[Bioc-devel] package build error probably due to Biomart unavailability

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Fri Apr 20 20:20:55 CEST 2018

There is this page


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

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




ETH Zurich
Dr. Peter Blattmann
Institute of Molecular Systems Biology
Aebersold group
Auguste-Piccard-Hof 1
8093 Zurich

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>

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