Account for bpiterate returning a list of remote_error objects #28
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Side note: I suspect the behavior of returning a list of errors without actually signaling an error might ultimately be a bug in one of the parallel backends (specifically BatchtoolsParam). But regardless, it is a possible case that should be handled. |
DarwinAwardWinner
force-pushed
the
misc-improvements
branch
from
4b9a97e to
5eb7e0c
Compare
|
I refactored this based on the BiocParallel error-handling documentation: https://bioconductor.org/packages/devel/bioc/vignettes/BiocParallel/inst/doc/Errors_Logs_And_Debugging.pdf Let me know if you want me to rebase it onto the latest master. |
DarwinAwardWinner
force-pushed
the
misc-improvements
branch
from
5eb7e0c to
59217be
Compare
Apparently bpiterate can sometimes return a list, but one or more elements of the list is a remote error object. The code now checks for this case using BiocParallel::bpok.
DarwinAwardWinner
force-pushed
the
misc-improvements
branch
from
59217be to
3edd25a
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Apparently bpiterate can sometimes return a list, but one or more elements of the list is a remote error object. The code now checks for this case.
I believe this error case was probably introduced by my previous pull request (#27), which removed the use of the
REDUCEargument tobpiterateas part of an optimization. This pull request now properly handles the case my code introduced.