985 22, MAIL=/var/mail/yat60124, R_LIB_PATH=/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data, JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun, HOST=rhskl2, BIG_HOME=/nfs/compdiag/user/yat60124/, TERM=xterm, R_LIBS=/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data, PATH=/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/nfs/compdiag/bin:/usr/lib/jvm/java-1.5.0-sun/bin:/nfs/compdiag/user/yat60124/applications/apache-ant-1.7.1/bin:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/nfs/compdiag/package/R/2.9.1/x86_64] [java] +rversion:R version 2.9.1 (2009-06-26) [java] +rlibraypath:/nfs/compdiag/package/R/2.9.1/x86_64 [java] +rjavapath:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64/rJava [java] +rinfo:[Ljava.lang.String;@31ad98ef [/nfs/compdiag/package/R/2.9.1/x86_64, R version 2.9.1 (2009-06-26), /nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64/rJava] [java] rpath:/nfs/compdiag/package/R/2.9.1/x86_64 [java] rversion:R version 2.9.1 (2009-06-26) [java] user rjava path:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64/rJava [java] >>R installation inspection done. [java] R_LIBS:/home/yat60124/RWorkbench/library/R-version-2.9.1:/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data [java] envVector:[XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt, R_HOME=/nfs/compdiag/package/R/2.9.1/x86_64/, LANG=en_US.ISO-8859-15, DISPLAY=localhost:16.0, PWD=/home/yat60124, NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat, VENDOR=unknown, USER=yat60124, HOME=/nfs/compdiag/user/yat60124, LD_LIBRARY_PATH=/nfs/compdiag/package/R/2.9.1/x86_64/lib, SSH_CONNECTION=132.199.132.238 51985 132.199.249.2 22, REMOTEHOST=pc56270.klinik.uni-regensburg.de, MACHTYPE=x86_64, LOGNAME=yat60124, SHELL=/bin/bash, SYSTEM_PATH=/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/nfs/compdiag/bin:/usr/lib/jvm/java-1.5.0-sun/bin:/nfs/compdiag/user/yat60124/applications/apache-ant-1.7.1/bin:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/nfs/compdiag/package/R/2.9.1/x86_64, OSTYPE=linux, PERL5LIB=/nfs/compdiag/user/thm09830/perl, SSH_TTY=/dev/pts/7, SHLVL=2, HOSTTYPE=x86_64-linux, GROUP=genomik, SSH_CLIENT=132.199.132.238 51985 22, MAIL=/var/mail/yat60124, R_LIB_PATH=/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data, Path=/nfs/compdiag/package/R/2.9.1/x86_64/lib:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/nfs/compdiag/bin:/usr/lib/jvm/java-1.5.0-sun/bin:/nfs/compdiag/user/yat60124/applications/apache-ant-1.7.1/bin:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/nfs/compdiag/package/R/2.9.1/x86_64, JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun, HOST=rhskl2, BIG_HOME=/nfs/compdiag/user/yat60124/, TERM=xterm, R_LIBS=/home/yat60124/RWorkbench/library/R-version-2.9.1:/nfs/compdiag/package/R/lib/cran/release2.9/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64:/nfs/compdiag/package/R/lib/bioconductor/release_2.4/data, PATH=/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/nfs/compdiag/bin:/usr/lib/jvm/java-1.5.0-sun/bin:/nfs/compdiag/user/yat60124/applications/apache-ant-1.7.1/bin:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64:/usr/lib/jvm/java-1.5.0-sun/jre/lib/amd64/server:/nfs/compdiag/package/R/2.9.1/x86_64] [java] >>Installing missing packages [rJava, JavaGD, iplots].. [java] This doesn't alter your R installation and may take several minutes. It will be done only once [java] [/nfs/compdiag/package/R/2.9.1/x86_64/bin/R, CMD, BATCH, --no-save, /home/yat60124/RWorkbench/installRequiredPackages.R, /home/yat60124/RWorkbench/installRequiredPackages.Rout] [java] WARNING: ignoring environment value of R_HOME [java] [java] R version 2.9.1 (2009-06-26) [java] Copyright (C) 2009 The R Foundation for Statistical Computing [java] ISBN 3-900051-07-0 [java] [java] R is free software and comes with ABSOLUTELY NO WARRANTY. [java] You are welcome to redistribute it under certain conditions. [java] Type 'license()' or 'licence()' for distribution details. [java] [java] Natural language support but running in an English locale [java] [java] R is a collaborative project with many contributors. [java] Type 'contributors()' for more information and [java] 'citation()' on how to cite R or R packages in publications. [java] [java] Type 'demo()' for some demos, 'help()' for on-line help, or [java] 'help.start()' for an HTML browser interface to help. [java] Type 'q()' to quit R. [java] [java] > source('http://bioconductor.org/biocLite.R') [java] > biocLite('rJava',lib='/home/yat60124/RWorkbench/library/R-version-2.9.1') [java] Running biocinstall version 2.4.11 with R version 2.9.1 [java] Your version of R requires version 2.4 of Bioconductor. [java] trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz' [java] Content type 'application/x-gzip' length 240527 bytes (234 Kb) [java] opened URL [java] ================================================== [java] downloaded 234 Kb [java] [java] * Installing *source* package 'rJava' ... [java] checking for gcc... gcc -std=gnu99 [java] checking for C compiler default output file name... a.out [java] checking whether the C compiler works... yes [java] checking whether we are cross compiling... no [java] checking for suffix of executables... [java] checking for suffix of object files... o [java] checking whether we are using the GNU C compiler... yes [java] checking whether gcc -std=gnu99 accepts -g... yes [java] checking for gcc -std=gnu99 option to accept ISO C89... none needed [java] checking how to run the C preprocessor... gcc -std=gnu99 -E [java] checking for grep that handles long lines and -e... /bin/grep [java] checking for egrep... /bin/grep -E [java] checking for ANSI C header files... yes [java] checking for sys/wait.h that is POSIX.1 compatible... yes [java] checking for sys/types.h... yes [java] checking for sys/stat.h... yes [java] checking for stdlib.h... yes [java] checking for string.h... yes [java] checking for memory.h... yes [java] checking for strings.h... yes [java] checking for inttypes.h... yes [java] checking for stdint.h... yes [java] checking for unistd.h... yes [java] checking for string.h... (cached) yes [java] checking sys/time.h usability... yes [java] checking sys/time.h presence... yes [java] checking for sys/time.h... yes [java] checking for unistd.h... (cached) yes [java] checking for an ANSI C-conforming const... yes [java] checking whether time.h and sys/time.h may both be included... yes [java] configure: checking whether gcc -std=gnu99 supports static inline... [java] yes [java] checking Java support in R... present: [java] interpreter : '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java' [java] archiver : '/usr/lib/jvm/java-1.5.0-sun/bin/jar' [java] compiler : '/usr/lib/jvm/java-1.5.0-sun/bin/javac' [java] header prep.: '/usr/lib/jvm/java-1.5.0-sun/bin/javah' [java] cpp flags : '-I/usr/lib/jvm/java-1.5.0-sun/include -I/usr/lib/jvm/java-1.5.0-sun/include/linux' [java] java libs : '-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64/server -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64 -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64 -L/usr/local/lib64 -ljvm' [java] checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. [java] [java] Make sure you have Java Development Kit installed and correctly registered in R. [java] If in doubt, re-run "R CMD javareconf" as root. [java] [java] ERROR: configuration failed for package 'rJava' [java] * Removing '/home/yat60124/RWorkbench/library/R-version-2.9.1/rJava' [java] [java] The downloaded packages are in [java] '/tmp/Rtmp2BsLTA/downloaded_packages' [java] Warning message: [java] In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : [java] installation of package 'rJava' had non-zero exit status [java] > biocLite('JavaGD',lib='/home/yat60124/RWorkbench/library/R-version-2.9.1') [java] Running biocinstall version 2.4.11 with R version 2.9.1 [java] Your version of R requires version 2.4 of Bioconductor. [java] trying URL 'http://cran.fhcrc.org/src/contrib/JavaGD_0.5-2.tar.gz' [java] Content type 'application/x-gzip' length 87076 bytes (85 Kb) [java] opened URL [java] ================================================== [java] downloaded 85 Kb [java] [java] * Installing *source* package 'JavaGD' ... [java] checking for gcc... gcc -std=gnu99 [java] checking for C compiler default output file name... a.out [java] checking whether the C compiler works... yes [java] Exception in thread "main" org.kchine.r.server.manager.ServantCreationFailed [java] checking whether we are cross compiling... no [java] at org.kchine.r.server.manager.ServerManager.createRInternal(ServerManager.java:804) [java] checking for suffix of executables... [java] at org.kchine.r.server.manager.ServerManager.createR(ServerManager.java:463) [java] checking for suffix of object files... o [java] at org.kchine.r.server.CoreMain.main(CoreMain.java:94) [java] checking whether we are using the GNU C compiler... yes [java] checking whether gcc -std=gnu99 accepts -g... yes [java] checking for gcc -std=gnu99 option to accept ISO C89... none needed [java] checking how to run the C preprocessor... gcc -std=gnu99 -E [java] checking for grep that handles long lines and -e... /bin/grep [java] checking for egrep... /bin/grep -E [java] checking for ANSI C header files... yes [java] checking for sys/wait.h that is POSIX.1 compatible... yes [java] checking for sys/types.h... yes [java] checking for sys/stat.h... yes [java] checking for stdlib.h... yes [java] checking for string.h... yes [java] checking for memory.h... yes [java] checking for strings.h... yes [java] checking for inttypes.h... yes [java] checking for stdint.h... yes [java] checking for unistd.h... yes [java] checking for string.h... (cached) yes [java] checking sys/time.h usability... yes [java] checking sys/time.h presence... yes [java] checking for sys/time.h... yes [java] checking for unistd.h... (cached) yes [java] checking for an ANSI C-conforming const... yes [java] checking whether time.h and sys/time.h may both be included... yes [java] checking for stdlib.h... (cached) yes [java] checking for GNU libc compatible malloc... yes [java] checking return type of signal handlers... void [java] checking for memset... yes [java] checking for mkdir... yes [java] checking for rmdir... yes [java] checking for select... yes [java] checking for socket... yes [java] checking Java support in R... present: [java] interpreter : '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java' [java] cpp flags : '-I/usr/lib/jvm/java-1.5.0-sun/include -I/usr/lib/jvm/java-1.5.0-sun/include/linux' [java] java libs : '-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64/server -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64 -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64 -L/usr/local/lib64 -ljvm' [java] checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. [java] ERROR: configuration failed for package 'JavaGD' [java] * Removing '/home/yat60124/RWorkbench/library/R-version-2.9.1/JavaGD' [java] [java] The downloaded packages are in [java] '/tmp/Rtmp2BsLTA/downloaded_packages' [java] Warning message: [java] In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : [java] installation of package 'JavaGD' had non-zero exit status [java] > biocLite('iplots',lib='/home/yat60124/RWorkbench/library/R-version-2.9.1') [java] Running biocinstall version 2.4.11 with R version 2.9.1 [java] Your version of R requires version 2.4 of Bioconductor. [java] trying URL 'http://cran.fhcrc.org/src/contrib/iplots_1.1-3.tar.gz' [java] Content type 'application/x-gzip' length 331100 bytes (323 Kb) [java] opened URL [java] ================================================== [java] downloaded 323 Kb [java] [java] * Installing *source* package 'iplots' ... [java] ** R [java] ** inst [java] ** preparing package for lazy loading [java] Error in dyn.load(file, DLLpath = DLLpath, ...) : [java] unable to load shared library '/nfs/compdiag/package/R/lib/bioconductor/release_2.4/x86_64/rJava/libs/rJava.so': [java] libjvm.so: cannot open shared object file: No such file or directory [java] Error : .onLoad failed in 'loadNamespace' for 'rJava' [java] Error : package 'rJava' could not be loaded [java] ERROR: lazy loading failed for package 'iplots' [java] * Removing '/home/yat60124/RWorkbench/library/R-version-2.9.1/iplots' [java] [java] The downloaded packages are in [java] '/tmp/Rtmp2BsLTA/downloaded_packages' [java] Warning message: [java] In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : [java] installation of package 'iplots' had non-zero exit status [java] > [java] > proc.time() [java] user system elapsed [java] 31.081 4.604 147.182 [java] The following packages probably couldn't be automatically installed [java] [rJava, JavaGD, iplots] [java] >>Installing missing packages [rJava, JavaGD, iplots].. [java] This doesn't alter your R installation and may take several minutes. It will be done only once [java] [/nfs/compdiag/package/R/2.9.1/x86_64/bin/R, CMD, BATCH, --no-save, /home/yat60124/RWorkbench/installRequiredPackages.R, /home/yat60124/RWorkbench/installRequiredPackages.Rout] [java] WARNING: ignoring environment value of R_HOME [java] [java] R version 2.9.1 (2009-06-26) [java] Copyright (C) 2009 The R Foundation for Statistical Computing [java] ISBN 3-900051-07-0 [java] [java] R is free software and comes with ABSOLUTELY NO WARRANTY. [java] You are welcome to redistribute it under certain conditions. [java] Type 'license()' or 'licence()' for distribution details. [java] [java] Natural language support but running in an English locale [java] [java] R is a collaborative project with many contributors. [java] Type 'contributors()' for more information and [java] 'citation()' on how to cite R or R packages in publications. [java] [java] Type 'demo()' for some demos, 'help()' for on-line help, or [java] 'help.start()' for an HTML browser interface to help. [java] Type 'q()' to quit R. [java] [java] > source('http://bioconductor.org/biocLite.R') [java] > biocLite('rJava',lib='/home/yat60124/RWorkbench/library/R-version-2.9.1') [java] Running biocinstall version 2.4.11 with R version 2.9.1 [java] Your version of R requires version 2.4 of Bioconductor. [java] trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz' [java] Content type 'application/x-gzip' length 240527 bytes (234 Kb) [java] opened URL [java] ================================================== [java] downloaded 234 Kb [java] [java] * Installing *source* package 'rJava' ... [java] checking for gcc... gcc -std=gnu99 [java] checking for C compiler default output file name... a.out [java] checking whether the C compiler works... yes [java] checking whether we are cross compiling... no [java] checking for suffix of executables... [java] checking for suffix of object files... o [java] checking whether we are using the GNU C compiler... yes [java] checking whether gcc -std=gnu99 accepts -g... yes [java] checking for gcc -std=gnu99 option to accept ISO C89... none needed [java] checking how to run the C preprocessor... gcc -std=gnu99 -E [java] checking for grep that handles long lines and -e... /bin/grep [java] checking for egrep... /bin/grep -E [java] checking for ANSI C header files... yes [java] checking for sys/wait.h that is POSIX.1 compatible... yes [java] checking for sys/types.h... yes [java] checking for sys/stat.h... yes [java] checking for stdlib.h... yes [java] checking for string.h... yes [java] checking for memory.h... yes [java] checking for strings.h... yes [java] checking for inttypes.h... yes [java] checking for stdint.h... yes [java] checking for unistd.h... yes [java] checking for string.h... (cached) yes [java] checking sys/time.h usability... yes [java] checking sys/time.h presence... yes [java] checking for sys/time.h... yes [java] checking for unistd.h... (cached) yes [java] checking for an ANSI C-conforming const... yes [java] checking whether time.h and sys/time.h may both be included... yes [java] configure: checking whether gcc -std=gnu99 supports static inline... [java] yes [java] checking Java support in R... present: [java] interpreter : '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java' [java] archiver : '/usr/lib/jvm/java-1.5.0-sun/bin/jar' [java] compiler : '/usr/lib/jvm/java-1.5.0-sun/bin/javac' [java] header prep.: '/usr/lib/jvm/java-1.5.0-sun/bin/javah' [java] cpp flags : '-I/usr/lib/jvm/java-1.5.0-sun/include -I/usr/lib/jvm/javaa-1.5.0-sun-1.5.0.14/jre/lib/amd64/server -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64 -L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64 -L/usr/local/lib64 -ljvm' [java] checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. [java] [java] Make sure you have Java Development Kit installed and correctly registered in R. [java] If in doubt, re-run "R CMD javareconf" as root. [java] [java] ERROR: configuration failed for package 'rJava' [java] * Removing '/home/yat60124/RWorkbench/library/R-version-2.9.1/rJava' [java] [java] The downloaded packages are in [java] '/tmp/Rtmp2BsLTA/downloaded_packages' [java] Warning message: [java] In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : [java] installation of package 'rJava' had non-zero exit status [java] > biocLite('JavaGD',lib='/home/yat60124/RWorkbench/library/R-version-2.9.1') [java] Running biocinstall version 2.4.11 with R version 2.9.1 [java] Your version of R requires version 2.4 of Bioconductor. [java] trying URL 'http://cran.fhcrc.org/src/contrib/JavaGD_0.5-2.tar.gz' [java] Content type 'application/x-gzip' length 87076 bytes (85 Kb) [java] opened URL [java] ================================================== [java] downloaded 85 Kb [java] [java] * Installing *source* package 'JavaGD' ... [java] checking for gcc... gcc -std=gnu99 [java] checking for C compiler default output file name... a.out [java] checking whether the C compiler works... yes [java] Exception in thread "main" org.kchine.r.server.manager.ServantCreationFailed [java] checking whether we are cross compiling... no [java] at org.kchine.r.server.manager.ServerManager.createRInternal(ServerManager.java:804) [java] checking for suffix of executables... [java] at org.kchine.r.server.manager.ServerManager.createR(ServerManager.java:463) [java] checking for suffix of object files... o [java] at org.kchine.r.server.CoreMain.main(CoreMain.java:94) [java] checking whether we are using the GNU C compiler... yes [java] checking whether gcc -std=gnu99 accepts -g... yes [java] checking for gcc -std=gnu99 option to accept ISO C89... none needed [java] checking how to run the C preprocessor... gcc -std=gnu99 -E [java] checking for grep that handles long lines and -e... /bin/grep [java] checking for egrep... /bin/grep -E [java] checking for ANSI C header files... yes [java] checking for sys/wait.h that is POSIX.1 compatible... yes [java] checking for sys/types.h... yes [java] checking for sys/stat.h... yes [java] checking for stdlib.h... yes [java] checking for string.h... yes [java] checking for memory.h... yes [java] checking for strings.h... yes [java] checking for inttypes.h... yes [java] checking for stdint.h... yes [java] checking for unistd.h... yes [java] checking for string.h... (cached) yes [java] checking sys/time.h usability... yes [java] checking sys/time.h presence... yes [java] checking for sys/time.h... yes [java] checking for unistd.h... (cached) yes [java] checking for an ANSI C-conforming const... yes [java] checking whether time.h and sys/time.h may both be included... yes [java] checking for stdlib.h... (cached) yes [java] checking for GNU libc compatible malloc... yes [java] checking return type of signal handlers... void [java] checking for memset... yes |
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