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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/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
* running ‘cleanup’
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ..
Creating pdf output from LaTeX ...
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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
[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/pt
m/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/ptm
/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-port
\T1/zi4/m/n/10 base::options()
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[]\T1/zi4/m/n/10 bpmapply(FUN,...,MoreArgs=NULL,SIMPLIFY=TRUE,USE.NAMES=TRUE,BP
PARAM=bpparam())
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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 An ob-ject con-tain-ing in-for-ma-tion about the clus-ter, re-
turned by \T1/zi4/m/n/10 bpbackend()\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 .prototype_update()\T1/ptm/m/n/10 , name-va
lue pairs to ini-tial-ize de-rived and base class
[27]
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\T1/ptm/m/n/10 value pairs pro-vid-ing de-fault pa-ram-e-teter ar-gu-ments. The
de-fault val-ues for the \T1/zi4/m/n/10 BiocParallelParam
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\T1/ptm/m/n/10 base class is pro-vided in a list \T1/zi4/m/n/10 .BiocParallelPa
ram_prototype\T1/ptm/m/n/10 , and the func-tion \T1/zi4/m/n/10 .prototype_updat
e()
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[]\T1/zi4/m/n/10 bpstop,BiocParallelParam-method \T1/ptm/m/n/10 (\T1/zi4/m/n/10
.bpstop_impl()\T1/ptm/m/n/10 ) en-sures ap-pro-pri-ate clean-up of stopped
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[]\T1/zi4/m/n/10 bplapply,ANY,BiocParallelParam-method \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 bpiterate,ANY,BiocParallelParam-method
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\T1/zi4/m/n/10 length() \T1/ptm/m/n/10 (num-ber of nodes). In ad-di-tion, the b
ack-ends must sup-port \T1/zi4/m/n/10 .send_to() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 .recv_any()
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\T1/ptm/m/n/10 man-ager and \T1/zi4/m/n/10 .send()\T1/ptm/m/n/10 , \T1/zi4/m/n/
10 .recv()\T1/ptm/m/n/10 , and \T1/zi4/m/n/10 .close() \T1/ptm/m/n/10 worker me
th-ods. De-fault \T1/zi4/m/n/10 .send_all() \T1/ptm/m/n/10 and \T1/zi4/m/n/10 .
recv_all()
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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 ;
[34]
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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,stop.on
.error = FALSE,tasks
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\T1/zi4/m/n/10 = 0L,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglob
als=TRUE,log = FALSE,threshold
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\T1/zi4/m/n/10 = "INFO",logdir = NA_character_,resultdir = NA_character_,manage
r.hostname = NA_character_,manager.port
[35]
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[36] [37]
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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 .
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\T1/ptm/m/n/10 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(showConnections(a
ll=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 ;
[43]
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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,stop.on.error =
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\T1/zi4/m/n/10 FALSE,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglo
bals = TRUE,log
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\T1/zi4/m/n/10 = FALSE,threshold = "INFO",logdir = NA_character_,resultdir = NA
_character_,jobname
[44]
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[45]
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[]\T1/zi4/m/n/10 as(from,"SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/10
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
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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/pt
m/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/ptm
/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-port
\T1/zi4/m/n/10 base::options()
[9]
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[]\T1/zi4/m/n/10 bpmapply(FUN,...,MoreArgs=NULL,SIMPLIFY=TRUE,USE.NAMES=TRUE,BP
PARAM=bpparam())
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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 An ob-ject con-tain-ing in-for-ma-tion about the clus-ter, re-
turned by \T1/zi4/m/n/10 bpbackend()\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 .prototype_update()\T1/ptm/m/n/10 , name-va
lue pairs to ini-tial-ize de-rived and base class
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\T1/ptm/m/n/10 value pairs pro-vid-ing de-fault pa-ram-e-teter ar-gu-ments. The
de-fault val-ues for the \T1/zi4/m/n/10 BiocParallelParam
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\T1/ptm/m/n/10 base class is pro-vided in a list \T1/zi4/m/n/10 .BiocParallelPa
ram_prototype\T1/ptm/m/n/10 , and the func-tion \T1/zi4/m/n/10 .prototype_updat
e()
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[]\T1/zi4/m/n/10 bpstop,BiocParallelParam-method \T1/ptm/m/n/10 (\T1/zi4/m/n/10
.bpstop_impl()\T1/ptm/m/n/10 ) en-sures ap-pro-pri-ate clean-up of stopped
[28]
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[]\T1/zi4/m/n/10 bplapply,ANY,BiocParallelParam-method \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 bpiterate,ANY,BiocParallelParam-method
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\T1/zi4/m/n/10 length() \T1/ptm/m/n/10 (num-ber of nodes). In ad-di-tion, the b
ack-ends must sup-port \T1/zi4/m/n/10 .send_to() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 .recv_any()
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\T1/ptm/m/n/10 man-ager and \T1/zi4/m/n/10 .send()\T1/ptm/m/n/10 , \T1/zi4/m/n/
10 .recv()\T1/ptm/m/n/10 , and \T1/zi4/m/n/10 .close() \T1/ptm/m/n/10 worker me
th-ods. De-fault \T1/zi4/m/n/10 .send_all() \T1/ptm/m/n/10 and \T1/zi4/m/n/10 .
recv_all()
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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 .
[34]
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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 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
[35]
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(),tasks = 0L,stop.on
.error = FALSE,tasks
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\T1/zi4/m/n/10 = 0L,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglob
als=TRUE,log = FALSE,threshold
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\T1/zi4/m/n/10 = "INFO",logdir = NA_character_,resultdir = NA_character_,manage
r.hostname = NA_character_,manager.port
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[36] [37]
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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 .
[43]
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\T1/ptm/m/n/10 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(showConnections(a
ll=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 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
[44]
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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,stop.on.error =
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\T1/zi4/m/n/10 FALSE,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglo
bals = TRUE,log
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\T1/zi4/m/n/10 = FALSE,threshold = "INFO",logdir = NA_character_,resultdir = NA
_character_,jobname
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[45]
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[]\T1/zi4/m/n/10 as(from,"SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/10
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 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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[]\T1/zi4/m/it/10 bpprogressbar,BiocParallelParam-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 bpthreshold<-,SerialParam,character-method
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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
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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
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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/pt
m/m/n/10 : Get or en-able log-ging, if avail-able. \T1/zi4/m/n/10 value \T1/ptm
/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-port
\T1/zi4/m/n/10 base::options()
[9]
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[]\T1/zi4/m/n/10 bpmapply(FUN,...,MoreArgs=NULL,SIMPLIFY=TRUE,USE.NAMES=TRUE,BP
PARAM=bpparam())
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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 An ob-ject con-tain-ing in-for-ma-tion about the clus-ter, re-
turned by \T1/zi4/m/n/10 bpbackend()\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 .prototype_update()\T1/ptm/m/n/10 , name-va
lue pairs to ini-tial-ize de-rived and base class
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\T1/ptm/m/n/10 value pairs pro-vid-ing de-fault pa-ram-e-teter ar-gu-ments. The
de-fault val-ues for the \T1/zi4/m/n/10 BiocParallelParam
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\T1/ptm/m/n/10 base class is pro-vided in a list \T1/zi4/m/n/10 .BiocParallelPa
ram_prototype\T1/ptm/m/n/10 , and the func-tion \T1/zi4/m/n/10 .prototype_updat
e()
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[]\T1/zi4/m/n/10 bpstop,BiocParallelParam-method \T1/ptm/m/n/10 (\T1/zi4/m/n/10
.bpstop_impl()\T1/ptm/m/n/10 ) en-sures ap-pro-pri-ate clean-up of stopped
[28]
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[]\T1/zi4/m/n/10 bplapply,ANY,BiocParallelParam-method \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 bpiterate,ANY,BiocParallelParam-method
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\T1/zi4/m/n/10 length() \T1/ptm/m/n/10 (num-ber of nodes). In ad-di-tion, the b
ack-ends must sup-port \T1/zi4/m/n/10 .send_to() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 .recv_any()
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\T1/ptm/m/n/10 man-ager and \T1/zi4/m/n/10 .send()\T1/ptm/m/n/10 , \T1/zi4/m/n/
10 .recv()\T1/ptm/m/n/10 , and \T1/zi4/m/n/10 .close() \T1/ptm/m/n/10 worker me
th-ods. De-fault \T1/zi4/m/n/10 .send_all() \T1/ptm/m/n/10 and \T1/zi4/m/n/10 .
recv_all()
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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 .
[34]
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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 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
[35]
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[]\T1/zi4/m/n/10 MulticoreParam(workers = multicoreWorkers(),tasks = 0L,stop.on
.error = FALSE,tasks
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\T1/zi4/m/n/10 = 0L,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglob
als=TRUE,log = FALSE,threshold
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\T1/zi4/m/n/10 = "INFO",logdir = NA_character_,resultdir = NA_character_,manage
r.hostname = NA_character_,manager.port
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[36] [37]
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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 .
[40] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [41]
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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 .
[43]
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\T1/ptm/m/n/10 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(showConnections(a
ll=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 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
[44]
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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,stop.on.error =
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\T1/zi4/m/n/10 FALSE,progressbar = FALSE,RNGseed = NULL,timeout = Inf,exportglo
bals = TRUE,log
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\T1/zi4/m/n/10 = FALSE,threshold = "INFO",logdir = NA_character_,resultdir = NA
_character_,jobname
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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/pt
m/m/n/10 : Get or set the value to en-able log-ging. \T1/zi4/m/n/10 value \T1/p
tm/m/n/10 must be a \T1/zi4/m/n/10 logical(1)\T1/ptm/m/n/10 .
[45]
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[]\T1/zi4/m/n/10 as(from,"SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/zi4/m/n/10
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 .
[46] [47]
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(./Rd2.ind [49]
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(Font) using `T1/zi4/m/n' instead on input line 27.
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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
[50]
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[]\T1/zi4/m/it/10 bpbackend<-,DoparParam,SOCKcluster-method
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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 bpiterate,ANY,ANY,BiocParallelParam-method
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[]\T1/zi4/m/it/10 bpjobname<-,BiocParallelParam,character-method
[51]
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[]\T1/zi4/m/it/10 bplogdir<-,BatchtoolsParam,character-method
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[]\T1/zi4/m/it/10 bplogdir<-,BiocParallelParam,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
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[]\T1/zi4/m/it/10 bpprogressbar<-,BiocParallelParam,logical-method
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[]\T1/zi4/m/it/10 bpresultdir<-,BiocParallelParam,character-method
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[]\T1/zi4/m/it/10 bpRNGseed<-,BatchtoolsParam,numeric-method
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[]\T1/zi4/m/it/10 bpRNGseed<-,BiocParallelParam,NULL-method
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[]\T1/zi4/m/it/10 bpRNGseed<-,BiocParallelParam,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
[52]
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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
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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
[53] [54]) (./Rd2.aux)
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Saving output to ‘/private/tmp/Rtmp1AacpU/Rbuildf9c4654156f1/BiocParallel/build/BiocParallel.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘BiocParallel_1.18.1.tar.gz’
