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

[James W. MacDonald]

Hi Karl,

On 11/23/2011 11:34 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:
>
> > 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)
> >

Tsk, tsk. What is this install.packages() of which you speak? I do 
believe you want

source("http://www.bioconductor.org/biocLite.R")
biocLite("DAVIDQuery")

Which is guaranteed to (find and) install the right thing, whereas 
install.packages() most likely will not.

>
> 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)).

I am not a fan of system-wide installs of R. I always just download the 
tarball to my personal directory, then do

tar xvfz <R-tarballname>
cd <R-whateverversion>
./configure && make

Then you will only have one library, and will not require sudo to do 
anything with it. When you upgrade you should always be upgrading your 
BioC install as well, and there is no profit in doing anything but 
installing biocLite() (which now comes in a package called 
BiocInstaller), and then re-installing all the packages you use in the 
new version of R.

Best,

Jim


>
> 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
> >
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues