That will be hard to do without your package. Note that I've suggested a work around in my first reply.
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.onkel...@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 19:51 schreef Jose Barrera <jose.barr...@isglobal.org>: > 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.barr...@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: *l...@isglobal.org > <l...@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, supresión, limitación del > tratamiento, portabilidad y oposición dirigiéndose a *l...@isglobal.org > <l...@isglobal.org>* . Política de privacidad en *www.isglobal.org > <http://www.isglobal.org/>*. > > > El lun, 1 feb 2021 a las 19:42, Thierry Onkelinx (< > thierry.onkel...@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.onkel...@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.barr...@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.barr...@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: >>> *l...@isglobal.org >>> <l...@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, supresión, limitación >>> del tratamiento, portabilidad y oposición dirigiéndose a *l...@isglobal.org >>> <l...@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.onkel...@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.onkel...@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.barr...@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.barr...@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: >>>>> l...@isglobal.org <mailto:l...@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 l...@isglobal.org <mailto:l...@isglobal.org>* *. >>>>> Política de >>>>> privacidad >>>>> en www.isglobal.org <http://www.isglobal.org/>. >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________________________ >>>>> R-package-devel@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: >>> l...@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 l...@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 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: > l...@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 l...@isglobal.org . Política de privacidad en > www.isglobal.org. > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
