CHANGES IN VERSION 1.7 ---------------------- BUG FIXES o (v. 1.7.4) Allow more than 125 MPI nodes, https://github.com/Bioconductor/BiocParallel/issues/55 NEW FEATURES o Throttle number of cores used on Bioconductor build systems (with environment variable BBS_HOME set) to 4 CHANGES IN VERSION 1.5 ---------------------- NEW FEATURES o stop.on.error returns catchable 'remote_error' o bplapply() signals a 'bplist_error' when any element is an error. o 'bplist_error' includes an attribute 'result' containing computed results; when stop.on.error = FALSE, the result vector is parallel to (has the same geometry as) the input vector. o bpvec() signals a 'bpvec_error' when length(FUN(X)) != length(X) USER-VISIBLE CHANGES o Rename bpslaveLoop to (S3 generic) bploop o bpiterate() returns values consistent with REDUCE, rather than wrapping in list() o BatchJobsParam() passes more arguments to BatchJobs' makeRegistry(), setConfig(), submitJobs() BUG FIXES o workers=1, tasks=0 assigns all elements of X in one chunk o SerialParam() respects stop.on.error o bpmapply,ANY,* methods did not honor all arguments, particularly MoreArgs. CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o Add support for iterative REDUCE in .bpiterate_serial() o Refactor BiocParallelParam class: - add 'log', 'tasks', 'threshold', 'logdir', 'resultdir' fields - 'tasks' is used by SnowParam and MulticoreParam only o MulticoreParam now uses SnowParam(..., type=FORK) o Add bpvalidate() MODIFICATIONS o Add check to bipiterate() for Windows o Invoke REDUCE without '...' in .bpiterate_serial() o Update README and bpvec() man page o Change default BPPARAM to SnowParam() for Windows o Update bpiterate() man pages for Windows o Add note to vignette re: module load in template file from Thomas Girke o SnowParam: - bpmapply() now dispatches to bplapply() - remove BPRESUME - logging, gc ouput on worker - write results or logs to file - new error handling with futile.logger o Lighten the NAMESPACE by importing only parallel, snow o Modify which params are registered at load time: - Windows: SnowParam(), SerialParam() - Non-Windows: MulticoreParam(), SnowParam(), SerialParam() o bpvalidate() looks for symbols in 'fun' environment, NAMESPACE of loaded libraries, and the search path BUG FIXES o Bug fix in bpiterate_multicore(); update doc examples o Bug fix in bpiterate() in ordering results from Martin o Bug fix in .bpiterate_serial() when REDUCE is given CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o Add vignette sections for cluster managers, AMI o Add bpiterate generic and methods o Add REDUCE to bpiterate() o Add 'reduce.in.order' to bpiterate() MODIFICATIONS o Update vignette examples, reorganize sections o Allow 'workers' in BiocParallelParam to be character or integer o Enhance bpresume() man page; add examples o Enhance register() man page; add examples o Improve default registration for SnowParam: - max 8 cores - use detectcores() / mc.cores if available o Modify .convertToSimpleError() to convert NULL to NA_character_ BUG FIXES o Fix recursion problem for BPPARAM as list o Modify bpaggregate() to run in parallel