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BioC 3.5: CHECK report for BiocParallel on veracruz2

This page was generated on 2017-10-18 14:30:47 -0400 (Wed, 18 Oct 2017).

Package 121/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.10.1
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_5
Last Commit: a76c58c
Last Changed Date: 2017-05-02 05:26:22 -0400 (Tue, 02 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.10.1.tar.gz
StartedAt: 2017-10-18 01:00:24 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:03:34 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 189.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocParallel.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘1.10.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocParallel’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::checkDir’ ‘parallel:::closeNode’ ‘parallel:::recvData’
  ‘parallel:::recvOneData’ ‘parallel:::sendData’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bpaggregate     7.507  0.275  10.530
SnowParam-class 0.389  0.039   6.238
register        0.039  0.082   5.314
bptry           0.032  0.062   5.240
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.


BiocParallel.Rcheck/00install.out:

* installing *source* package ‘BiocParallel’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)

BiocParallel.Rcheck/BiocParallel-Ex.timings:

nameusersystemelapsed
BatchJobsParam-class2.9920.0783.208
BiocParallelParam-class0.0030.0000.003
DoparParam-class0.0000.0000.001
MulticoreParam-class0.4750.1504.158
SerialParam-class0.0080.0120.020
SnowParam-class0.3890.0396.238
bpaggregate 7.507 0.27510.530
bpiterate0.0030.0000.004
bplapply0.0180.0172.917
bploop0.0010.0000.001
bpmapply0.0260.0932.234
bpok0.0600.0333.016
bpschedule0.0310.0192.217
bptry0.0320.0625.240
bpvalidate0.3490.0870.446
bpvec0.4920.1433.509
bpvectorize0.0270.0192.805
register0.0390.0825.314