Errors, Logs and Debugging in BiocParallel

This vignette is part of the BiocParallel package and focuses on error handling and logging. A section at the end demonstrates how the two can be used together as part of an effective debugging routine. BiocParallel provides a unified interface to the parallel infrastructure in several packages including snow , parallel , BatchJobs and foreach. When implementing error handling in BiocParallel the primary goals were to enable the return of partial results when an error is thrown (vs just the error) and to establish logging on the workers. In cases where error handling existed, such as BatchJobs and foreach, those behaviors were preserved. Clusters created with snow and parallel now have flexible error handling and logging available through SnowParam and MulticoreParam objects. In this document the term “job” is used to describe a single call to a bp*apply function (e.g., the X in bplapply). A “job” consists of one or more “tasks”, where each “task” is run separately on a worker. The BiocParallel package is available at bioconductor.org and can be downloaded via biocLite: source("http://bioconductor.org/biocLite.R") biocLite("BiocParallel")