[Bioc-devel] Help with tokay2 errors

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Apr 2 21:34:31 CEST 2020

On quick glance into the logs on tokay2 it looks like it may be an issue with MotifDb and not your package.
In merge_motif it doesn't get to evaluating the code as it is hung up on trying to load the MotifDb library.  Once this library is called,
There are numerous:

*** recursive gc invocation

and somewhere in the middle of all these repeated lines is

Error: package or namespace load failed for 'MotifDb':
 .onLoad failed in loadNamespace() for 'MotifDb', details:
  call: base::colSums(x, na.rm = na.rm, dims = dims, ...)
  error: bad binding access
Execution halted

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Benjamin Jean-Marie Tremblay <benjamin.tremblay using uwaterloo.ca>
Sent: Saturday, March 28, 2020 4:22 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Help with tokay2 errors


Recently I've been having several examples fail on the tokay2 test machine,
specifically the i386 examples. Unfortunately I don't have access to a
windows machine to diagnose these failures right now, and the output that I
can see shows no errors; the examples just end abruptly. I don't see these
failures on my own computer (regular macOS, also docker bioc-devel image), so
I�m at a bit of a loss as to how to go about fixing these.


Any help would be greatly appreciated.


Benjamin Tremblay
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