Re: [R-pkg-devel] Inconsistent R CMD Check results

[Ying Li via R-package-devel]

That makes sense, thanks very much for your explanation and advice, Tomas and 
Uwe!

Best,
Ying

From: Uwe Ligges 
Sent: Wednesday, January 25, 2023 9:52
To: Tomas Kalibera ; Ying Li 
; r-package-devel@r-project.org 

Cc: Arindam RoyChoudhury 
Subject: [EXTERNAL] Re: [R-pkg-devel] Inconsistent R CMD Check results



On 24.01.2023 22:03, Tomas Kalibera wrote:
> On 1/23/23 17:51, Ying Li via R-package-devel wrote:
>> Dear all,
>>
>> Hope you are well! Recently, in the check before a re-submission, I
>> got an unexpected note when doing R CMD Check using
>> rhub::check_for_cran(), saying that "Examples with CPU (user + system)
>> or elapsed time > 5s".
>>
>> I didn't expect this note to appear because the same examples didn't
>> cause this note in the previous submission last December. Compared
>> with the previous submission, we only edited documentation, there was
>> no change in the R code for functions of our package.
>>
>> To double-check, I downloaded our previous submission from CRAN and
>> checked it again. It's strange that this current CRAN version also has
>> this note now. However, when submitting it last December, there were
>> no such notes. Do you have any idea why the R CMD Check results are
>> inconsistent?
>
> You could check on Winbuilder as that is a concrete setup used for
> incoming checks. But in principle, the computation may take longer
> because of changes in dependencies, external software and R. Which can
> be due to a performance regression, a bugfix, etc. Only
> debugging/profiling could reveal the true cause.

Yes, it may even be some OS update, or just coincidence that the system
was idling the last time your package got checked.
Note that CRAN systems are expected to be slower than, e.g., your
laptop, as the servers use multi core CPUs with rather low frequencies.

Best,
Uwe Ligges




>> Since the examples caused no note in the last submission and were
>> successfully submitted to CRAN, I'm not sure whether I should change
>> the examples in this re-submission to eliminate this sudden note. Any
>> suggestions will be appreciated!
> If you were close to the limit last time, it may be a coincidence and
> you might simply reduce the examples to be on the safe side.
>
> Tomas
>
>>
>> Thank you!
>> Ying
>>
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>>
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[R-pkg-devel] Inconsistent R CMD Check results

[Ying Li via R-package-devel]

Dear all,

Hope you are well! Recently, in the check before a re-submission, I got an 
unexpected note when doing R CMD Check using rhub::check_for_cran(), saying 
that "Examples with CPU (user + system) or elapsed time > 5s".

I didn't expect this note to appear because the same examples didn't cause this 
note in the previous submission last December. Compared with the previous 
submission, we only edited documentation, there was no change in the R code for 
functions of our package.

To double-check, I downloaded our previous submission from CRAN and checked it 
again. It's strange that this current CRAN version also has this note now. 
However, when submitting it last December, there were no such notes. Do you 
have any idea why the R CMD Check results are inconsistent?

Since the examples caused no note in the last submission and were successfully 
submitted to CRAN, I'm not sure whether I should change the examples in this 
re-submission to eliminate this sudden note. Any suggestions will be 
appreciated!

Thank you!
Ying

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

[Ying Li via R-package-devel]

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-submissi...@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 
> mailto:arr2...@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



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