[R-pkg-devel] Cannot submit package due to false-positive rejection

[Roy Mendelssohn - NOAA Federal]

I run into this all the time.  The trick is to find a minimal example that the package will work with that shows how to make a call,  and allows for CRAN, especially on new submissions,  to test to some extent that the function works.  For more real-life examples,  write a good vignette that uses the larger dataset,  but remember that the build of the vignette also has a time limit, I think it is 10 minutes but don't quote me on that.

I may mis-state this a little,  but I believe CRAN does a nightly build of the entire environment.  If things take too long,  the build would never finish.  I am certain there are several reasons for doing this,  but one reason is to attempt to insure that all packages work together so that they will work when you install them into your environment.  As compared to another,  unnamed language where even using the package manager I have had to trash the entire environment due to inconsistencies, so packages wouldn't load. Once even after a clean install and an "update all",  several major packages wouldn't load due to inconsistencies.  If that ever has happened in R I don't remember it,  and why I go to the trouble to get my packages into CRAN,  because a lot of users just want things to work when they install the package,  and CRAN helps with that.

HTH,

-Roy



> On Oct 28, 2022, at 3:02 PM, Jeff Newmiller <jdnewmil using dcn.davis.ca.us> wrote:
> 
> This is definitely not a false positive. Find a way to not run long calcs during the CRAN build. There is no alternative.
> 
> One way this can be done is by only running your examples when an environment variable of your choosing exists. Since CRAN machines won't configure that variable, you can get around this hard requirement.
> 
> On October 28, 2022 12:48:44 PM PDT, Ying Li via R-package-devel <r-package-devel using r-project.org> wrote:
>> Hello all,
>> 
>> Our package did not pass the automagical checks when submitted to CRAN. We think the rejection is a false positive, so we �reply-all to that message and explain� as following the official instruction. We provided explanation for all notes in that email (replied to cran-submissions using r-project.org<mailto:cran-submissions using r-project.org>) but did not receive any message after 9 days.
>> 
>> I am looking for suggestions on what to do in this case: should we continue waiting for CRAN team�s reply? Or is it necessary to eliminate those notes and then submit the package again?
>> 
>> Below are the notes from CRAN teams' auto-check service and our explanation send to CRAN team:
>> 
>>> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
>>> Check: CRAN incoming feasibility, Result: NOTE
>>> Maintainer: 'Arindam RoyChoudhury <arr2014 using med.cornell.edu<mailto:arr2014 using med.cornell.edu>>'
>> 
>>> New submission
>> 
>>> Possibly misspelled words in DESCRIPTION:
>>>   Peng (17:5)
>>>   Phylogenetics (17:32)
>>>  al (17:13)
>>>   et (17:10)
>> 
>>> Size of tarball: 14208488 bytes
>> 
>> Explain:  This is a new submission. These words are not misspelled.
>> 
>>> Flavor: r-devel-windows-x86_64
>>> Check: examples, Result: NOTE
>>> Examples with CPU (user + system) or elapsed time > 10s
>>>      user system elapsed
>>> RDM 40.05   0.89   40.94
>> 
>> Explain:  This is because a large dataset is used in the example. An example with large dataset is necessary, as this package is meant for analyzing large datasets.
>> 
>> 
>>> Flavor: r-devel-linux-x86_64-debian-gcc
>>> Check: examples, Result: NOTE
>>> Examples with CPU (user + system) or elapsed time > 5s
>>>     user system elapsed
>>> RDM 24.399  0.888  25.289
>> 
>> Explain:  This is because a large dataset is used in the example. An example with large dataset is necessary, as this package is meant for analyzing large datasets.
>> 
>> Any suggestions or comments would be appreciated. Thank you in advance!
>> 
>> Best,
>> Ying
>> 
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
> 
> -- 
> Sent from my phone. Please excuse my brevity.
> 
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**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
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Santa Cruz, CA 95060
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e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/

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