[Bioc-devel] SummarizedExperiment

[Martin Morgan]

On 10/24/2016 07:48 AM, Rodriguez Martinez, Andrea wrote:
> Hi,
>
>
> I am developing a package based on the SummarizedExperiment package. I have included the SummarizedExperiment package in both DESCRIPTION and NAMESPACE files. In some functions of my package, and also in the vignette, I use the function "assays()" from the SummarizedExperiment package. However, when I try to build the vignette, it says: function "assays()" not found. The same happens when checking my package.
>
>

Imports: SummarizedExperiment

and

importFrom(SummarizedExperiment, assays)

or

import(SummarizedExperiment)

is sufficient for R functions defined in your package.

The code in a vignette is run as if it were a script source'd in to R, 
so if you use assays() at the 'top level' (seen by the user) then you 
need to ensure that assays() is visible -- include SummarizedExperiment 
in the Depends: field of your package and library(yourpackage) in the 
vignette, or library(SummarizedExperiment) in your vignette, or 
SummarizedExperiment::assays() in your vignette, etc.

If that doesn't help, feel free to point to the specific vignette in github.

Martin

> Any idea for this ?
>
>
> Thanks,
>
>
> Andrea
>
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>
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