[Bioc-devel] error in bumphunter unit test

Samuela Pollack @po||@ck @end|ng |rom j|mmy@h@rv@rd@edu
Tue Apr 2 16:17:57 CEST 2019

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

More information about the Bioc-devel mailing list