[R-pkg-devel] no visible global function definition for ‘par’

Mon Jan 30 19:00:34 CET 2017

On 30/01/2017 12:04 PM, Cathy Lee Gierke wrote:
> That is the obvious solution, but it doesn't seem correct:  I have pdf
> included in the description, and namespace files, yet it is being called
> out.  Additionally, aren't most of these pkgs in the packages included by
> default?
>
> And up until yesterday, I didn't have any of these problems.  I've been
> compiling and running this for several years.  But now I want to release to
> CRAN, so I've been fixing minor issues....and suddenly this mass of Notes.

For several years R would allow functions from base packages to be 
assumed to be on the search list, but it no longer does so (and hasn't 
since R 3.3.0).  This is a good thing:  if your user says library(foo), 
and the foo package happens to export a pdf() function, your package may 
end up using that one, even though you really mean grDevices::pdf().  If 
you explicitly import pdf() from grDevices, that won't happen.

Duncan Murdoch

>
> Thank you,
>
> Cathy Lee Gierke
>
>
> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
> drive out hate: only love can do that.” *
> *“The arc of the moral universe is long, but it bends towards justice.”*
> *“Nothing in the world is more dangerous than sincere ignorance and
> conscientious stupidity.” *
> *“Never forget that everything Hitler did in Germany was legal.”   *
> *“Forgiveness is not an occasional act, it is a constant attitude.” *
> *“Injustice anywhere is a threat to justice everywhere.”  *
>
> ― Martin Luther King Jr.
>
> <http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>
>
> On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson <brian at braverock.com>
> wrote:
>
>> The error you reference below is pretty clear, I think.
>>
>> You need to add imports for all the functions you're using from other
>> packages.
>>
>> See: https://cran.r-project.org/doc/manuals/r-release/R-exts.
>> html#Specifying-imports-and-exports
>>
>> Regards,
>>
>> Brian
>>
>>
>> --
>> Brian G. Petersonhttp://braverock.com/brian/
>> Ph: 773-459-4973 <(773)%20459-4973>
>> IM: bgpbraverock
>>
>>
>> On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
>>
>> Yes, that seemed to get rid of the NOTE....but it doesn't seem to make
>> much difference other than that.  i.e., it seems to process the same using
>> CATkit vs CATkit_2.06.tar.gz!
>>
>> Here is the main error that I am getting.  I just upgraded to the latest R
>> version, fyi.
>>
>> Everything was fine, a few minor warnings...now this.  Description and
>> namespace are proper.  These pkgs should all be part of the R base, aren't
>> they? Anyone know why I should get these errors?  Thanks!
>>
>> * checking R code for possible problems ... NOTE
>>
>> Actogram: no visible global function definition for ‘par’
>>
>> Actogram: no visible global function definition for ‘barplot’
>>
>> Actogram: no visible global function definition for ‘box’
>>
>> Actogram: no visible global function definition for ‘text’
>>
>> Actogram: no visible global function definition for ‘mtext’
>>
>> Actogram: no visible binding for global variable ‘end’
>>
>> AutoCorr: no visible global function definition for ‘par’
>>
>> AutoCorr: no visible global function definition for ‘layout’
>>
>> AutoCorr: no visible global function definition for ‘acf’
>>
>> AutoCorr: no visible global function definition for ‘abline’
>>
>> AutoCorr: no visible global function definition for ‘title’
>>
>> AutoCorr: no visible global function definition for ‘mtext’
>>
>> AutoCorr: no visible global function definition for ‘var’
>>
>> AutoCorr: no visible binding for global variable ‘end’
>>
>> CATCosinor: no visible global function definition for ‘par’
>>
>> CATCosinor: no visible global function definition for ‘pdf’
>>
>> CATCosinor: no visible global function definition for ‘jpeg’
>>
>> CATCosinor: no visible global function definition for ‘png’
>>
>> CATCosinor: no visible global function definition for ‘tiff’
>>
>> ......... A zillion more for every function I have......
>>
>> periCosinor: no visible global function definition for ‘par’
>>
>> periCosinor: no visible global function definition for ‘fft’
>>
>> Undefined global functions or variables:
>>
>>   TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
>>
>>   coefficients dev.cur dev.off drop1 end fft gray heat.colors image
>>
>>   jpeg layout legend lines median model.tables mtext na.action na.omit
>>
>>   palette par pdf pf plot plot.new png points rainbow rasterImage
>>
>>   read.table str strwidth tail terrain.colors text tiff title ts var
>>
>>   write.table
>>
>> Consider adding
>>
>>   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
>>
>>              "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",
>>
>>              "terrain.colors", "tiff")
>>
>>   importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
>>
>>              "image", "layout", "legend", "lines", "mtext", "par",
>>
>>              "plot", "plot.new", "points", "rasterImage", "strwidth",
>>
>>              "text", "title")
>>
>>   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",
>>
>>              "drop1", "end", "fft", "median", "model.tables",
>>
>>              "na.action", "na.omit", "pf", "ts", "var")
>>
>>   importFrom("utils", "read.table", "str", "tail", "write.table")
>>
>> to your NAMESPACE file.
>>
>> Cathy Lee Gierke
>>
>>
>> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
>> drive out hate: only love can do that.” *
>> *“The arc of the moral universe is long, but it bends towards justice.”*
>> *“Nothing in the world is more dangerous than sincere ignorance and
>> conscientious stupidity.” *
>> *“Never forget that everything Hitler did in Germany was legal.”   *
>> *“Forgiveness is not an occasional act, it is a constant attitude.” *
>> *“Injustice anywhere is a threat to justice everywhere.”  *
>>
>> ― Martin Luther King Jr.
>>
>> <http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>
>>
>> On Mon, Jan 30, 2017 at 10:05 AM, Brian G. Peterson <brian at braverock.com>
>> wrote:
>>
>> On Mon, 2017-01-30 at 09:45 -0600, Cathy Lee Gierke wrote:
>>>  building ‘CATkit_2.06.tar.gz’
>>
>> R CMD build creates a tarball
>>
>>> x-134-84-0-217:CATkit user$ *R CMD check CATkit*
>>
>> but you are checknig the directory, not the tarball.
>>
>> do
>>
>> R CMD check CATkit_2.06.tar.gz
>>
>> instead.
>>
>> Regards,
>>
>> Brian
>>
>>
>>
>
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