[BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)

Karl Brand k.brand at erasmusmc.nl
Wed Nov 23 17:34:38 CET 2011

Esteemed BioC UseRs and Devs,

I'm trying (and failing) to install the BioC package "DAVIDQuery". There 
must be a simple way to solve this issue, but my googling failed to 
solve this issue.

Within (ESS/Emacs) R --vanilla i tried:

 > install.packages("DAVIDQuery", dependencies=TRUE)
Installing package(s) into ‘/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
   package ‘DAVIDQuery’ is not available (for R version 2.14.0)

This makes me wonder if i need to specify a different library (path). If 
so, which one?

 > .libPaths()
[1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"

(This is a bigger area of ignorance for me - why has R set up four 
separate libraries by default? Where some require use of sudo to 
install/update packages, whilst others do not? And what are the 
implications when it comes time to upgrade to the next version of R? I 
have obtained some advice on this before - 
https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but 
have failed to implement this given my focus on just using R, neglecting 
its proper maintenance, and all round inexperience with linux).

I'd really appreciate responses on getting "DAVIDQuery" running on my 
currently installed R 2.14.0 (as well as any tips on 'good practice' 
when it comes to R library management on linux (ubuntu)).



 > sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_DK.UTF-8"       LC_COLLATE=en_AU.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.14.0 tools_2.14.0

Karl Brand <k.brand at erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268

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