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BioC 3.0: CHECK report for BiocParallel on moscato1

This page was generated on 2015-04-10 09:48:22 -0700 (Fri, 10 Apr 2015).

Package 92/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.0.3
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiocParallel
Last Changed Rev: 99195 / Revision: 102249
Last Changed Date: 2015-02-07 12:52:56 -0800 (Sat, 07 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: BiocParallel
Version: 1.0.3
Command: rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.0.3.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.0.3.tar.gz
StartedAt: 2015-04-09 23:02:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:08:25 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 384.7 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.0.3.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/BiocParallel.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.0.3'
* 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 object imported by a ':::' call: 'parallel:::getClusterOption'
  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 ... NOTE
bpiterate,ANY-ANY-MulticoreParam: no visible global function definition
  for '.bpiterate_multicore'
* 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' ... [26s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
bpaggregate 6.71   0.11    6.82
register    0.10   0.00    5.52
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
bpaggregate 8.35   0.13    8.49
register    0.07   0.02    5.29
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [131s]
 [132s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [136s]
 [137s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.0.3.zip
* DONE (BiocParallel)

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

nameusersystemelapsed
AllClasses000
BatchJobsParam-class1.810.132.56
DoparParam-class0.180.012.28
MulticoreParam-class000
SerialParam-class0.010.000.02
SnowParam-class0.050.053.82
bpaggregate6.710.116.82
bpcontrols000
bpiterate2.810.082.88
bplapply0.240.000.24
bpmapply0.010.000.01
bpresume0.020.000.02
bpschedule0.010.000.01
bpvec0.220.000.22
bpvectorize000
register0.100.005.52

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

nameusersystemelapsed
AllClasses000
BatchJobsParam-class2.780.133.52
DoparParam-class0.210.011.57
MulticoreParam-class0.020.000.02
SerialParam-class0.020.000.02
SnowParam-class0.010.024.30
bpaggregate8.350.138.49
bpcontrols000
bpiterate3.510.073.59
bplapply0.360.000.36
bpmapply0.020.000.02
bpresume0.010.000.01
bpschedule0.020.000.02
bpvec0.330.000.32
bpvectorize000
register0.070.025.29