[Bioc-devel] affycoretools in devel failed to install

[James W. MacDonald]

Hi Vojtech,


On 7/25/2014 7:32 AM, Vojtech Kulvait wrote:
> Hello,
> when I try to install affycoretools in devel i get an error:
>
> * installing *source* package ‘affycoretools’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : object ‘symbols2indices’ is not exported by 'namespace:limma'
> ERROR: lazy loading failed for package ‘affycoretools’

Cutting out just what you think is important from the output from 
biocLite isn't really helpful. Instead, please give us everything.

I cannot see how this has anything to do with affycoretools anyway. I 
don't import symbols2indices, nor do I call that function in any code in 
affycoretools. Plus, limma exports every function except those that 
begin with a period, so symbols2indices is for sure exported. And to top 
it all off, the build report for affycoretools is clean, except for some 
warnings I will have to clean up sometime 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/affycoretools/zin1-checksrc.html)

If I were to make a haphazard guess, I would think your limma package 
install is borked somehow and you might be better off re-installing it.

Best,

Jim


>
> I think I have up to date instalation of all packages.
> Vojtech.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099