[Bioc-devel] SummarizedExperiment

Rodriguez Martinez, Andrea andrea.rodriguez-martinez13 at imperial.ac.uk
Mon Oct 24 15:07:00 CEST 2016

Thanks very much. I will do that.

Best wishes,

From: Martin Morgan <martin.morgan at roswellpark.org>
Sent: 24 October 2016 13:58:28
To: Rodriguez Martinez, Andrea; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] SummarizedExperiment

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
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