Missing packages in conda environment

[BerndDoser]

Two linux workstations are showing following error message calling the pipeline within the conda environment:

Warning message:
In options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
Error: package or namespace load failed for ‘methods’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘datasets’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘utils’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘grDevices’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘graphics’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘stats’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Error: package or namespace load failed for ‘methods’:
 .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
During startup - Warning messages:
1: package "methods" in options("defaultPackages") was not found 
2: package ‘datasets’ in options("defaultPackages") was not found 
3: package ‘utils’ in options("defaultPackages") was not found 
4: package ‘grDevices’ in options("defaultPackages") was not found 
5: package ‘graphics’ in options("defaultPackages") was not found 
6: package ‘stats’ in options("defaultPackages") was not found 
7: package ‘methods’ in options("defaultPackages") was not found 
Error: .onLoad failed in loadNamespace() for 'methods', details:
  call: assign(".methodsNamespace", where, baseenv())
  error: cannot add binding of '.methodsNamespace' to the base environment
Fatal error: unable to initialize the JIT

It was not possible to reproduce this error on a developer machine. Therefore, we will keep this issue under observation for the moment.

[BerndDoser]

Some references found so far:

• https://stackoverflow.com/questions/36963671/some-packages-were-not-found
• Fatal error: unable to initialize the JIT when R in the PATH but libR.so not found. rpy2/rpy2#870