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

Tue Feb 2 12:00:10 CET 2021

On 01/02/2021 1:51 p.m., Jose Barrera wrote:
> 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"?

Where is the cache on your local system?  I think if it is in the 
vignettes/<vignettename>_cache directory, it would be installed (unless 
your .Rbuildignore file says to ignore it).

If you extract the tar.gz file into a new directory, does the cache end 
up in the same directory as the main vignette file?

Duncan Murdoch

> 
> 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
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>>> 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/>*.
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>>>
>>> -----------------------------------------------------------------------------------------------------------------------------
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>>> envío, incluida su dirección de e-mail, forman parte de ficheros de
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>>> <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,
>>>>> 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 <mailto:lopd using isglobal.org>* *.
>>>>> Política de
>>>>> privacidad
>>>>> en www.isglobal.org <http://www.isglobal.org/>.
>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>
>>> 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.
>>>
>>
>