Hi Lori, I made some changes to the MEAL vignettes and now MEAL successfully passes tests on Linux and Windows (build time: 1854 and 1613 seconds respectively). However, it still times out in OSX. Should I try to reduce the building time in merida2?
Thanks, Carlos Ruiz El 13/04/2018 a las 19:39, Shepherd, Lori escribió: > > It is by fluke that the windows did not time out... The > builders timeout occur at 2400 sec and you are right up against the > edge at 2145.4 seconds on windows. > > > The build reports include an EllapsedTime indication in the summary > section for each builder ... > > > Your package does not meet the requirement (<2400 (40min!!) and your > vignette needs to be altered to fit the time constraints of the builders. > > > You should easily be able to test R CMD build on your system and log > the time to debug this issue. On linux there is the `time <command>` > option. > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ------------------------------------------------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Carlos Ruiz <carlos.r...@isglobal.org> > *Sent:* Friday, April 13, 2018 11:26:03 AM > *To:* Turaga, Nitesh; Bioc-devel > *Subject:* Re: [Bioc-devel] TIMEOUT on package MEAL > Hi BiocDevel, > > Could you help me with this issue? The report is not very informative. I > suspect that the vignettes are taking too long but I have two vignettes > and I don't know which one is more problematic. I don't understand > either why I have a timeout in OS and Linux but not in Windows. > > When I had to deal with warnings or errors, I was able to reproduce them > in my computer and solve them. Is there any way to reproduce the timeouts? > > Thank you, > > Carlos Ruiz > > > El 12/04/2018 a las 18:22, Turaga, Nitesh escribió: > > Dear maintainer, > > > > I'd like to bring to your attention that the your package is > getting a TIMEOUT 'R CMD build' on platforms in the devel version of > Bioconductor (i.e. BioC 3.7): > > > > > http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.html > > > > Would you mind taking a look at this? Don't hesitate to ask on the > bioc-devel mailing list if you have any question or need help. > > > > The package is failing on devel which is very problematic. If it is > not fixed in devel in a timely manner we would also consider this > package for potential deprecation in the next cycle. The deadline for > passing R CMD build and check in devel is April 25. > > > > Thanks for your contribution to Bioconductor. > > > > Pleae be advised that Bioconductor has switched from svn to Git. > Some helpful > > links can be found here: > > https://bioconductor.org/developers/how-to/git/ > > > > Best, > > > > Nitesh Turaga > > Bioconductor Core Team > > > > This email message may contain legally privileged and/or > confidential information. If you are not the intended recipient(s), > or the employee or agent responsible for the delivery of this message > to the intended recipient(s), you are hereby notified that any > disclosure, copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please notify > the sender immediately by e-mail and delete this email message from > your computer. Thank you. > > -- > Carlos Ruiz > PhD Student > ISGlobal > Barcelona Institute for Global Health - Campus MAR > Barcelona Biomedical Research Park (PRBB) (office 001) > Doctor Aiguader, 88 > 08003 Barcelona, Spain > Tel. +34 93 214 7309 > carlos.r...@isglobal.org > www.isglobal.org <http://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 <http://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> <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> <http://www.isglobal.org/>. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee > or agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately > by e-mail and delete this email message from your computer. Thank you. -- Carlos Ruiz PhD Student ISGlobal Barcelona Institute for Global Health - Campus MAR Barcelona Biomedical Research Park (PRBB) (office 001) Doctor Aiguader, 88 08003 Barcelona, Spain Tel. +34 93 214 7309 carlos.r...@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. ISGlobal Privacy Policy at 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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel