Many thanks Vincent! The Biobase upgrade solved the problem. Best, Kristen
-----Original Message----- From: Vincent Carey [mailto:[email protected]] Sent: Wednesday, September 01, 2010 11:58 AM To: Dang Kristen USRE Cc: [email protected] Subject: Re: [Bioc-sig-seq] problems installing ShortRead on Linux The current version of R is 2.11.1 and an upgrade is advisable. If the installation was attempted using biocLite() which is the most recommended approach, a full transcript of the installation messages would be useful. I believe your Biobase may be out of date. > getAnywhere("mkScalar") A single object matching 'mkScalar' was found It was found in the following places package:Biobase namespace:Biobase with value function (obj) { switch(typeof(obj), character = new("ScalarCharacter", obj), logical = new("ScalarLogical", obj), integer = new("ScalarInteger", obj), double = new("ScalarNumeric", obj), stop("no scalar class implemented for type: ", typeof(obj))) } <environment: namespace:Biobase> > mkScalar(FALSE) FALSE > class(.Last.value) [1] "ScalarLogical" attr(,"package") [1] "Biobase" > sessionInfo() R version 2.11.1 Patched (2010-06-08 r52234) x86_64-apple-darwin10.3.0 locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] ShortRead_1.6.2 Rsamtools_1.0.5 lattice_0.18-5 [4] Biostrings_2.16.0 GenomicRanges_1.0.3 IRanges_1.6.14 [7] Biobase_2.8.0 weaver_1.14.0 codetools_0.2-2 [10] digest_0.4.2 loaded via a namespace (and not attached): [1] grid_2.11.1 hwriter_1.2 On Wed, Sep 1, 2010 at 10:55 AM, <[email protected]> wrote: > Dear List Members, > I asked my sysadmin to install the ShortRead package on one of our Linux > servers and he ran into a problem. He reports that all the dependencies for > Shortread installed fine, but the install of ShortRead itself failed. The > error message he receives is below: > > "Error in mkScalar(FALSE) : no scalar class implemented for type: logical > Error : unable to load R code in package 'ShortRead'" > > I have included the output of sessionInfo at the bottom of this message. > > We have previously successfully installed ShortRead on another Linux machine > that is running the same version of R, so it seems as though there is a > machine-specific difference, perhaps something to do with the R installation. > However from the error message, I cannot guess what the problem might be. > > If anyone has any suggestions, I would greatly appreciate it. > >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > Best regards, > > Kristen Dang > Computational Biologist > Syngenta Biotechnology > 3054 E. Cornwallis Rd. > Research Triangle Park, NC 27709 > www.syngenta.com > > > > > -------------------------------------------------------------------------- > This message may contain confidential information. If ...{{dropped:19}} _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
