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BioC 3.4: CHECK report for BiocParallel on malbec1

This page was generated on 2017-04-15 16:11:11 -0400 (Sat, 15 Apr 2017).

Package 116/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.8.2
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BiocParallel
Last Changed Rev: 128057 / Revision: 128728
Last Changed Date: 2017-04-05 02:56:24 -0400 (Wed, 05 Apr 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  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.8.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.8.2.tar.gz
StartedAt: 2017-04-14 21:14:59 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:17:34 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 155.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BiocParallel.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.2’
* 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
--------------------------------------------------------------------------
[[27981,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
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 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     5.140  0.092   7.106
SnowParam-class 0.248  0.020   5.342
* 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
  ‘/home/biocbuild/bbs-3.4-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-class2.0520.0162.091
BiocParallelParam-class0.0040.0000.002
DoparParam-class000
MulticoreParam-class0.2600.0483.547
SerialParam-class0.0120.0000.012
SnowParam-class0.2480.0205.342
bpaggregate5.1400.0927.106
bpiterate0.0040.0000.004
bplapply0.0280.0161.921
bploop0.0000.0000.001
bpmapply0.0160.0641.720
bpok0.0640.0842.844
bpschedule0.0320.0521.753
bptry0.0200.0843.630
bpvalidate0.2800.0080.305
bpvec0.4360.0642.351
bpvectorize0.0160.0521.922
register0.0400.0803.661