Dear all, Our package DominoEffect failed the most recent tests and I suspect the problem was that Biomart was unavailable while the package was packaged and tested (we rely on the biomaRt package). I believe this because I cannot reproduce the error on my own machine and the commit aa9212c has been working fine since two months. However, regarding the upcoming release it would be good to not rely on chance that biomart is up and running (if my hypothesis is correct that this was the problem). Therefore, has anyone an idea how to prevent such errors in the future or has experience with biomaRt functions in their test or vignettes? Thank you very much for your help. Best regards Peter http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/merida2-checksrc.html http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/tokay2-buildsrc.html http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/malbec2-buildsrc.html ___________________________________________________________ ETH Zurich Dr. Peter Blattmann Institute of Molecular Systems Biology Aebersold group HPT E58 Auguste-Piccard-Hof 1 8093 Zurich Switzerland phone: +41 44 633 26 97 cellphone: +41 79 745 80 61 fax: +41 44 633 15 32 E-mail: blattmann at imsb.biol.ethz.ch<mailto:blattmann at imsb.biol.ethz.ch>
[Bioc-devel] package build error probably due to Biomart unavailability
2 messages · Blattmann Peter, Shepherd, Lori
There is this page http://bioconductor.org/developers/how-to/web-query/ That suggests some try catch loops to at least try and fail gracefully 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-bounces at r-project.org> on behalf of Blattmann Peter <blattmann at imsb.biol.ethz.ch>
Sent: Friday, April 20, 2018 1:44:08 PM
To: mailman, bioc-devel; grimbough at gmail.com
Cc: Buljan Marija
Subject: [Bioc-devel] package build error probably due to Biomart unavailability
Sent: Friday, April 20, 2018 1:44:08 PM
To: mailman, bioc-devel; grimbough at gmail.com
Cc: Buljan Marija
Subject: [Bioc-devel] package build error probably due to Biomart unavailability
Dear all, Our package DominoEffect failed the most recent tests and I suspect the problem was that Biomart was unavailable while the package was packaged and tested (we rely on the biomaRt package). I believe this because I cannot reproduce the error on my own machine and the commit aa9212c has been working fine since two months. However, regarding the upcoming release it would be good to not rely on chance that biomart is up and running (if my hypothesis is correct that this was the problem). Therefore, has anyone an idea how to prevent such errors in the future or has experience with biomaRt functions in their test or vignettes? Thank you very much for your help. Best regards Peter http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/merida2-checksrc.html http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/tokay2-buildsrc.html http://bioconductor.org/checkResults/devel/bioc-LATEST/DominoEffect/malbec2-buildsrc.html ___________________________________________________________ ETH Zurich Dr. Peter Blattmann Institute of Molecular Systems Biology Aebersold group HPT E58 Auguste-Piccard-Hof 1 8093 Zurich Switzerland phone: +41 44 633 26 97 cellphone: +41 79 745 80 61 fax: +41 44 633 15 32 E-mail: blattmann at imsb.biol.ethz.ch<mailto:blattmann at imsb.biol.ethz.ch> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at 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.