[Bioc-devel] Odd behavior by R CMD check

[Dan Tenenbaum]

----- Original Message -----
> From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hartley at nih.gov>
> To: "Henrik Bengtsson" <henrik.bengtsson at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, March 14, 2016 6:58:04 AM
> Subject: Re: [Bioc-devel] Odd behavior by R CMD check

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

No. SPB does not use "--as-cran". As was pointed out earlier in this thread, R-devel is now emitting this information by default (i.e. with or without the --as-cran flag).

Dan


> -----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]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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