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Fixes for package installation error with BiocParallel version 1.30.0 #8

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Fixes for package installation error with BiocParallel version 1.30.0 #8

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09324f7
Ignore RStudio project files
jasenfinch Apr 29, 2022
ba79e22
add missing arguments to bpiterate
jasenfinch Apr 29, 2022
7d71ea8
fix arguments declared to .composeTry
jasenfinch Apr 30, 2022
af0a8af
fix argument declared to .composeTry in bpiterate
jasenfinch Apr 30, 2022
8e898f9
update NAMESPACE
jasenfinch Apr 30, 2022
df883be
add future.batchtools to DESCRIPTION suggests field
jasenfinch Apr 30, 2022
5b8fd78
add missing function import. Update NAMESPACE
jasenfinch Apr 30, 2022
9f871c9
Add BiocParallel to remotes field in DESCRIPTION
jasenfinch Dec 1, 2022
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2 changes: 2 additions & 0 deletions .Rbuildignore
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Original file line number Diff line number Diff line change
Expand Up @@ -60,3 +60,5 @@ Rplots.pdf$
#----------------------------
^.ghi
^.issues
^.*\.Rproj$
^\.Rproj\.user$
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -10,3 +10,5 @@
.make/*.md.rsp
docs/
.Rdump
.Rproj.user
BiocParallel.FutureParam.Rproj
7 changes: 5 additions & 2 deletions DESCRIPTION
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Expand Up @@ -8,7 +8,10 @@ Imports:
methods
Suggests:
markdown,
R.rsp
R.rsp,
future.batchtools
Remotes:
bioc::BiocParallel
VignetteBuilder:
R.rsp
Title: Use Futures with BiocParallel
Expand All @@ -21,5 +24,5 @@ License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://BiocParallel.FutureParam.futureverse.org, https://github.com/HenrikBengtsson/BiocParallel.FutureParam
BugReports: https://github.com/HenrikBengtsson/BiocParallel.FutureParam/issues
RoxygenNote: 7.1.1
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE)
3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -6,10 +6,13 @@ if (getRversion() >= "3.6.0") {
importFrom(BiocParallel,.BiocParallelParam_prototype)
}
export(FutureParam)
importFrom(BiocParallel,bpRNGseed)
importFrom(BiocParallel,bpexportglobals)
importFrom(BiocParallel,bplog)
importFrom(BiocParallel,bplogdir)
importFrom(BiocParallel,bploop)
importFrom(BiocParallel,bpok)
importFrom(BiocParallel,bpoptions)
importFrom(BiocParallel,bpparam)
importFrom(BiocParallel,bpstopOnError)
importFrom(BiocParallel,bpthreshold)
Expand Down
31 changes: 22 additions & 9 deletions R/FutureParam-class.R
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Expand Up @@ -121,10 +121,11 @@ setReplaceMethod("bplogdir", c("FutureParam", "character"), function(x, value) {
###

#' @importFrom methods setMethod
#' @importFrom BiocParallel bplog bpok bpparam bpstopOnError bpthreshold bptimeout
#' @importFrom BiocParallel bplog bpok bpparam bpstopOnError bpthreshold bptimeout bpexportglobals
#' @importFrom future future resolve value
setMethod("bplapply", c("ANY", "FutureParam"), function(X, FUN, ..., BPREDO=list(), BPPARAM=bpparam()) {
.composeTry <- importBP(".composeTry")
.workerOptions <- importBP('.workerOptions')
.error_bplist <- importBP(".error_bplist")
.log_load <- importBP(".log_load")
.redo_index <- importBP(".redo_index")
Expand All @@ -140,9 +141,14 @@ setMethod("bplapply", c("ANY", "FutureParam"), function(X, FUN, ..., BPREDO=list

.log_load(bplog(BPPARAM), bpthreshold(BPPARAM))

FUN <- .composeTry(FUN, bplog(BPPARAM), bpstopOnError(BPPARAM),
stop.immediate=bpstopOnError(BPPARAM),
timeout=bptimeout(BPPARAM))
OPTIONS <- .workerOptions(
log = bplog(BPPARAM),
stop.on.error = bpstopOnError(BPPARAM),
timeout = bptimeout(BPPARAM),
exportglobals = bpexportglobals(BPPARAM)
)

FUN <- .composeTry(FUN, OPTIONS, bpRNGseed(BPPARAM))

## Create futures
fs <- list()
Expand Down Expand Up @@ -173,11 +179,12 @@ setMethod("bplapply", c("ANY", "FutureParam"), function(X, FUN, ..., BPREDO=list


#' @importFrom methods setMethod
#' @importFrom BiocParallel bploop bplog bptimeout bpstopOnError
#' @importFrom BiocParallel bploop bplog bptimeout bpstopOnError bpoptions bpRNGseed
#' @importFrom future future resolve value
setMethod("bpiterate", c("ANY", "ANY", "FutureParam"), function(ITER, FUN, ..., REDUCE, init, reduce.in.order=FALSE, BPPARAM=bpparam()) {
setMethod("bpiterate", c("ANY", "ANY", "FutureParam"), function(ITER, FUN, ..., REDUCE, init, reduce.in.order=FALSE, BPREDO = list(),BPPARAM=bpparam(),BPOPTIONS = bpoptions()) {
.composeTry <- importBP(".composeTry")

.workerOptions <- importBP(".workerOptions")

ITER <- match.fun(ITER)
FUN <- match.fun(FUN)
hasREDUCE <- !missing(REDUCE)
Expand All @@ -192,8 +199,14 @@ setMethod("bpiterate", c("ANY", "ANY", "FutureParam"), function(ITER, FUN, ...,
}
}

FUN <- .composeTry(FUN, bplog(BPPARAM), bpstopOnError(BPPARAM),
timeout=bptimeout(BPPARAM))
OPTIONS <- .workerOptions(
log = bplog(BPPARAM),
stop.on.error = bpstopOnError(BPPARAM),
timeout = bptimeout(BPPARAM),
exportglobals = bpexportglobals(BPPARAM)
)

FUN <- .composeTry(FUN, OPTIONS, bpRNGseed(BPPARAM))
ARGFUN <- function(value) c(list(value), list(...))


Expand Down