CHANGES IN VERSION 1.26 ----------------------- USER VISIBLE CHANGES o (v 1.25.2) bpvalidate() gains an argument to control warning / error / silent signaling, and returns a 'BPValidate' object. BUG FIXES o (v 1.26.1) bptry(bplapply(X, ...)) returns a list of length X, appropriately annotated, when SerialParam(stop.on.error = TRUE). See https://github.com/Bioconductor/BiocParallel/issues/142 CHANGES IN VERSION 1.24 ----------------------- BUG FIXES o (v.1.23.1) bpvalidate() detects variables defined in parent environments; warns on use of global variables. o (v.1.23.2) bplapply() runs gc() after each evaluation of `FUN()`, so that workers do not accumulate excessive memory allocations (memory on a per-process basis is not excessive, but cluster-wise could be). See https://github.com/Bioconductor/BiocParallel/pull/124 o (v.1.24.1) Add 'topLevelEnvironment' to list of blocked global variable exports to address performance regression introduced by testthat 3.0. See https://github.com/Bioconductor/BiocParallel/issues/127 CHANGES IN VERSION 1.22 ----------------------- USER VISIBLE CHANGES o (v 1.20.2) don't advance random number stream when used 'internally'. This behavior alters reproducibility of existing scripts relying (probably implicitly) on the advancing stream. https://github.com/Bioconductor/BiocParallel/issues/110 BUG FIXES o (v 1.20.1) bplapply(), bpmapply(), bpvec() propagate names on arguments more correctly, https://github.com/Bioconductor/BiocParallel/issues/108 CHANGES IN VERSION 1.20 ----------------------- BUG FIXES o (v 1.19.2) Improve efficiency of MulticoreParam() when state does not persist across calls to bplapply(). CHANGES IN VERSION 1.18 ----------------------- USER VISIBLE CHANGES o (v 1.17.6) Initial use of registered BPPARAM does not advance random number seed, see https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014526.html o (v 1.17.7) Loading package does not advance random number seed, see https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014535.html o (v. 1.17.7) removed deprecated functions bplasterror(), bpresume(), bpcatchError() and field catch.error. o (v. 1.17.7) Make logdir, resultdir fields of BiocParallelParam. o (v. 1.17.7) replaced internal use of BatchJobs:::checkDir() (testing existence and read / write ability of log and other directories) with BiocParallelParam validity check. o (v. 1.17.7) expose 'developer' interface, `?DeveloperInterface` o (v. 1.17.11) on Windows, coerce `MulticoreParam(n)` to `MulticoreParam(1)` == SerialParam()` BUG FIXES o (v 1.17.4) port 1.16.3 (no '>' on SnowParam() worker end) and 1.16.4 (bpRNGseed<-() accepts NULL) o (v 1.17.5) port 1.16.4 (bpRNGseed() can reset seed to NULL), 1.16.5 (number of available cores defaults to 1 if cannot be determined). CHANGES IN VERSION 1.16 ----------------------- NEW FEATURES o (v 1.15.9) BatchtoolsParam() gains resources=list() for template file substitution. o (v 1.15.12) bpexportglobals() for all BPPARAM exports global options (i.e., base::options()) to workers. Default TRUE. BUG FIXES o (v 1.15.6) bpiterate,serial-method does not return a list() when REDUCE present (https://github.com/Bioconductor/BiocParallel/issues/77) o (v 1.15.7) bpaggregate,formula-method failed to find BPREDO (https://support.bioconductor.org/p/110784) o (v 1.15.13) bplappy,BatchtoolsParam() coerces List to list (https://github.com/Bioconductor/BiocParallel/issues/82) o (v 1.15.14) implicit loading of BiocParallel when loading a third- party package failed because reference class `initialize()` methods are not installed correctly. This bug fix results in signficant revision in the implementation, so that valid objects must be constructed through the public constructors, e.g., `BatchtoolsParam()` o (v 1.16.3) do not print '>' for each terminating SnowParam() worker o (v 1.16.4) allow bpRNGseed() to reset seed to NULL o (v 1.16.5) number of available cores defaults to 1 on machines where number of cores available cannot be determined. See https://github.com/Bioconductor/BiocParallel/issues/91. CHANGES IN VERSION 1.14 ----------------------- BUG FIXES o (v 1.13.1) bpiterate,serial-method does not unlist the result of FUN before passing to REDUCE. CHANGES IN VERSION 1.12 ----------------------- BUG FIXES o (v. 1.11.1) Change registered backend initialization to first invocation, rather than on load. o (v 1.11.8) Ensure registry is initiailized before (public) use. Issue #65 NEW FEATURES o (v. 1.11.2) bpiterate() gains a progress counter. o (v. 1.11.5) ipclock(), etc: inter-process locks and counters CHANGES IN VERSION 1.10 ---------------------- BUG FIXES o (v. 1.9.6) use of logdir= no longer tries to double-close log file. CHANGES IN VERSION 1.8 ---------------------- 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 1.6 ---------------------- 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 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