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BioC 3.4: BUILD report for BiocParallel on malbec1

This page was generated on 2017-04-15 16:11:11 -0400 (Sat, 15 Apr 2017).

Package 116/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.8.2
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BiocParallel
Last Changed Rev: 128057 / Revision: 128728
Last Changed Date: 2017-04-05 02:56:24 -0400 (Wed, 05 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK [ OK ] OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.8.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocParallel
StartedAt: 2017-04-14 19:16:39 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 19:17:28 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 48.4 seconds
RetCode: 0
Status:  OK 
PackageFile: BiocParallel_1.8.2.tar.gz
PackageFileSize: 610.3 KiB

Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.4-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
* 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 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
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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 Identifies un-suc-cess-ful re-sults re-turned from \T1/zi4/m/n
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n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
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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 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,      
                     catch.errors = TRUE, stop.on.error = FALSE,               
            tasks = 0L, progressbar = FALSE, RNGseed = NULL,                   
        timeout = Inf, log = FALSE, threshold = "INFO",                        
   logdir = NA_character_, resultdir = NA_character_,                          
 jobname = "BPJOB", ...)\T1/ptm/m/n/10 : 
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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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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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tm/m/n/10 . 
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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
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[]\T1/zi4/m/n/10 SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),     
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               progressbar = FALSE, RNGseed = NULL, timeout = Inf,             
         log = FALSE, threshold = "INFO", logdir = NA_character_,              
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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/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
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n/10 bpvec\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/zi4
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m/n/10 bpworkers[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 bpnworkers[][][]\T1/p
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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
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bmitJobs
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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 . 
[5]
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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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-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 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,      
                     catch.errors = TRUE, stop.on.error = FALSE,               
            tasks = 0L, progressbar = FALSE, RNGseed = NULL,                   
        timeout = Inf, log = FALSE, threshold = "INFO",                        
   logdir = NA_character_, resultdir = NA_character_,                          
 jobname = "BPJOB", ...)\T1/ptm/m/n/10 : 
[27]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,              
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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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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/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
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               progressbar = FALSE, RNGseed = NULL, timeout = Inf,             
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[36]
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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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[40]
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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
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRU
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-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
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][]\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 MulticoreParam(workers = multicoreWorkers(), tasks = 0L,      
                     catch.errors = TRUE, stop.on.error = FALSE,               
            tasks = 0L, progressbar = FALSE, RNGseed = NULL,                   
        timeout = Inf, log = FALSE, threshold = "INFO",                        
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 jobname = "BPJOB", ...)\T1/ptm/m/n/10 : 
[27]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,              
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/zi4/m/n/10 BiocParallelParam \T1/pt
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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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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/ptm/m/n/10 NOTE: The \T1/zi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
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               progressbar = FALSE, RNGseed = NULL, timeout = Inf,             
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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 where the re-sources de-fined in the con-fig-u-ra-tion are used.
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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 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 . 
[5]
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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 each worker re-turns, the data are com-bined with the \T1/zi4/m/
n/10 REDUCE \T1/ptm/m/n/10 func-tion. \T1/zi4/m/n/10 REDUCE
[9]
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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/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, log = FALSE, threshold = "INFO",                        
   logdir = NA_character_, resultdir = NA_character_,                          
 jobname = "BPJOB", ...)\T1/ptm/m/n/10 : 
[27]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,              
       USE.NAMES=TRUE, BPPARAM=bpparam()) 
[28] [29]
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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/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
[35]
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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, timeout = Inf,             
         log = FALSE, threshold = "INFO", logdir = NA_character_,              
        resultdir = NA_character_, jobname = "BPJOB", ...)\T1/ptm/m/n/10 : 
[36]
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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
[37] [38] (./Rd2.ind [39]

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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 
[40]
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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,BiocParallelParam-method 

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[]\T1/zi4/m/it/10 bpjobname<-,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<-,SnowParam,character-method 
[41]
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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 

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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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