[Bioc-devel] Odd behavior by R CMD check

Hartley, Stephen (NIH/NHGRI) [F] stephen.hartley at nih.gov
Mon Mar 14 14:58:04 CET 2016


Why didn't this show up before in the SPB reports until recently? Is "--as-cran" a new addition to the SPB?

-----Original Message-----
From: Henrik Bengtsson [mailto:henrik.bengtsson at gmail.com] 
Sent: Friday, March 11, 2016 6:06 PM
To: Hartley, Stephen (NIH/NHGRI) [F]
Cc: Martin Morgan; bioc-devel
Subject: Re: [Bioc-devel] Odd behavior by R CMD check

If you have R-devel you can get those NOTEs using:

R CMD check --as-cran *.tar.gz

(It's been reported by --as-cran since Oct 2015 or so).

/Henrik

On Fri, Mar 11, 2016 at 2:45 PM, Hartley, Stephen (NIH/NHGRI) [F] <stephen.hartley at nih.gov> 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.
>
> -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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