[Bioc-devel] some new warnings in a package

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.

Best,

R.

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.

Martin

Best,

R.

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