Vignette Run Time
Entering edit mode
Last seen 5 months ago
United States

Hi, I am working on a package and the run time for my vignette, given I run all the code which is a requirement, during the CMD build exceeds the time limit of 10 minutes. I have looked into the long tests bioconductor feature but that only seems to cover unit tests that need a long time to run. The reason why the code takes so long to run is, in order for the code to produce results full sample data is needed, as our code is based on a pipeline included in a paper. I have tried to make a smaller dataset, however, the attempts have led to incomplete/inaccurate results. Is there a way to extend the time limit on the CMD build?

Best, Matt Moravec

software error • 231 views
Entering edit mode
Last seen 10 weeks ago
United States

Please ask questions about package development on the bioc-devel mailing list

The run time limit is firm; you'll need to adjust your vignette / example data. It's disconcerting that your package only 'works' for a particular data set, it makes it seem like the code is not really meant for general use. Bioconductor is probably not the right venue if the goal is to archive your source code as an example of reproducible research, rather than to make code available for others to apply your methods to their data.


Login before adding your answer.

Traffic: 256 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6