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k. brand
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@k-brand-1874
Last seen 10.0 years ago
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)).
Sincerely,
Karl
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=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