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

2022-10-28 Thread Roy Mendelssohn - NOAA Federal via R-package-devel 
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  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 
>  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-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
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
> 
> -- 
> Sent from my phone. Please excuse my brevity.
> 
> __
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**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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

2022-10-28 Thread Jeff Newmiller 
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 
 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-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
>
>
>
>   [[alternative HTML version deleted]]
>

-- 
Sent from my phone. Please excuse my brevity.

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

2022-10-28 Thread 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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