Hi, I am trying to install, on a linux machine, biomaRt I used: biocLite("biomaRt") the installation however fails due to the foolwing error: > biocLite("biomaRt") Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor. also installing the dependency ?XML? trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz' I tryed to download XML package directly from R CRAN but I get: IWSS Security Event (itdmzas055) InterScan Web Security detected the following in HTTP traffic: Item: http://cran.r-project.org/src/contrib/XML_1.95-3.tar.gz Action: deleted Reason: Violation of a compressed file restriction -- File: XML_1.95-3.tar.gz, security warning: Corrupted_Zip_file The uncleanable file is deleted This happen also for older versions of the library. Any idea where an uncorrupted version of the XML library can be found? > sessionInfo() R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.0 Cheers Raffaele

raffaele.calogero at unito.it writes: > Hi, > I am trying to install, on a linux machine, biomaRt > I used: > biocLite("biomaRt") > the installation however fails due to the foolwing error: >> biocLite("biomaRt") > Running biocinstall version 2.2.9 with R version 2.7.0 > Your version of R requires version 2.2 of BioConductor. > also installing the dependency XML > > trying URL > 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz' > Error in download.file(url, destfile, method, mode = "wb", > ...) : > cannot open URL > 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz' > > I tryed to download XML package directly from R CRAN but I > get: > IWSS Security Event (itdmzas055) > InterScan Web Security detected the following in HTTP > traffic: > Item: http://cran.r-project.org/src/contrib/XML_1.95-3.tar.gz > Action: deleted > Reason: Violation of a compressed file restriction > -- File: XML_1.95-3.tar.gz, security warning: > Corrupted_Zip_file > The uncleanable file is deleted This sounds like your organization has some security software that is getting in the way. You'll need to speak with your local IT people; perhaps the source cran.r-project.org) is different from most of the other Bioconductor packages? Martin > This happen also for older versions of the library. > > Any idea where an uncorrupted version of the XML library > can be found? > >> sessionInfo() > R version 2.7.0 (2008-04-22) > x86_64-unknown-linux-gnu > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets > methods base > loaded via a namespace (and not attached): > [1] tools_2.7.0 > > > Cheers > Raffaele > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793