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

[Karl Brand]

Hi Iain, (Martin and James),

Yes, Ubuntu. Yes, i've upgraded R versions at least once, and ubuntu 
version once. Also given

@Martin's comments, this could be the outcome of working with R on 
Ubuntu without paying attention to what goes where during package 
installation and R upgrading (as applies to here).

@James' suggestion to manually download and install packages will solve 
this issue as well as the appealing avoidance of using sudo. Definitely 
worth trying out.

thanks again for sharing these thoughts,

Karl

On 2011-11-23 20:21, Iain Gallagher wrote:
> Hi Karl
>
> Are you using Ubuntu? I just looked at my installation and see the same four libs. I wonder if this is due to initially installing R from the official Ubuntu repos and then updating R (to the current version) using the CRAN repos?
>
> Just a thought.
>
> Best
>
> Iain
>
>
>
> ________________________________
>   From: Martin Morgan<mtmorgan at fhcrc.org>
> To: Karl Brand<k.brand at erasmusmc.nl>
> Cc: bioconductor at r-project.org
> Sent: Wednesday, 23 November 2011, 17:39
> Subject: Re: [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)
>
> On 11/23/2011 08:34 AM, Karl Brand wrote:
>>
>> 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:
>>
>> Â>  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)
>
> DAVIDQuery is a Bioconductor package, but it sounds like you're choosing
> a 'CRAN' archive. The recommended installation process is
>
> Â   source("http://bioconductor.org/biocLite.R")
> Â   biocLite("DAVIDQuery")
>
>
>> Â>
>>
>> This makes me wonder if i need to specify a different library (path). If
>> so, which one?
>>
>> Â>  .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"
>
> That there are four is due to someone / thing other than R; see ?Startup
> for hints on how these libraries are identified.
>
> Martin
>
>>
>> (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
>>
>> Â>  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
>> Â>
>>
>
>
>
>
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-- 
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