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BUILD report for BiocParallel on veracruz1

This page was generated on 2018-04-12 13:36:15 -0400 (Thu, 12 Apr 2018).

Package 127/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.12.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_6
Last Commit: 2143a9a
Last Changed Date: 2017-10-30 12:39:55 -0400 (Mon, 30 Oct 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  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK [ OK ] OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocParallel
StartedAt: 2018-04-11 20:12:54 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 20:14:01 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 67.2 seconds
RetCode: 0
Status:  OK 
PackageFile: BiocParallel_1.12.0.tar.gz
PackageFileSize: 684.8 KiB

Command output

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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
* 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 ...

This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
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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 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/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 of mul-ti-core work-ers is al-ways 1. Oth-er-wise, the de-fault 
is the max-i-mum of 1 and \T1/zi4/m/n/10 parallel::detectCores() - 2\T1/ptm/m/n
/10 ;
[28]
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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
[29]
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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_,                          
 manager.hostname = NA_character_,                           manager.port = NA_
integer_, ...)\T1/ptm/m/n/10 : 
[30]
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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
 ,
[33]
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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 op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used to sp
ec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.core
s=4L)\T1/ptm/m/n/10 ;
[37]
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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, timeout = Inf,             
         log = FALSE, threshold = "INFO", logdir = NA_character_,              
        resultdir = NA_character_, jobname = "BPJOB",                      mana
ger.hostname = NA_character_,                      manager.port = NA_integer_, 
                     ...)\T1/ptm/m/n/10 : 
[38]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,              
       USE.NAMES=TRUE, BPPARAM=bpparam()) 
[39]
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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 . 
[40]
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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.
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[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 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
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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 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 of mul-ti-core work-ers is al-ways 1. Oth-er-wise, the de-fault 
is the max-i-mum of 1 and \T1/zi4/m/n/10 parallel::detectCores() - 2\T1/ptm/m/n
/10 ;
[28]
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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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\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
[29]
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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_,                          
 manager.hostname = NA_character_,                           manager.port = NA_
integer_, ...)\T1/ptm/m/n/10 : 
[30]
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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
 ,
[33]
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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 op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used to sp
ec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.core
s=4L)\T1/ptm/m/n/10 ;
[37]
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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, timeout = Inf,             
         log = FALSE, threshold = "INFO", logdir = NA_character_,              
        resultdir = NA_character_, jobname = "BPJOB",                      mana
ger.hostname = NA_character_,                      manager.port = NA_integer_, 
                     ...)\T1/ptm/m/n/10 : 
[38]
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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/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 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 bpstopOnError,BiocParallelParam-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.
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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
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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/
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 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 of mul-ti-core work-ers is al-ways 1. Oth-er-wise, the de-fault 
is the max-i-mum of 1 and \T1/zi4/m/n/10 parallel::detectCores() - 2\T1/ptm/m/n
/10 ;
[28]
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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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\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
[29]
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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_,                          
 manager.hostname = NA_character_,                           manager.port = NA_
integer_, ...)\T1/ptm/m/n/10 : 
[30]
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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
 ,
[33]
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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 op-tion \T1/zi4/m/n/10 mc.cores \T1/ptm/m/n/10 can be used to sp
ec-ify an ar-bi-trary num-ber of work-ers, e.g., \T1/zi4/m/n/10 options(mc.core
s=4L)\T1/ptm/m/n/10 ;
[37]
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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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\T1/ptm/m/n/10 these are di-verted to the log out-put. Those fa-mil-iar with th
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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, timeout = Inf,             
         log = FALSE, threshold = "INFO", logdir = NA_character_,              
        resultdir = NA_character_, jobname = "BPJOB",                      mana
ger.hostname = NA_character_,                      manager.port = NA_integer_, 
                     ...)\T1/ptm/m/n/10 : 
[38]
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[]\T1/zi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,              
       USE.NAMES=TRUE, BPPARAM=bpparam()) 
[39]
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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 bpcatchErrors<-,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,BiocParallelParam-method 

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Saving output to ‘/private/tmp/RtmpsDhn9u/Rbuilddc9922f0b9de/BiocParallel/build/BiocParallel.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
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* building ‘BiocParallel_1.12.0.tar.gz’