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BioC 3.4: CHECK report for BiocParallel on tokay1

This page was generated on 2017-04-15 16:17:33 -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: rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.8.2.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.8.2.tar.gz
StartedAt: 2017-04-14 21:11:48 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:14:44 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 175.4 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.8.2.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/BiocParallel.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.8.2'
* 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 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 4.53   0.16   11.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bpaggregate     5.55   0.10   13.83
SnowParam-class 0.22   0.03    5.15
* 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-3.4-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_1.8.2.zip
* DONE (BiocParallel)

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

nameusersystemelapsed
BatchJobsParam-class1.780.112.08
BiocParallelParam-class000
DoparParam-class000
MulticoreParam-class0.070.002.13
SerialParam-class000
SnowParam-class0.250.014.55
bpaggregate 4.53 0.1611.31
bpiterate000
bplapply0.010.001.05
bploop000
bpmapply0.000.010.64
bpok0.050.022.23
bpschedule0.020.000.02
bptry0.000.001.72
bpvalidate0.170.000.17
bpvec0.310.011.37
bpvectorize0.020.011.06
register0.040.001.08

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

nameusersystemelapsed
BatchJobsParam-class2.520.092.61
BiocParallelParam-class000
DoparParam-class000
MulticoreParam-class0.060.002.12
SerialParam-class0.010.000.02
SnowParam-class0.220.035.15
bpaggregate 5.55 0.1013.83
bpiterate000
bplapply0.030.011.34
bploop000
bpmapply0.010.000.72
bpok0.050.002.49
bpschedule0.020.000.02
bptry0.010.002.15
bpvalidate0.170.010.19
bpvec0.410.001.77
bpvectorize0.010.021.26
register0.070.001.69