[R-pkg-devel] Cache in vignette not working when checking a package

Mon Feb 1 19:41:57 CET 2021

Probably because the cache is not installed into the package. I'd check the
tar.gz file to see if the cache is present.

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////

<https://www.inbo.be>

Op ma 1 feb. 2021 om 19:01 schreef Jose Barrera <jose.barrera using isglobal.org>:

> Dear Thierry,
>
> Thanks for your advice. However, I would like to understand why when I
> build the vignette to get the pdf from the Rnw, it takes just 8 seconds
> once the "cache" folder has been created instead of the initial 4 minutes,
> but this time reduction does not happen when checking the package.
>
> Best,
>
> Jose Barrera
> Statistician, Associate Lecturer
>
> *IS**Global*
> Barcelona Institute for Global Health - Campus MAR
> Barcelona Biomedical Research Park (PRBB) (Room Hypatia)
>
> Doctor Aiguader, 88
> 08003 Barcelona, Spain
> Tel. +34 93 2147383
> jose.barrera using isglobal.org
> <https://www.linkedin.com/in/josebarrera>
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> www.isglobal.org
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> El lun, 1 feb 2021 a las 13:02, Thierry Onkelinx (<
> thierry.onkelinx using inbo.be>) escribió:
>
>> Dear Jose,
>>
>> I store the results of CPU intensive chunks in the package. Have a look
>> at
>> https://github.com/ropensci/git2rdata/blob/master/vignettes/efficiency.Rmd
>> .
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkelinx using inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be
>>
>>
>> ///////////////////////////////////////////////////////////////////////////////////////////
>> To call in the statistician after the experiment is done may be no more
>> than asking him to perform a post-mortem examination: he may be able to say
>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does not
>> ensure that a reasonable answer can be extracted from a given body of data.
>> ~ John Tukey
>>
>> ///////////////////////////////////////////////////////////////////////////////////////////
>>
>> <https://www.inbo.be>
>>
>>
>> Op ma 1 feb. 2021 om 12:49 schreef Jose Barrera <
>> jose.barrera using isglobal.org>:
>>
>>> Dear all,
>>>
>>> I have an issue when checking a package that includes a vignette using
>>> cache = TRUE in some chunks. The vignette is generated with knit from an
>>> Rnw document. The issue is that cache works when building the vignette
>>> locally but it seems not working when checking the package.
>>>
>>> I have proceeded as follows:
>>>
>>> 1) R CMD build collin --resave-data
>>>       * creating vignettes...  --->  4 minutes
>>> 2) R CMD check --as-cran collin_0.0.1.tar.gz
>>>       * checking re-building of vignette outputs ...  --->  4 minutes
>>> 3) I install "collin_0.0.1.tar.gz" in my laptop
>>> 4) In an R session, I build the vignette "collin/vignettes/collin.Rnw".
>>> It
>>> takes 4.7 minutes and the "cache" folder is created in
>>> "collin/vignettes/"
>>> 5) I remove all aux files in "collin/vignettes/" (now, the only extra
>>> item
>>> is the "cache" folder)
>>> 6) I re-build the vignette in the R session and now it takes only 8
>>> seconds, so the cache is working
>>> 7) Repeat 5)
>>> 8) Repeat 1) and 2) but it still takes 4 minutes so it seems like R CMD
>>> build and R CMD check are ignoring the "cache" folder in
>>> "collin/vignettes/".
>>>
>>> I would be very grateful if you could provide some advice on how to fix
>>> the
>>> problem.
>>>
>>> Best,
>>>
>>> Jose Barrera
>>> Statistician, Associate Lecturer
>>>
>>> ISGlobal
>>> Barcelona Institute for Global Health - Campus MAR
>>> Barcelona Biomedical Research Park (PRBB) (Room Hypatia)
>>>
>>> Doctor Aiguader, 88
>>> 08003 Barcelona, Spain
>>> Tel. +34 93 2147383
>>> jose.barrera using isglobal.org
>>> www.isglobal.org
>>>
>>> --
>>>
>>>
>>> This message is intended exclusively for its addressee and may contain
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>>> If
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>>
> This message is intended exclusively for its addressee and may contain
> information that is CONFIDENTIAL and protected by professional privilege.
> If you are not the intended recipient you are hereby notified that any
> dissemination, copy or disclosure of this communication is strictly
> prohibited by law. If this message has been received in error, please
> immediately notify us via e-mail and delete it.
>
> DATA PROTECTION. We inform you that your personal data, including your
> e-mail address and data included in your email correspondence, are included
> in the ISGlobal Foundation files. Your personal data will be used for the
> purpose of contacting you and sending information on the activities of the
> above foundations. You can exercise your rights of access, rectification,
> cancellation and opposition by contacting the following address:
> lopd using isglobal.org. ISGlobal Privacy Policy at www.isglobal.org.
>
>
> -----------------------------------------------------------------------------------------------------------------------------
>
> CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a su
> destinatario y puede contener información confidencial, por lo que la
> utilización, divulgación y/o copia sin autorización está prohibida por la
> legislación vigente. Si ha recibido este mensaje por error, le rogamos lo
> comunique inmediatamente por esta misma vía y proceda a su destrucción.
>
> PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este
> envío, incluida su dirección de e-mail, forman parte de ficheros de
> titularidad de la Fundación ISGlobal  para cualquier finalidades de
> contacto, relación institucional y/o envío de información sobre sus
> actividades. Los datos que usted nos pueda facilitar contestando este
> correo quedarán incorporados en los correspondientes ficheros, autorizando
> el uso de su dirección de e-mail para las finalidades citadas. Puede
> ejercer los derechos de acceso, rectificación, cancelación y oposición
> dirigiéndose a lopd using isglobal.org . Política de privacidad en
> www.isglobal.org.
>

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