[Rd] solve.default(): solve.qr() or qr.solve() in warning

[Henrik Bengtsson]

If base::solve.default() is called with a 'qr' object, the following
will take place:

if(inherits(a, "qr")) {
warning("solve.default called with a \"qr\" object: use 'qr.solve'")
return(solve.qr(a, b, tol))
}

Note how the warning says that qr.solve() should be used, whereas
solve.qr() is called.

Should the warning just say:

warning("solve.default called with a \"qr\" object: use 'solve.qr'")

or

warning("solve.default called directly with a \"qr\" object: use 'solve'")?

/Henrik

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Re: [Bioc-devel] Update of miRBaseVersions.db annotation package

[Stefan Haunsberger]

Hi,

thanks for your fast reply. I've fixed the issues and get no error messages
when running BiocCheck.
This is the updated version:
https://drive.google.com/open?id=1rJcs2W5fcfc0Cq74QHfNfk0mu2xJ5JJ9

Thanks and kind regards,

Stefan

On Fri, Apr 6, 2018 at 7:58 PM Van Twisk, Daniel <
daniel.vantw...@roswellpark.org> wrote:

> I'd be happy to update your annotation package.  The package, however,
> appears to have multiple warnings and errors occurring on check and
> BiocCheck.  There appear to be some documentation issues and a test failure
> in check.  For BiocCheck, just be sure the BiocViews you are using are from
> one category, the other warning is fine.
>
>
> Please email once these issues are addressed and I can propagate the
> changes.
> --
> *From:* Bioc-devel  on behalf of Stefan
> Haunsberger 
> *Sent:* Thursday, April 5, 2018 1:39:21 PM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] Update of miRBaseVersions.db annotation package
>
> Hi everyone,
>
> I would like to update the miRBaseVersions.db annotation package in devel
> version.
> It now contains the most recent miRBase release version 22, from the 12th
> of March 2018, for mature miRNAs as well as precursor miRNAs.
>
> It can be downloaded from the following google drive repository:
>
> https://drive.google.com/file/d/1J7CFiJut-0ODDePa7oO1IY7L4JycLyX7/view?usp=sharing
>
> The most recently developed version is also available on GitHub:
> https://github.com/StefanHaunsberger/mirbaseversions.db
>
> Thanks,
>
> Stefan
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] Cannot submit package due to misspell note

[David Sterratt]

|On the subject of spell-checking, to avoid false positives when I'm 
checking the package, in the directory above the package directory I 
create a file called .spell_ignore with one word per line, and then run|:
|||devtools::spell_check("pkg/", dict="en_GB", 
ignore=read.table(".spell_ignore", stringsAsFactors=FALSE)$V1)
All the false positives still come through in the CRAN check, but it 
makes checking easier for me.


David.
|
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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