[BioC] problem while loading affycoretools

[Henrik Bengtsson]

On Sun, Sep 15, 2013 at 2:51 PM, Steve Lianoglou
<lianoglou.steve at gene.com> wrote:
> Hi,
>
> On Sun, Sep 15, 2013 at 1:57 PM, Mayte Suarez-Farinas
> <farinam at mail.rockefeller.edu> wrote:
>> I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools:
>>
>> library(affycoretools)
>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
>>   there is no package called ‘ff’
>> Error: package or namespace load failed for ‘affycoretools’
>
> This is strange -- for some reason R is trying to load the ff package,
> but as far as I am aware, affycoretools does not depend on this
> package.

FYI, 'affycoretools' imports 'oligoClasses' which in turn imports
'ff'.  Maybe there are other paths to 'ff' as well.

/Henrik

>
> You can try to install ff first and see if affycoretools will load:
>
> http://cran.r-project.org/web/packages/ff/index.html
>
> I'm curious if you have trouble loading any other package? Perhaps you
> can try something completely out of bioconductor land like ggplot2 or
> plyr.
>
> Do those work?
>
> You might want to start R via `R --vanilla` in your terminal. Perhaps
> there's some weirdness in an ~/.Rdata file that is being loaded and is
> tripping you up (I'd try this first, actually).
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
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