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BioC 2.13: BUILD report for BiocParallel on zin1

This page was generated on 2014-04-05 09:48:29 -0700 (Sat, 05 Apr 2014).

Package 82/750HostnameOS / ArchBUILDCHECKBUILD BIN
BiocParallel 0.4.1
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/BiocParallel
Last Changed Rev: 81898 / Revision: 88450
Last Changed Date: 2013-10-20 10:07:38 -0700 (Sun, 20 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64 [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  TIMEOUT  OK 

Summary

Package: BiocParallel
Version: 0.4.1
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocParallel
StartedAt: 2014-04-04 22:30:53 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 22:30:58 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 4.8 seconds
RetCode: 0
Status:  OK 
PackageFile: BiocParallel_0.4.1.tar.gz
PackageFileSize: 153.3 KiB

Command output

* 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
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Converting Rd files to LaTeX .
Creating pdf output from LaTeX ...

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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{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/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 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 in-di-cat-ing whether forked chil-dr
en will be ter-mi-nated be-fore \T1/fi4/m/n/10 bplapply
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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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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 Use \T1/fi4/m/n/10 as(cl, "SnowParam") \T1/ptm/m/n/10 to co-er
ce a clus-ter cre-ated di-rectly by \T1/fi4/m/n/10 parallel::param \T1/ptm/m/n/
10 to a \T1/fi4/m/n/10 SnowParam
[20] (./Rd2.ind [21]

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