[Bioc-devel] Bioconductor Issue 395: An R package OPWeight

Martin Morgan martin.morgan at roswellpark.org
Tue Jul 4 00:27:35 CEST 2017

On 07/03/2017 11:27 AM, Shakil Mohamad wrote:
> Hi,
> I have a "Timeout" problem in my package building. If I use cache = TRUE in
> the vignette, the package builds smoothly; however, chache=FALSE faces
> timeout problem. Can anyone know why?

superficially, this suggests that you should be less ambitious in the 
examples or data analysis in the vignette.

More deeply, this usually means that your code is written inefficiently. 
You should try to identify the slowest functions, and try to improve 
their performance, usually by writing them as 'vectorized' (e.g., 
colSums(x)) rather than 'iterative' (e.g., apply(x, 2, sum)).


> I was recommended to uses cache=FALSE so that the tarball size become
> <=5MB.
> Another option, can I use chache=TRUE then during the push to
> Biconductor, I manually delete cache folder to save the space? It worked
> well before with me.
> Note that, the following code I used in the vignette
> knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, autodep = TRUE)
> Thank you
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