[Bioc-devel] Bioconductor package build fails

Hoffman, Gabriel g@briel@hoffm@n @ending from m@@m@edu
Thu Oct 11 20:38:15 CEST 2018

I am the developer of the variancePartition package, and I recently made some very small changes to the documentation of my package.  The latest version 1.10.3 builds correctly on Bioconductor's Windows and OS X machines but fails on Ubuntu:


The code in the package has been stable, and I am not able to reproduce the error on by Ubuntu machine 14.04.5 LTS with R 3.5.1.

The issue has something to do with multithreading using doParallel.  The error is:

Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  :
  port 11104 cannot be opened
Quitting from lines 102-154 (variancePartition.Rnw)
Error: processing vignette 'variancePartition.Rnw' failed with diagnostics:
cannot open the connection
Execution halted

With the Bioconductor 3.7 Freeze coming, I�m concerned about getting stuck with a broken package.

 - Gabriel

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