An error while installing RWebService
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MLSC MANIPAL ▴ 120
@mlsc-manipal-4543
Last seen 8.1 years ago
*Dear Sir, I want to use RWebServices package. I have already installed BioMart, Biostrings, ChipPeakAnno, Iranges, Genomic features, MicroRNA, Limma, RJava, TypeInfo, But when i try to install the RWebServices it is asking to install the SJava package. But I find following error when I start to install SJava: * Using R version 2.11.1, biocinstall version 2.6.9. Installing Bioconductor version 2.6 packages: [1] "SJava" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/home/student/R/i686-pc-linux-gnu-library/2.11' trying URL ' http://www.bioconductor.org/packages/2.6/bioc/src/contrib/SJava_0.74.0 .tar.gz ' Content type 'application/x-gzip' length 2208965 bytes (2.1 Mb) opened URL ================================================== downloaded 2.1 Mb * installing *source* package ‘SJava’ ... checking shlib support in R... checking Java support in R... present: interpreter : '/usr/bin/java' archiver : '/usr/bin/jar' compiler : '/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags : '' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L/usr/java/packages/lib/i386 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. R was configured without full Java support (including JDK). Please run R CMD javareconf as root to add Java support to R. If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables. ERROR: configuration failed for package ‘SJava’ * removing ‘/home/student/R/i686-pc-linux-gnu-library/2.11/SJava’ The downloaded packages are in ‘/tmp/RtmpKKfFj5/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'SJava' had non-zero exit status *Hence, Can you please suggest me a solution for this?* * * *Thanking you in anticipation.* * * *Regards,* *Rayan* [[alternative HTML version deleted]]
limma biomaRt RWebServices IRanges microRNA SJava ChIPpeakAnno limma biomaRt RWebServices • 826 views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States
On Tue, Mar 15, 2011 at 1:59 AM, MLSC MANIPAL <mlscmahe@gmail.com> wrote: > *Dear Sir, > > I want to use RWebServices package. I have already installed BioMart, > Biostrings, ChipPeakAnno, Iranges, Genomic features, MicroRNA, Limma, > RJava, > TypeInfo, But when i try to install the RWebServices it is asking to > install the SJava package. > > But I find following error when I start to install SJava: > * > Using R version 2.11.1, biocinstall version 2.6.9. > Installing Bioconductor version 2.6 packages: > [1] "SJava" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using > '/home/student/R/i686-pc-linux-gnu-library/2.11' > trying URL ' > > http://www.bioconductor.org/packages/2.6/bioc/src/contrib/SJava_0.74 .0.tar.gz > ' > Content type 'application/x-gzip' length 2208965 bytes (2.1 Mb) > opened URL > ================================================== > downloaded 2.1 Mb > > * installing *source* package ‘SJava’ ... > checking shlib support in R... checking Java support in R... present: > interpreter : '/usr/bin/java' > archiver : '/usr/bin/jar' > compiler : '/usr/bin/javac' > header prep.: '/usr/bin/javah' > cpp flags : '' > java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server > -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 > -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L/usr/java/packages/lib/i386 > -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' > configure: error: One or more Java configuration variables are not set. > R was configured without full Java support (including JDK). Please run > > R CMD javareconf > > as root to add Java support to R. If you don't have root privileges, > run > > R CMD javareconf -e > > to set all Java-related variables. > ERROR: configuration failed for package ‘SJava’ > * removing ‘/home/student/R/i686-pc-linux-gnu-library/2.11/SJava’ > > The downloaded packages are in > ‘/tmp/RtmpKKfFj5/downloaded_packages’ > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'SJava' had non-zero exit status > > > > *Hence, Can you please suggest me a solution for this?* > Did you try the suggested commands? Running R CMD javareconf as root, or if you don't have root access: R CMD javareconf -e Then try running R and installing SJava again. Dan > * * > > *Thanking you in anticipation.* > > * * > > *Regards,* > > *Rayan* > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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