[BioC] installation of org.Hs.eg.db

[axel.klenk at actelion.com]

Dear Andreia,

the warning is simply informing you that the package
will be installed into the default library because you
have not specified a 'lib' argument. No need to worry
about that. Try:

library("org.Hs.eg.db")

and you will see that it works... hopefully... :-)

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland



                                                                           
             Andreia Fonseca                                               
             <andreia.fonseca@                                             
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             Sent by:                  bioconductor at stat.math.ethz.ch      
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             z.ch                                                  Subject 
                                       [BioC] installation of org.Hs.eg.db 
                                                                           
             11/26/2009 04:31                                              
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Dear Forum,


I have installed biomart, in the begining I had problems because some
libraries the Rcurl and the xml were missing. But now I am getting the same
error with biocLite("org.Hs.eg.db")

I get that is missing a library but I am not understanding which, can
someone help me? I run Ubuntu 9.04

Thanks Andreia

Below is the messages after

> source ("http://bioconductor.org/biocLite.R")
> biocLite("org.Hs.eg.db")

Running biocinstall version 2.3.14 with R version 2.8.1
Your version of R requires version 2.3 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/user/R/x86_64-pc-linux-gnu-library/2.8'
trying URL '
http://bioconductor.org/packages/2.3/data/annotation/src/contrib/org.Hs.eg.db_2.2.6.tar.gz

'
Content type 'application/x-gzip' length 31989336 bytes (30.5 Mb)
opened URL
==================================================
downloaded 30.5 Mb

* Installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
 >>> Building/Updating help pages for package 'org.Hs.eg.db'
     Formats: text html latex example
  org.Hs.egACCNUM                   text    html    latex   example
  org.Hs.egALIAS2EG                 text    html    latex   example
  org.Hs.egBASE                     text    html    latex   example
  org.Hs.egCHR                      text    html    latex   example
  org.Hs.egCHRLENGTHS               text    html    latex   example
  org.Hs.egCHRLOC                   text    html    latex   example
  org.Hs.egENSEMBL                  text    html    latex   example
  org.Hs.egENSEMBLPROT              text    html    latex   example
  org.Hs.egENSEMBLTRANS             text    html    latex   example
  org.Hs.egENZYME                   text    html    latex   example
  org.Hs.egGENENAME                 text    html    latex   example
  org.Hs.egGO                       text    html    latex   example
  org.Hs.egGO2ALLEGS                text    html    latex   example
  org.Hs.egMAP                      text    html    latex   example
  org.Hs.egMAPCOUNTS                text    html    latex   example
  org.Hs.egOMIM                     text    html    latex   example
  org.Hs.egORGANISM                 text    html    latex   example
  org.Hs.egPATH                     text    html    latex   example
  org.Hs.egPFAM                     text    html    latex   example
  org.Hs.egPMID                     text    html    latex   example
  org.Hs.egPROSITE                  text    html    latex   example
  org.Hs.egREFSEQ                   text    html    latex   example
  org.Hs.egSYMBOL                   text    html    latex   example
  org.Hs.egUNIGENE                  text    html    latex   example
  org.Hs.egUNIPROT                  text    html    latex   example
  org.Hs.eg_dbconn                  text    html    latex   example
** building package indices ...
* DONE (org.Hs.eg.db)

The downloaded packages are in
    /tmp/RtmpqsEDGq/downloaded_packages

             [[alternative HTML version deleted]]

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