Skip to content

Fixes for package installation error with BiocParallel version 1.30.0 #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 8 commits into
base: develop
Choose a base branch
from
Open

Fixes for package installation error with BiocParallel version 1.30.0 #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
09324f7
Ignore RStudio project files
Apr 29, 2022
ba79e22
add missing arguments to bpiterate
Apr 29, 2022
7d71ea8
fix arguments declared to .composeTry
Apr 30, 2022
af0a8af
fix argument declared to .composeTry in bpiterate
Apr 30, 2022
8e898f9
update NAMESPACE
Apr 30, 2022
df883be
add future.batchtools to DESCRIPTION suggests field
Apr 30, 2022
5b8fd78
add missing function import. Update NAMESPACE
Apr 30, 2022
9f871c9
Add BiocParallel to remotes field in DESCRIPTION
Dec 1, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions .Rbuildignore
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,5 @@
.make/*.md.rsp
docs/
.Rdump
.Rproj.user
BiocParallel.FutureParam.Rproj
7 changes: 5 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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