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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
* 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 3.1415926-2.5-1.40.14 (TeX Live 2013)
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 Flag to de-ter-mine in apply-like fun
c-tions (see e.g. [][]\T1/fi4/m/n/10 bplapply[][][]\T1/ptm/m/n/10 ) whether
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/fi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/fi4/m/n/10 clean
up
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[]\T1/fi4/m/n/10 bpstopOnError(x, ...)\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpstopOnE
rror(x) <- value\T1/ptm/m/n/10 : \T1/fi4/m/n/10 logical()\T1/ptm/m/n/10 . Con-t
rols if the job stops
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[]\T1/fi4/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/fi4/m/
n/10 REDUCE \T1/ptm/m/n/10 func-tion. \T1/fi4/m/n/10 REDUCE
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/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/fi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/fi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/fi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 Flag to de-ter-mine in apply-like fun
c-tions (see e.g. [][]\T1/fi4/m/n/10 bplapply[][][]\T1/ptm/m/n/10 ) whether
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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/fi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/fi4/m/n/10 makeCluste
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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/fi4/m/n/10 clusterSetRNGStream
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[]\T1/fi4/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 :
[24]
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[]\T1/fi4/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/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/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/fi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/fi4/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/fi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/fi4/m/n/10 registered(bpparamClass)\T1/p
tm/m/n/10 .
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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/fi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/fi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/fi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/fi4/m/n/10 scriptdir
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[]\T1/fi4/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 :
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[]\T1/fi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
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[]\T1/fi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/fi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/fi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/fi4/m/n/10 spawnedMPIcluster
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 Flag to de-ter-mine in apply-like fun
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 BatchJobs cre-ates tem-po-rary di-rec
-to-ries in the \T1/fi4/m/n/10 work.dir\T1/ptm/m/n/10 . If \T1/fi4/m/n/10 clean
up
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[]\T1/fi4/m/n/10 bpstopOnError(x, ...)\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpstopOnE
rror(x) <- value\T1/ptm/m/n/10 : \T1/fi4/m/n/10 logical()\T1/ptm/m/n/10 . Con-t
rols if the job stops
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[]\T1/fi4/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/fi4/m/
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/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/fi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/fi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/fi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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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/fi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/fi4/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/fi4/m/n/10 clusterSetRNGStream
[24]
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[]\T1/fi4/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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[]\T1/fi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/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/fi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/fi4/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/fi4/m/n/10 registered(bpparamClass)\T1/p
tm/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/fi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/fi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/fi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
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[]\T1/fi4/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 :
[33]
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[]\T1/fi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/fi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/fi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/fi4/m/n/10 spawnedMPIcluster
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 .
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[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bpmapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/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/fi4/m/n
/10 bplapply\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpmapply\T1/ptm/m/n/10 , \T1/fi4/m/
n/10 bpvec\T1/ptm/m/n/10 , \T1/fi4/m/n/10 bpaggregate \T1/ptm/m/n/10 or \T1/fi4
/m/n/10 bpvectorize\T1/ptm/m/n/10 .
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[]\T1/fi4/m/n/10 logical(1)\T1/ptm/m/n/10 Flag to de-ter-mine in apply-like fun
c-tions (see e.g. [][]\T1/fi4/m/n/10 bplapply[][][]\T1/ptm/m/n/10 ) whether
[21] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [22] [23]
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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/fi4/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/fi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/fi4/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/fi4/m/n/10 clusterSetRNGStream
[24]
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[]\T1/fi4/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 :
[25]
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[]\T1/fi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
[26]
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[]\T1/ptm/m/n/10 Make this the de-fault \T1/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/m/n/10 FALSE\T1/ptm/m/n/10
,
[28]
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\T1/ptm/m/n/10 tomiza-tions dur-ing start-up (e.g., in an \T1/fi4/m/n/10 .Rprof
ile \T1/ptm/m/n/10 file) with, for in-stance, \T1/fi4/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/fi4/m/n/10 options(MulticoreParam=MulticoreParam()) \T
1/ptm/m/n/10 and then the value of \T1/fi4/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/fi4/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/fi4/m/n/10 outfile \T1/ptm/m/n/10 ar-gu-ment to \T1/fi4/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/fi4/m/n/10 clusterSetRNGStream
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[]\T1/ptm/m/n/10 NOTE: The \T1/fi4/m/n/10 PSOCK \T1/ptm/m/n/10 clus-ter from th
e \T1/fi4/m/n/10 parallel \T1/ptm/m/n/10 pack-age does not sup-port clus-ter op
-tions \T1/fi4/m/n/10 scriptdir
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[]\T1/fi4/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 :
[33]
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[]\T1/fi4/m/n/10 bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())
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[]\T1/fi4/m/n/10 as(from, "SnowParam")\T1/ptm/m/n/10 : Cre-ates a \T1/fi4/m/n/1
0 SnowParam \T1/ptm/m/n/10 ob-ject from a \T1/fi4/m/n/10 SOCKcluster \T1/ptm/m/
n/10 or \T1/fi4/m/n/10 spawnedMPIcluster
[34] [35] (./Rd2.ind [36]
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[]\T1/fi4/m/it/10 bpaggregate,data.frame,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpaggregate,formula,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpaggregate,matrix,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpbackend<-,DoparParam,SOCKcluster-method
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[]\T1/fi4/m/it/10 bpcatchErrors,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpcatchErrors<-,BiocParallelParam,logical-method
[37]
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[]\T1/fi4/m/it/10 bpiterate,ANY,ANY,BatchJobsParam-method
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[]\T1/fi4/m/it/10 bpiterate,ANY,ANY,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpjobname<-,BiocParallelParam,character-method
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[]\T1/fi4/m/it/10 bpprogressbar,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpprogressbar<-,BiocParallelParam,logical-method
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[]\T1/fi4/m/it/10 bpresultdir<-,SnowParam,character-method
[38]
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[]\T1/fi4/m/it/10 bpstopOnError,BiocParallelParam-method
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[]\T1/fi4/m/it/10 bpstopOnError<-,BiocParallelParam,logical-method
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[]\T1/fi4/m/it/10 bpstopOnError<-,DoparParam,logical-method
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[]\T1/fi4/m/it/10 bptasks<-,BiocParallelParam,numeric-method
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[]\T1/fi4/m/it/10 bpthreshold<-,SerialParam,character-method
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[]\T1/fi4/m/it/10 bpthreshold<-,SnowParam,character-method
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[]\T1/fi4/m/it/10 bpworkers<-,MulticoreParam,numeric-method
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[]\T1/fi4/m/it/10 bpworkers<-,SnowParam,character-method
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[]\T1/fi4/m/it/10 coerce,spawnedMPIcluster,SnowParam-method
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Saving output to ‘/private/tmp/RtmpYwfga2/Rbuild10478736fb635/BiocParallel/build/BiocParallel.pdf’ ...
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* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘BiocParallel_1.2.22.tar.gz’
