[Bioc-devel] some new warnings in a package

So yes, you should update the NAMESPACE file following the warning
message you see in your build report.
Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.
yes, these warnings are relative new.
However all remaining NOTEs and WARNINGs that appeared in the latest build
persist, for example

* checking for code/documentation mismatches ... WARNING

just issues a warning with any further details.
ok thanks for pointing that out.

I believe this is a change in R, but the immediate culprit is 
BiocInstaller (indirectly loaded by AnnotationHub and other dependencies 
of your package). R CMD check would try and capture the 'stderr' stream 
to check for errors. BiocInstaller would try and capture the 'stderr' 
stream on package load to check for https capabilities [primarily a 
left-over from earlier version of R, where a output went directly to 
stderr rather than to a message or warning). BiocInstaller interfered 
with R CMD check.

This is fixed in BiocInstaller 1.21.7.

Thanks for the bug report and your persistence.

Martin
Thx,
Ludwig

On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...

The warnings seem to be, at first glance, linked to messages e.g. for
masking:

-----------------------------------------------------------------------

* checking S3 generic/method consistency ... WARNING

Attaching package: 'EnrichmentBrowser'

The following object is masked from 'package:BiocGenerics':

      normalize

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

------------------------------------------------------------------------

However, even when renaming the function, so that masking is not
necessary
(and the message is thus not given anymore), the issue persists.

There seems to be something weird with the current R-devel (2016-04-29
r70565), as R CMD check as prompts me to import from base packages:

-------------------------------------------------------------------------
Undefined global functions or variables:
    available.packages browseURL capture.output col2rgb data dev.off
    formula head mad median memory.limit model.matrix p.adjust par pchisq
    phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
    segments symbols text unzip write.table
Consider adding
    importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
    importFrom("graphics", "par", "segments", "symbols", "text")
    importFrom("stats", "formula", "mad", "median", "model.matrix",
               "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
               "quantile", "rnorm", "runif", "sd")
    importFrom("utils", "available.packages", "browseURL",
               "capture.output", "data", "head", "memory.limit",
               "read.delim", "unzip", "write.table")
to your NAMESPACE file.
---------------------------------------------------------------------------
the advice here -- to import from base packages -- is correct. This
ensures that a user cannot define a function, e.g., col2rgb, that masks
the one in grDevices. It is appropriate because these base packages are
not by default imported into your package namespace, so symbols are
resolved by looking on the search() path. The only exception to this is
the actual 'base' package, which _is_ imported by default.

The advice is conservative, in that it does not say that you should add
Imports: grDevices etc to your NAMESPACE file. This is also correct, in
that the grDevices package is always installed.

Martin

Somebody an idea? Or just waiting for the next R-devel snapshot?

Thx,
Ludwig

On Fri, 29-04-2016, at 23:49, Martin Morgan
<martin.morgan at roswellpark.org> wrote:
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, thanks for the reply and details. And sorry for my
not-particularly-explicit message; yes, GLAD is the package that I
moved
to
Depends. And I did not say (though I had intended too ---time to go to
bed)
that I had committed my changes to svn.

Anyway, should I revert my changes to keep GLAD in Imports?

Best,

R.

Martin

Best,

R.

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         ramon.diaz at iib.uam.es

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[Bioc-devel] some new warnings in a package

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