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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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Bug report: 4 arguments passed to .Internal(nchar) #23

Closed HenrikBengtsson closed 9 years ago

HenrikBengtsson commented 9 years ago

Received the following error in a batch jobs:

Error: 2 errors; first error:
  Error in asSamList.SamReadGroup(other): 4 arguments passed to .Internal(nchar)
 which requires 3
HenrikBengtsson commented 9 years ago

This is probably because nchar() was exported from an R 3.2.0 patched with:

> nchar
function (x, type = "chars", allowNA = FALSE, keepNA = FALSE)
.Internal(nchar(x, type, allowNA, keepNA))
<bytecode: 0x1db8008>
<environment: namespace:base>

which the compute node uses an earlier version (R 3.2.0) with:

> nchar
function (x, type = "chars", allowNA = FALSE)
.Internal(nchar(x, type, allowNA))
<bytecode: 0x1c8bc70>
<environment: namespace:base>
HenrikBengtsson commented 9 years ago

This would not be a problem if functions from the base package would be exported. Also, we should automatically filter out globals that call .Internal().

HenrikBengtsson commented 9 years ago

Created globals Issue #6 for this.