[Bioc-devel] SummarizedExperiment

Martin Morgan martin.morgan at roswellpark.org
Mon Oct 24 14:58:28 CEST 2016

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


importFrom(SummarizedExperiment, assays)



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.


> Any idea for this ?
> Thanks,
> Andrea
> 	[[alternative HTML version deleted]]
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