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BioC 3.5: CHECK report for BiocParallel on tokay2

This page was generated on 2017-10-18 14:22:13 -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: rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.10.1.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.10.1.tar.gz
StartedAt: 2017-10-17 22:19:53 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:23:53 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 239.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.10.1.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BiocParallel.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bpaggregate     5.87   0.22   14.09
SnowParam-class 0.51   0.02    6.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bpaggregate     8.55   0.19   17.22
SnowParam-class 0.62   0.03    6.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.


BiocParallel.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'BiocParallel' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocParallel' as BiocParallel_1.10.1.zip
* DONE (BiocParallel)

BiocParallel.Rcheck/examples_i386/BiocParallel-Ex.timings:

nameusersystemelapsed
BatchJobsParam-class2.890.143.44
BiocParallelParam-class000
DoparParam-class000
MulticoreParam-class0.370.012.45
SerialParam-class0.020.000.02
SnowParam-class0.510.026.48
bpaggregate 5.87 0.2214.09
bpiterate0.020.000.02
bplapply0.030.011.53
bploop000
bpmapply0.030.000.92
bpok0.050.023.20
bpschedule0.010.000.02
bptry0.050.032.59
bpvalidate0.350.060.41
bpvec0.350.022.03
bpvectorize0.040.001.66
register0.030.011.59

BiocParallel.Rcheck/examples_x64/BiocParallel-Ex.timings:

nameusersystemelapsed
BatchJobsParam-class3.970.134.39
BiocParallelParam-class000
DoparParam-class000
MulticoreParam-class0.650.002.67
SerialParam-class000
SnowParam-class0.620.036.66
bpaggregate 8.55 0.1917.22
bpiterate000
bplapply0.020.021.82
bploop000
bpmapply0.030.001.03
bpok0.080.003.48
bpschedule0.020.000.01
bptry0.010.002.86
bpvalidate0.350.060.41
bpvec0.530.012.36
bpvectorize0.030.041.83
register0.030.001.75