[Bioc-devel] error in bumphunter unit test

[Shepherd, Lori]

The version of R devel being used could be significant.  There have been a number of changes in R devel that could be the culprit.


Could be completely unrelated but one such example is the random number generator updates:

https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html



Please make sure you are using the most recent R-devel.


The version of packages being utilized on the build system will be the versions listed in the build report page:

http://bioconductor.org/checkResults/3.9/bioc-LATEST/


You could always do a BiocManager::valid() to test a valid install and if any packages should be updated.



Are you using a bioconductor provided devel docker images?  If you are, the devel docker image are updated weekly. You might want to pull the latest version. A locally pull docker image does not update automatically.


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 using r-project.org> on behalf of Samuela Pollack <spollack using jimmy.harvard.edu>
Sent: Tuesday, April 2, 2019 10:17:57 AM
To: Bioc-devel
Subject: [Bioc-devel] error in bumphunter unit test

Dear Bioconductor,

Our bumphunter package is failing its unit tests fairly spectacularly:
the pval algorithm seems to be returning a data frame full of zeroes.
Unfortunately, I have not been able to reproduce this behavior. I have
instantiated an EC2 instance with the devel AMI, updated all the
packages, installed bumphunter and its dependencies, and run the unit
tests without errors.

My sessionInfo indicates all R dependencies are identical to the
snapshot on the devel build report. However, two things may be causing
the disparity in results:

(i) bumphunter uses 'doParallel' and 'foreach' at the point that it is
failing; is it possible for me to confirm that I am using the same
version of these as the build system used. (Note: we are failing even
when doParallel defaults to sequential execution, so the low-level
interface does not seem to be relevant.)

(ii) The devel AMI is running R 3.6 release 75543 and the build system
is running release 76205. Could this be the discrepancy we're looking
for? We are reluctant to reinstall all of R+Bioc unless it looks relevant.

Any other suggestions would be very helpful. We haven't touched the
package in months and are totally buffaloed why it has decided to fail
just days before the new release.

thanks in advance for any advice you can offer,

- Sam

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