BiocParallel 1.4.3
Bioconductor Package Maintainer
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiocParallel | | Last Changed Rev: 111519 / Revision: 116712 | | Last Changed Date: 2015-12-15 11:34:18 -0800 (Tue, 15 Dec 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | [ OK ] | OK | OK | |
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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 ...
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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.
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/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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[]\T1/ptm/m/n/10 Messages sent to \T1/ptm/m/it/10 std-out \T1/ptm/m/n/10 and \T
1/ptm/m/it/10 stderr \T1/ptm/m/n/10 are re-turned to the workspace by de-fault.
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e \T1/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 :
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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
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(see the transcript file for additional information)pdfTeX warning (dest): name
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Output written on Rd2.pdf (36 pages, 156727 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpqbCeNz/Rbuild131777491b01d/BiocParallel/build/BiocParallel.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘BiocParallel_1.4.3.tar.gz’