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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocParallel
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* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* preparing ‘BiocParallel’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
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[]\T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/zi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/zi4/m/n/10 clean
up
[2]
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\T1/ptm/m/n/10 where the re-sources de-fined in the con-fig-u-ra-tion are used.
Ig-nored when \T1/zi4/m/n/10 submit.pars
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\T1/ptm/m/n/10 user-supplied ar-gu-ment \T1/zi4/m/n/10 resources \T1/ptm/m/n/10
to \T1/zi4/m/n/10 BatchJobsParam \T1/ptm/m/n/10 is ig-nored. \T1/zi4/m/n/10 su
bmitJobs
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[]\T1/zi4/m/n/10 named list()\T1/ptm/m/n/10 Arguments passed to the \T1/zi4/m/n
/10 resources \T1/ptm/m/n/10 ar-gu-ment of \T1/zi4/m/n/10 batchtools::submitJob
s
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\T1/zi4/m/n/10 value \T1/ptm/m/n/10 must be a scalar in-te-ger >= 0L. This ar-g
u-ment ap-plies to \T1/zi4/m/n/10 SnowParam \T1/ptm/m/n/10 and \T1/zi4/m/n/10 M
ulticoreParam
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[]\T1/zi4/m/n/10 bplog(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bplog(x) <- value\T1/p
tm/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/pt
m/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 bpexportglobals(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpexportglob
als(x) <- value\T1/ptm/m/n/10 : \T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-por
t \T1/zi4/m/n/10 base::options()
[8]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRU
E, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bpmapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Identifies un-suc-cess-ful re-sults re-turned from \T1/zi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 page (e.g., \T1/zi4/m/n/10 ?bpisup\T1/ptm/m/n/10 ): [][]\T1/zi4/
m/n/10 bpworkers[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpnworkers[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 bpstart[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
bpstop[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpisup[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 bpbackend[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpbackend<
-[][][]\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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[]\T1/zi4/m/n/10 character(1) \T1/ptm/m/n/10 Host name of man-ager node. See 'G
lobal Op-tions', in [][]\T1/zi4/m/n/10 SnowParam[][][]\T1/ptm/m/n/10 .
[31]
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\T1/ptm/m/n/10 limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the num-ber of
open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnections(all=TRU
E))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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\T1/ptm/m/n/10 these are di-verted to the log out-put. Those fa-mil-iar with th
e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
[32]
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,
catch.errors = TRUE, stop.on.error = FALSE,
tasks = 0L, progressbar = FALSE, RNGseed = NULL,
timeout = Inf, exportglobals=TRUE, log = FALS
E, threshold = "INFO", logdir = NA_character_, result
dir = NA_character_, manager.hostname = NA_character_
, manager.port = NA_integer_, ...)\T1/ptm/m/n/10 :
[33]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[34]
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/zi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/zi4/m/n/10 FALSE\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 tomiza-tions dur-ing start-up (e.g., in an \T1/zi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/zi4/m/n/10 options(MulticoreP
aram=quote(MulticoreParam(workers=8)))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 e.g., \T1/zi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/zi4/m/n/10 registered(bpparamClass)\T1/p
tm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
[40]
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\T1/ptm/m/n/10 hard-coded limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the
num-ber of open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnecti
ons(all=TRUE))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
[41]
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/zi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/zi4/m/n/10 scriptdir
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[]\T1/zi4/m/n/10 SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),
tasks = 0L, catch.errors = TRUE, stop.on.error = FALSE,
progressbar = FALSE, RNGseed = NULL, timeou
t = Inf, exportglobals = TRUE, log = FALSE, threshold = "I
NFO", logdir = NA_character_, resultdir = NA_character_, j
obname = "BPJOB", manager.hostname = NA_character_,
manager.port = NA_integer_, ...)\T1/ptm/m/n
/10 :
[42]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
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[]\T1/zi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/zi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/zi4/m/n/10 spawnedMPIcluster
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[]\T1/ptm/m/n/10 The de-fault man-ager host-name is "lo-cal-host" when the num-
ber of work-ers are spec-i-fied as a \T1/zi4/m/n/10 numeric(1)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 vari-able \T1/zi4/m/n/10 MASTER\T1/ptm/m/n/10 , or the global op
-tion \T1/zi4/m/n/10 bphost \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 options(bphost
=Sys.info()[["nodename"]])\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/zi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/zi4/m/n/10 clean
up
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\T1/ptm/m/n/10 where the re-sources de-fined in the con-fig-u-ra-tion are used.
Ig-nored when \T1/zi4/m/n/10 submit.pars
[3]
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\T1/ptm/m/n/10 user-supplied ar-gu-ment \T1/zi4/m/n/10 resources \T1/ptm/m/n/10
to \T1/zi4/m/n/10 BatchJobsParam \T1/ptm/m/n/10 is ig-nored. \T1/zi4/m/n/10 su
bmitJobs
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[]\T1/zi4/m/n/10 named list()\T1/ptm/m/n/10 Arguments passed to the \T1/zi4/m/n
/10 resources \T1/ptm/m/n/10 ar-gu-ment of \T1/zi4/m/n/10 batchtools::submitJob
s
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\T1/zi4/m/n/10 value \T1/ptm/m/n/10 must be a scalar in-te-ger >= 0L. This ar-g
u-ment ap-plies to \T1/zi4/m/n/10 SnowParam \T1/ptm/m/n/10 and \T1/zi4/m/n/10 M
ulticoreParam
[8]
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[]\T1/zi4/m/n/10 bplog(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bplog(x) <- value\T1/p
tm/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/pt
m/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 bpexportglobals(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpexportglob
als(x) <- value\T1/ptm/m/n/10 : \T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-por
t \T1/zi4/m/n/10 base::options()
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRU
E, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bpmapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Identifies un-suc-cess-ful re-sults re-turned from \T1/zi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 page (e.g., \T1/zi4/m/n/10 ?bpisup\T1/ptm/m/n/10 ): [][]\T1/zi4/
m/n/10 bpworkers[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpnworkers[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 bpstart[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
bpstop[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpisup[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 bpbackend[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpbackend<
-[][][]\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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[]\T1/zi4/m/n/10 character(1) \T1/ptm/m/n/10 Host name of man-ager node. See 'G
lobal Op-tions', in [][]\T1/zi4/m/n/10 SnowParam[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the num-ber of
open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnections(all=TRU
E))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[32]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,
catch.errors = TRUE, stop.on.error = FALSE,
tasks = 0L, progressbar = FALSE, RNGseed = NULL,
timeout = Inf, exportglobals=TRUE, log = FALS
E, threshold = "INFO", logdir = NA_character_, result
dir = NA_character_, manager.hostname = NA_character_
, manager.port = NA_integer_, ...)\T1/ptm/m/n/10 :
[33]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[34] [35]
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/zi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/zi4/m/n/10 FALSE\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 tomiza-tions dur-ing start-up (e.g., in an \T1/zi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/zi4/m/n/10 options(MulticoreP
aram=quote(MulticoreParam(workers=8)))\T1/ptm/m/n/10 .
[37]
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\T1/ptm/m/n/10 e.g., \T1/zi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/zi4/m/n/10 registered(bpparamClass)\T1/p
tm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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\T1/ptm/m/n/10 hard-coded limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the
num-ber of open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnecti
ons(all=TRUE))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[41]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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\T1/ptm/m/n/10 these are di-verted to the log out-put. Those fa-mil-iar with th
e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/zi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/zi4/m/n/10 scriptdir
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[]\T1/zi4/m/n/10 SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),
tasks = 0L, catch.errors = TRUE, stop.on.error = FALSE,
progressbar = FALSE, RNGseed = NULL, timeou
t = Inf, exportglobals = TRUE, log = FALSE, threshold = "I
NFO", logdir = NA_character_, resultdir = NA_character_, j
obname = "BPJOB", manager.hostname = NA_character_,
manager.port = NA_integer_, ...)\T1/ptm/m/n
/10 :
[42]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[43]
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[]\T1/zi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/zi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/zi4/m/n/10 spawnedMPIcluster
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[]\T1/ptm/m/n/10 The de-fault man-ager host-name is "lo-cal-host" when the num-
ber of work-ers are spec-i-fied as a \T1/zi4/m/n/10 numeric(1)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 vari-able \T1/zi4/m/n/10 MASTER\T1/ptm/m/n/10 , or the global op
-tion \T1/zi4/m/n/10 bphost \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 options(bphost
=Sys.info()[["nodename"]])\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/zi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/zi4/m/n/10 clean
up
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\T1/ptm/m/n/10 user-supplied ar-gu-ment \T1/zi4/m/n/10 resources \T1/ptm/m/n/10
to \T1/zi4/m/n/10 BatchJobsParam \T1/ptm/m/n/10 is ig-nored. \T1/zi4/m/n/10 su
bmitJobs
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[]\T1/zi4/m/n/10 named list()\T1/ptm/m/n/10 Arguments passed to the \T1/zi4/m/n
/10 resources \T1/ptm/m/n/10 ar-gu-ment of \T1/zi4/m/n/10 batchtools::submitJob
s
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\T1/zi4/m/n/10 value \T1/ptm/m/n/10 must be a scalar in-te-ger >= 0L. This ar-g
u-ment ap-plies to \T1/zi4/m/n/10 SnowParam \T1/ptm/m/n/10 and \T1/zi4/m/n/10 M
ulticoreParam
[8]
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[]\T1/zi4/m/n/10 bplog(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bplog(x) <- value\T1/p
tm/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/pt
m/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 bpexportglobals(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpexportglob
als(x) <- value\T1/ptm/m/n/10 : \T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-por
t \T1/zi4/m/n/10 base::options()
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRU
E, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bpmapply("MulticoreParam")\T1/
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[]\T1/ptm/m/n/10 Identifies un-suc-cess-ful re-sults re-turned from \T1/zi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 page (e.g., \T1/zi4/m/n/10 ?bpisup\T1/ptm/m/n/10 ): [][]\T1/zi4/
m/n/10 bpworkers[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpnworkers[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 bpstart[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
bpstop[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpisup[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 bpbackend[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpbackend<
-[][][]\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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[]\T1/zi4/m/n/10 character(1) \T1/ptm/m/n/10 Host name of man-ager node. See 'G
lobal Op-tions', in [][]\T1/zi4/m/n/10 SnowParam[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the num-ber of
open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnections(all=TRU
E))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[32]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
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e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,
catch.errors = TRUE, stop.on.error = FALSE,
tasks = 0L, progressbar = FALSE, RNGseed = NULL,
timeout = Inf, exportglobals=TRUE, log = FALS
E, threshold = "INFO", logdir = NA_character_, result
dir = NA_character_, manager.hostname = NA_character_
, manager.port = NA_integer_, ...)\T1/ptm/m/n/10 :
[33]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/zi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/zi4/m/n/10 FALSE\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 tomiza-tions dur-ing start-up (e.g., in an \T1/zi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/zi4/m/n/10 options(MulticoreP
aram=quote(MulticoreParam(workers=8)))\T1/ptm/m/n/10 .
[37]
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\T1/ptm/m/n/10 e.g., \T1/zi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/zi4/m/n/10 registered(bpparamClass)\T1/p
tm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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\T1/ptm/m/n/10 hard-coded limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the
num-ber of open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnecti
ons(all=TRUE))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[41]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
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r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/zi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/zi4/m/n/10 scriptdir
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[]\T1/zi4/m/n/10 SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),
tasks = 0L, catch.errors = TRUE, stop.on.error = FALSE,
progressbar = FALSE, RNGseed = NULL, timeou
t = Inf, exportglobals = TRUE, log = FALSE, threshold = "I
NFO", logdir = NA_character_, resultdir = NA_character_, j
obname = "BPJOB", manager.hostname = NA_character_,
manager.port = NA_integer_, ...)\T1/ptm/m/n
/10 :
[42]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[43]
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[]\T1/zi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/zi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/zi4/m/n/10 spawnedMPIcluster
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[]\T1/ptm/m/n/10 The de-fault man-ager host-name is "lo-cal-host" when the num-
ber of work-ers are spec-i-fied as a \T1/zi4/m/n/10 numeric(1)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 vari-able \T1/zi4/m/n/10 MASTER\T1/ptm/m/n/10 , or the global op
-tion \T1/zi4/m/n/10 bphost \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 options(bphost
=Sys.info()[["nodename"]])\T1/ptm/m/n/10 .
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[]\T1/zi4/m/it/10 bpaggregate,data.frame,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpaggregate,formula,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpaggregate,matrix,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpbackend<-,DoparParam,SOCKcluster-method
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[]\T1/zi4/m/it/10 bpcatchErrors,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpexportglobals,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpiterate,ANY,ANY,BatchJobsParam-method
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[]\T1/zi4/m/it/10 bpiterate,ANY,ANY,BatchtoolsParam-method
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[]\T1/zi4/m/it/10 bplogdir<-,SerialParam,character-method
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[48]
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[]\T1/zi4/m/it/10 bpresultdir<-,SnowParam,character-method
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[]\T1/zi4/m/it/10 bpRNGseed<-,BatchtoolsParam,numeric-method
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[49]
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[]\T1/zi4/m/it/10 coerce,spawnedMPIcluster,SnowParam-method
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[]\T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/zi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/zi4/m/n/10 clean
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\T1/ptm/m/n/10 user-supplied ar-gu-ment \T1/zi4/m/n/10 resources \T1/ptm/m/n/10
to \T1/zi4/m/n/10 BatchJobsParam \T1/ptm/m/n/10 is ig-nored. \T1/zi4/m/n/10 su
bmitJobs
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[]\T1/zi4/m/n/10 named list()\T1/ptm/m/n/10 Arguments passed to the \T1/zi4/m/n
/10 resources \T1/ptm/m/n/10 ar-gu-ment of \T1/zi4/m/n/10 batchtools::submitJob
s
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\T1/zi4/m/n/10 value \T1/ptm/m/n/10 must be a scalar in-te-ger >= 0L. This ar-g
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ulticoreParam
[8]
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[]\T1/zi4/m/n/10 bplog(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bplog(x) <- value\T1/p
tm/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/pt
m/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
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[]\T1/zi4/m/n/10 bpexportglobals(x)\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpexportglob
als(x) <- value\T1/ptm/m/n/10 : \T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-por
t \T1/zi4/m/n/10 base::options()
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRU
E, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bplapply("MulticoreParam")\T1/
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[]\T1/ptm/m/n/10 See \T1/zi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/zi4/m/n/10 method?bpmapply("MulticoreParam")\T1/
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[]\T1/ptm/m/n/10 Identifies un-suc-cess-ful re-sults re-turned from \T1/zi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 page (e.g., \T1/zi4/m/n/10 ?bpisup\T1/ptm/m/n/10 ): [][]\T1/zi4/
m/n/10 bpworkers[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpnworkers[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 bpstart[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
bpstop[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpisup[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 bpbackend[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpbackend<
-[][][]\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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[]\T1/zi4/m/n/10 character(1) \T1/ptm/m/n/10 Host name of man-ager node. See 'G
lobal Op-tions', in [][]\T1/zi4/m/n/10 SnowParam[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 limit in \T1/ptm/m/it/10 R\T1/ptm/m/n/10 ) mi-nus the num-ber of
open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnections(all=TRU
E))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[32]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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\T1/ptm/m/n/10 these are di-verted to the log out-put. Those fa-mil-iar with th
e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,
catch.errors = TRUE, stop.on.error = FALSE,
tasks = 0L, progressbar = FALSE, RNGseed = NULL,
timeout = Inf, exportglobals=TRUE, log = FALS
E, threshold = "INFO", logdir = NA_character_, result
dir = NA_character_, manager.hostname = NA_character_
, manager.port = NA_integer_, ...)\T1/ptm/m/n/10 :
[33]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/zi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/zi4/m/n/10 FALSE\T1/ptm/m/n/10
,
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\T1/ptm/m/n/10 tomiza-tions dur-ing start-up (e.g., in an \T1/zi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/zi4/m/n/10 options(MulticoreP
aram=quote(MulticoreParam(workers=8)))\T1/ptm/m/n/10 .
[37]
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\T1/ptm/m/n/10 e.g., \T1/zi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/zi4/m/n/10 registered(bpparamClass)\T1/p
tm/m/n/10 .
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[]\T1/zi4/m/n/10 logical(1) \T1/ptm/m/n/10 Ex-port \T1/zi4/m/n/10 base::options
() \T1/ptm/m/n/10 from man-ager to work-ers? De-fault \T1/zi4/m/n/10 TRUE\T1/pt
m/m/n/10 .
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num-ber of open con-nec-tions as re-turned by \T1/zi4/m/n/10 nrow(showConnecti
ons(all=TRUE))\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 The op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used t
o spec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.
cores=4L)\T1/ptm/m/n/10 ;
[41]
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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
When \T1/zi4/m/n/10 log = TRUE
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\T1/ptm/m/n/10 these are di-verted to the log out-put. Those fa-mil-iar with th
e \T1/zi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/zi4/m/n/10 makeCluste
r
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\T1/ptm/m/n/10 seed of the mas-ter pro-cess af-ter se-lect-ing the L'Ecuyer gen
-er-a-tor. See ?\T1/zi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/zi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/zi4/m/n/10 scriptdir
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[]\T1/zi4/m/n/10 SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),
tasks = 0L, catch.errors = TRUE, stop.on.error = FALSE,
progressbar = FALSE, RNGseed = NULL, timeou
t = Inf, exportglobals = TRUE, log = FALSE, threshold = "I
NFO", logdir = NA_character_, resultdir = NA_character_, j
obname = "BPJOB", manager.hostname = NA_character_,
manager.port = NA_integer_, ...)\T1/ptm/m/n
/10 :
[42]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[43]
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[]\T1/zi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/zi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/zi4/m/n/10 spawnedMPIcluster
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[]\T1/ptm/m/n/10 The de-fault man-ager host-name is "lo-cal-host" when the num-
ber of work-ers are spec-i-fied as a \T1/zi4/m/n/10 numeric(1)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 vari-able \T1/zi4/m/n/10 MASTER\T1/ptm/m/n/10 , or the global op
-tion \T1/zi4/m/n/10 bphost \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 options(bphost
=Sys.info()[["nodename"]])\T1/ptm/m/n/10 .
[44]
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[]\T1/zi4/m/it/10 bpaggregate,data.frame,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpaggregate,formula,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpaggregate,matrix,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpbackend<-,DoparParam,SOCKcluster-method
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[]\T1/zi4/m/it/10 bpcatchErrors,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpcatchErrors<-,BiocParallelParam,logical-method
[47]
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[]\T1/zi4/m/it/10 bpexportglobals,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpexportglobals<-,BiocParallelParam,logical-method
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[]\T1/zi4/m/it/10 bpiterate,ANY,ANY,BatchJobsParam-method
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[]\T1/zi4/m/it/10 bpiterate,ANY,ANY,BatchtoolsParam-method
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[]\T1/zi4/m/it/10 bpjobname<-,BiocParallelParam,character-method
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[]\T1/zi4/m/it/10 bplogdir<-,BatchtoolsParam,character-method
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[]\T1/zi4/m/it/10 bplogdir<-,SerialParam,character-method
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[]\T1/zi4/m/it/10 bpprogressbar,BiocParallelParam-method
[48]
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[]\T1/zi4/m/it/10 bpprogressbar<-,BiocParallelParam,logical-method
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[]\T1/zi4/m/it/10 bpresultdir<-,SnowParam,character-method
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[]\T1/zi4/m/it/10 bpRNGseed<-,BatchtoolsParam,numeric-method
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[]\T1/zi4/m/it/10 bpstopOnError,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpstopOnError<-,BiocParallelParam,logical-method
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[]\T1/zi4/m/it/10 bpstopOnError<-,DoparParam,logical-method
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[]\T1/zi4/m/it/10 bptasks<-,BiocParallelParam,numeric-method
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[]\T1/zi4/m/it/10 bpthreshold<-,SerialParam,character-method
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[]\T1/zi4/m/it/10 bpthreshold<-,SnowParam,character-method
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[]\T1/zi4/m/it/10 bptimeout<-,BiocParallelParam,numeric-method
[49]
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[]\T1/zi4/m/it/10 bpworkers<-,MulticoreParam,numeric-method
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[]\T1/zi4/m/it/10 bpworkers<-,SnowParam,character-method
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[]\T1/zi4/m/it/10 coerce,spawnedMPIcluster,SnowParam-method
[50]) (/tmp/RtmpvsSgJ3/Rbuild46fb430ead01/BiocParallel/.Rd2pdf18171/Rd2.aux)
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