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NEWS
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CHANGES IN VERSION 1.42
-----------------------
BUG FIXES
o (1.41.3) Patch a compiler error under Apple clang 17.0.0; see
<https://github.com/Bioconductor/BiocParallel/issues/271>
o (1.41.2) Set options (via `do.call()`) in package namespace,
rather than base environment / search path. Thanks Charlotte
Soneson!
<https://github.com/Bioconductor/BiocParallel/issues/266>
CHANGES IN VERSION 1.34
-----------------------
NEW FEATURES
o (1.33.2) limit worker number via environment variables.
https://github.com/Bioconductor/BiocParallel/issues/229
o (v1.33.3) bpmapply() does not send the whole list of arguments
to all workers. Instead, it takes the arguments and slices them,
passing the corresponding slice to each worker. Thanks Sergio Oller!
https://github.com/Bioconductor/BiocParallel/issues/229
USER VISIBLE CHANGES
o (1.33.1) Mark BatchJobsParam, bprunMPIslave as defunct.
o (1.33.9) Change default force.GC= to FALSE in MulticoreParam().
<https://github.com/Bioconductor/BiocParallel/issues/238>
o (1.33.11) change content of 'traceback' on error to include the
stack from the location of the error up to the invokation of
FUN. Previously, the traceback was from FUN to the top-level of
worker code, providing limited insight into nested errors.
o (1.33.12) 'force' function arguments to avoid consequences of
lazy evaluation discussed in
<https://github.com/Bioconductor/BiocParallel/issues/241#issuecomment-1445006892>
BUG FIXES
o (1.33.6) Restore 'exported' global variables in SerialParam()
https://github.com/Bioconductor/BiocParallel/issues/234
o (1.33.7) 'configure.ac' uses C++ compiler and checks for existence
of required header
<https://github.com/Bioconductor/BiocParallel/pull/236>
o (1.33.8 / v 1.32.5) set socket idle timeout to a large value, to
avoid premature worker termination and to be consistent with snow
/ parallel defaults.
<https://github.com/Bioconductor/BiocParallel/issues/237>
o (1.33.10 / v 1.32.6) be sure to clean up TransientMulticoreParam
state at start of each job.
<https://github.com/Bioconductor/BiocParallel/issues/243>
CHANGES IN VERSION 1.32
-----------------------
NEW FEATURES
o (v 1.31.10) bpiterate() when ITER is not a function will use
bpiterateAlong() to attempt to iterate over elements ITER[[1]],
ITER[[2]], etc.
https://stat.ethz.ch/pipermail/bioc-devel/2022-July/019075.html
USER VISIBLE CHANGES
o (v 1.31.3) Deprecate BatchJobsParam in favor of BatchtoolsParam
o (v 1.31.11) Replace Random Number .Rnw vignette with Rmd (html)
version (thanks Madelyn Carlson!)
https://github.com/Bioconductor/BiocParallel/pull/215
o (v 1.31.12) clarify default number of cores, and use on shared
clusters (thanks Dario Strbenac)
https://github.com/Bioconductor/BiocParallel/pull/218
https://github.com/Bioconductor/BiocParallel/issues/217
o (v 1.31.15) Replace Introduction to BiocParallel .Rnw vignette
with Rmd (html) version (thanks Phylis Atieno!)
https://github.com/Bioconductor/BiocParallel/pull/226
BUG FIXES
o (v 1.31.1) suppress package startup messages on workers
https://github.com/Bioconductor/BiocParallel/issues/198
o (v 1.31.1) coerce timeout to integer (typically from numeric)
https://github.com/Bioconductor/BiocParallel/issues/200
o (v 1.31.2) avoid segfault when ipcmutex() functions generate C++
errors. This occurs very rarely, for instance when the directory
used by boost for file locking (under /tmp) was created by another
user.
https://github.com/Bioconductor/BiocParallel/pull/202
o (v 1.31.2) resetting bpRNGseed() after bpstart() is reproducible
https://github.com/Bioconductor/BiocParallel/pull/204
o (v 1.31.5) enable logs for multiple managers sharing the same
workers.
https://github.com/Bioconductor/BiocParallel/pull/207
o (v 1.31.13 / v 1.30.4) only export variables in `.GlobalEnv` or
`package:`
<https://github.com/Bioconductor/BiocParallel/issues/223>
<https://github.com/Bioconductor/BiocParallel/pull/224>
o (v 1.31.14) Reduce bpmapply memory usage. Thanks Sergio Oller.
<https://github.com/Bioconductor/BiocParallel/pull/227>
CHANGES IN VERSION 1.30
-----------------------
USER VISIBLE CHANGES
o (v 1.29.1) Report first remote error in its entirety.
https://github.com/Bioconductor/BiocParallel/issues/165
o (v 1.29.4) Add bpresult() (extract result vector from return value
of tryCatch(bplapply(...))) and allow direct use of tryCatch(bplapply(...))
return value as arugment to bplapply(BPREDO= ...). Closes #157
o (v 1.29.8) The default timeout for worker computation changes
from 30 days to .Machine$integer.max (no timeout), allowing for
performance improvements when not set.
o (v 1.29.11) The timeout for establishing a socket connection is
set to getOption("timeout") (default 60 seconds).
o (v 1.29.15) Check for and report failed attempts to open SnowParam
ports.
o (v 1.29.18) add bpfallback= option to control use of `lapply()`
(fallback) when 0 or 1 workers are available.
o (v 1.29.19) add bpexportvariables= option to automatically
export global variables, or variables found in packages on the
search path, in user-provided `FUN=` functions.
BUG FIXES
o (v 1.29.2) Fix regression in use of debug() with SerialParam.
https://github.com/Bioconductor/BiocParallel/issues/128
o (v 1.29.3) Fix regression in progress bar display with bplapply().
https://github.com/Bioconductor/BiocParallel/issues/172
o (v 1.29.5) Fix default seed generation when user has non-default
generator. https://github.com/Bioconductor/BiocParallel/pull/176
o (v 1.29.9) Fix validity when workers, specified as character(),
are more numerous than (non-zero) tasks.
https://github.com/Bioconductor/BiocParallel/pull/181
CHANGES IN VERSION 1.28
-----------------------
USER VISIBLE CHANGES
o (v 1.27.3) Setting `progressbar = TRUE` for SnowParam() or
MulticoreParam() changes the default value of `tasks` from 0 to
`.Machine$integer.max`, so that progress on each element of `X` is
reported.
o (v 1.27.3) `tasks` greater than `length(X)` are set to
`length(X)`. Thus `.Machine$integer.max`, for instance, assures
that each element of `X` is a separate task.
o (v 1.27.5) Use of random numbers is robust to the distribution
of jobs across tasks for SerialParam(), SnowParam(), and
MulticoreParam(), for both bplapply() and bpiterate(), using the
RNGseed= argument to each *Param(). The change is NOT backward
compatible -- users wishing to exactly reproduce earlier results
should use a previous version of the package.
o (v 1.27.8) Standardize SerialParam() construct to enable setting
additional fields. Standardize coercion of other BiocParallelParam types
(e.g., SnowParam(), MulticoreParam()) to SerialParam() with
as(., "SerialParam").
o (v. 1.27.9) By defualt, do _not_ only run garbage collection
after every call to FUN(), except under MulticoreParam(). R's
garbage collection algorithm only fails to do well when forked
processes (i.e., MulticoreParam) assume that they are the only
consumers of process memory.
o (v 1.27.11) Developer-oriented functions bploop.*() arguments changed.
o (v 1.27.12) Ignore set.seed() and never increment the global random
number stream. This reverts a side-effect of behavior introduced in v.
1.27.5 to behavior more consistent with version 1.26.
o (v 1.27.16) Better BPREDO support for previously started BPPARAM, and
'transient' BPPARAM without RNGseed.
BUG FIXES
o (v 1.27.10) Typo in coercion to SerialParam when only a single worker
specified. https://github.com/Bioconductor/BiocParallel/issues/151
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