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CHECK report for skewr on celaya2

This page was generated on 2020-01-16 13:41:28 -0500 (Thu, 16 Jan 2020).

Package 1607/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
skewr 1.19.0
Ryan Putney
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/skewr
Branch: master
Last Commit: 6419cf4
Last Changed Date: 2019-10-29 13:39:02 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: skewr
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:skewr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings skewr_1.19.0.tar.gz
StartedAt: 2020-01-16 09:01:10 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:09:16 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 486.6 seconds
RetCode: 0
Status:  OK 
CheckDir: skewr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:skewr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings skewr_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/skewr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘skewr/DESCRIPTION’ ... OK
* this is package ‘skewr’ version ‘1.19.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
subsetProbes 6.862  0.393   7.256
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/skewr.Rcheck/00check.log’
for details.



Installation output

skewr.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL skewr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘skewr’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (skewr)

Tests output


Example timings

skewr.Rcheck/skewr-Ex.timings

nameusersystemelapsed
getBarcodes0.0490.0040.055
getMethyLumiSet0.0000.0000.001
getSNparams0.0000.0000.001
panelPlots000
preprocess0.0010.0010.001
subsetProbes6.8620.3937.256