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