[Bioc-devel] Odd behavior by R CMD check

[Martin Morgan]

On 03/11/2016 05:45 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:
> Thanks.  I'll try that. I'm surprised, as my local R-Devel install
> isn't that old.
>
> I used to have a few specific imports like this, but I was told to
> remove them because BiocCheck did not like them (because these
> packages were not declared in the "imports" line of the DESCRIPTION).
> I don't know if the newest version of BiocCheck still complains about
> them now.

The right solution is to declare them in the Imports: line, too.

Martin

>
> -Steve
>
> -----Original Message----- From: Martin Morgan
> [mailto:martin.morgan at roswellpark.org] Sent: Friday, March 11, 2016
> 2:24 PM To: Hartley, Stephen (NIH/NHGRI) [F]; bioc-devel Subject: Re:
> [Bioc-devel] Odd behavior by R CMD check
>
>
>
> On 03/11/2016 02:17 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:
>> I'm seeing some odd behavior by the R CMD check command for my
>> package, JunctionSeq.
>>
>> http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-
>>
>>
checksrc.html
>>
>> It's not technically throwing warnings (just a "NOTE"), but it is
>> claiming that there's no global definition for functions belonging
>> to the default R packages (grDevices, utils, stats, and graphics).
>>
>> So I get lines like this: drawGene: no visible global function
>> definition for 'plot.new'
>>
>> drawGene: no visible global function definition for 'plot.window'
>>
>> drawGene: no visible global function definition for 'par'
>>
>> drawGene: no visible global function definition for 'strwidth'
>>
>> drawGene: no visible global function definition for 'lines'
>>
>> drawGene: no visible global function definition for 'rect'
>>
>> drawGene: no visible global function definition for 'segments'
>>
>> drawGene: no visible global function definition for 'strheight'
>>
>> Since it's still able to compile the vignette and everything it's
>> clearly not actually having a problem finding these functions at
>> runtime, but I can't figure out what would cause it to throw these
>> notes. I don't get these notes when I run R CMD check locally on
>> any of my test machines (windows, CentOS5 linux and scientific
>> linux 6). And I've had it build with no issues before. I can't see
>> how my recent changes could possibly have caused this ...
>>
>> Has anyone ever seen this before?
>
> This is the behavior with a recent version of R-devel; likely you are
> using an older version or R-3.2.*. Things 'work' because the relevant
> packages are on the search path, but would fail if for instance the
> user or another package were to define a 'strheight' function that
> did something different from graphics::strheight.
>
> The solution is to import the relevant functions, as indicated in the
> build report.
>
> importFrom("grDevices", "cairo_ps", "col2rgb", "colorRamp",
> "dev.off", "png", "rgb", "svg", "tiff", "x11") importFrom("graphics",
> "abline", "axis", "box", "hist", "layout", "legend", "lines", "par",
> "plot", "plot.new", "plot.window", "points", "rect", "segments",
> "smoothScatter", "strheight", "strwidth", "text", "title")
> importFrom("stats", "Gamma", "as.formula", "coef", "coefficients",
> "deviance", "dnbinom", "fitted.values", "formula", "glm", "loess",
> "model.matrix", "optimize", "p.adjust", "pchisq", "predict", "qf",
> "rchisq", "rnorm", "runif", "terms", "weighted.mean")
> importFrom("utils", "object.size", "packageVersion", "read.delim",
> "read.table", "write.table")
>
> Martin
>
>>
>> Regards, Steve Hartley
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
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