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

Mon Feb 1 19:51:47 CET 2021

Indeed, the "cache" folder is not present in the tar.gz file. Could you
please help me on how to fix "the cache is not installed into the package"?

Thanks,

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>
Personal website: sites.google.com/view/josebarrera
www.isglobal.org

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El lun, 1 feb 2021 a las 19:42, Thierry Onkelinx (<thierry.onkelinx using inbo.be>)
escribió:

> 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>
>> Personal website: sites.google.com/view/josebarrera
>> www.isglobal.org
>>
>> 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 filing system. 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 to
>> access to personal data, rectification, erasure, restriction of processing,
>> data portability and object by contacting the following address: *lopd using isglobal.org
>> <lopd using isglobal.org>*. ISGlobal Privacy Policy at *www.isglobal.org
>> <http://www.isglobal.org/>*.
>>
>>
>> -----------------------------------------------------------------------------------------------------------------------------
>>
>> CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a
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>> 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
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>> <lopd using isglobal.org>* . Política de privacidad en *www.isglobal.org
>> <http://www.isglobal.org/>*.
>>
>>
>> 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
>>>> 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 <mailto:lopd using isglobal.org>. ISGlobal
>>>> Privacy Policy at
>>>> www.isglobal.org <http://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,
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>>>> el
>>>> uso de su dirección de e-mail para las finalidades citadas. Puede
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>>>> privacidad
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>>>>
>>>> ______________________________________________
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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.
>>
>

-- 

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
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immediately notify
us via e-mail and delete it.

DATA PROTECTION. We 
inform you that your personal data, including your
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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 <mailto:lopd using isglobal.org>. ISGlobal
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www.isglobal.org <http://www.isglobal.org/>.

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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 
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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 
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dirigiéndose a lopd using isglobal.org <mailto:lopd using isglobal.org>* *. Política de 
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en www.isglobal.org <http://www.isglobal.org/>.

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