[Bioc-devel] some new warnings in a package

Martin Morgan martin.morgan at roswellpark.org
Fri Apr 29 23:49:06 CEST 2016

On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
> Dear All,
> In case it matters, and since we are past the 22, I just noticed that a
> package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g.,
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
> that, if I recall correctly, were not being given around the 22nd. I think
> these warnings have started appearing with the latest Rs in BioC (around
> r70549?). I haven't been able to understand the ultimate cause of the
> warnings (as they seem to refer to issues that are not in the code of my
> package), but they disappear when I move a package from Imports to Depends.

They seem to come from GLAD's use of packageStartupMessage() in .onLoad 
(e.g., when the package is imported) rather than the recommended 
.onAttach (when the package is attached to the search() path, e.g., via 
library() or Depends: in the DESCRIPTION file).

I updated GLAD to use packageStartuupMessage() in .onAttach; I think the 
warnings will go away.


> Best,
> R.

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