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CHECK report for skewr on malbec1

This page was generated on 2019-04-16 11:51:07 -0400 (Tue, 16 Apr 2019).

Package 1462/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
skewr 1.14.0
Ryan Putney
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/skewr
Branch: RELEASE_3_8
Last Commit: f354f7a
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: skewr
Version: 1.14.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:skewr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings skewr_1.14.0.tar.gz
StartedAt: 2019-04-16 03:07:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:12:49 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 294.5 seconds
RetCode: 0
Status:  OK 
CheckDir: skewr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:skewr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings skewr_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/skewr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘skewr/DESCRIPTION’ ... OK
* this is package ‘skewr’ version ‘1.14.0’
* 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 ‘skewr’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dSN: no visible global function definition for ‘dnorm’
dSN: no visible global function definition for ‘pnorm’
panelPlots: no visible global function definition for ‘data’
panelPlots : finishPlot: no visible global function definition for
  ‘mtext’
panelPlots : finishPlot: no visible global function definition for
  ‘par’
panelPlots: no visible global function definition for ‘par’
panelPlots: no visible global function definition for ‘density’
panelPlots: no visible global function definition for ‘axis’
panelPlots: no visible global function definition for ‘lines’
panelPlots: no visible global function definition for ‘segments’
panelPlots: no visible global function definition for ‘mtext’
plotComponents: no visible global function definition for ‘hist’
plotComponents: no visible global function definition for ‘lines’
plotComponents: no visible global function definition for ‘segments’
plotComponents: no visible global function definition for ‘density’
subsetProbes: no visible global function definition for ‘data’
subsetProbes: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
subsetProbes: no visible binding for global variable ‘Color’
Undefined global functions or variables:
  Color IlluminaHumanMethylation450kmanifest axis data density dnorm
  hist lines mtext par pnorm segments
Consider adding
  importFrom("graphics", "axis", "hist", "lines", "mtext", "par",
             "segments")
  importFrom("stats", "density", "dnorm", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
subsetProbes 5.432  0.156   5.861
* 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-3.8-bioc/meat/skewr.Rcheck/00check.log’
for details.



Installation output

skewr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL skewr
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘skewr’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (skewr)

Tests output


Example timings

skewr.Rcheck/skewr-Ex.timings

nameusersystemelapsed
getBarcodes0.0320.0000.031
getMethyLumiSet000
getSNparams0.0040.0000.000
panelPlots000
preprocess000
subsetProbes5.4320.1565.861