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CHECK report for MiChip on celaya2

This page was generated on 2020-01-16 13:32:09 -0500 (Thu, 16 Jan 2020).

Package 1035/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiChip 1.41.0
Jonathon Blake
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/MiChip
Branch: master
Last Commit: bb4cc16
Last Changed Date: 2019-10-29 13:35:05 -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 UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MiChip
Version: 1.41.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MiChip.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MiChip_1.41.0.tar.gz
StartedAt: 2020-01-16 06:27:58 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 06:28:48 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 50.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MiChip.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MiChip.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MiChip_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MiChip.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 ‘MiChip/DESCRIPTION’ ... OK
* this is package ‘MiChip’ version ‘1.41.0’
* 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 ‘MiChip’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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
boxplotData: no visible global function definition for ‘jpeg’
boxplotData: no visible global function definition for ‘boxplot’
boxplotData: no visible global function definition for ‘rainbow’
boxplotData: no visible global function definition for ‘dev.off’
boxplotDataNoFile: no visible global function definition for ‘boxplot’
boxplotDataNoFile: no visible global function definition for ‘rainbow’
correctForFlags: no visible global function definition for ‘new’
myForgivingMedian: no visible global function definition for ‘na.omit’
myForgivingMedian: no visible global function definition for ‘median’
myForgivingMedian: no visible global function definition for ‘sd’
naOmitMedian: no visible global function definition for ‘na.omit’
naOmitMedian: no visible global function definition for ‘mad’
naOmitMedian: no visible global function definition for ‘median’
normalizePerChipMedian: no visible global function definition for
  ‘na.omit’
normalizePerChipMedian: no visible global function definition for
  ‘median’
normalizePerChipMedian: no visible global function definition for ‘new’
outputAnnotatedDataMatrix: no visible global function definition for
  ‘write.table’
panelCor: no visible global function definition for ‘cor.test’
panelCor: no visible binding for global variable ‘na.omit’
panelCor: no visible global function definition for ‘strwidth’
panelCor: no visible global function definition for ‘text’
parseRawData: no visible global function definition for ‘read.table’
parseRawData: no visible global function definition for ‘new’
plotIntensitiesScatter: no visible global function definition for
  ‘jpeg’
plotIntensitiesScatter: no visible global function definition for
  ‘pairs’
plotIntensitiesScatter : <anonymous>: no visible global function
  definition for ‘points’
plotIntensitiesScatter : <anonymous>: no visible global function
  definition for ‘abline’
plotIntensitiesScatter: no visible global function definition for
  ‘dev.off’
removeUnwantedRows: no visible global function definition for ‘new’
summarizeIntensitiesAsMedian: no visible binding for global variable
  ‘median’
summarizeIntensitiesAsMedian: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  abline boxplot cor.test dev.off jpeg mad median na.omit new pairs
  points rainbow read.table sd strwidth text write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "rainbow")
  importFrom("graphics", "abline", "boxplot", "pairs", "points",
             "strwidth", "text")
  importFrom("methods", "new")
  importFrom("stats", "cor.test", "mad", "median", "na.omit", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MiChip.Rcheck/00check.log’
for details.



Installation output

MiChip.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MiChip
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MiChip’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MiChip)

Tests output


Example timings

MiChip.Rcheck/MiChip-Ex.timings

nameusersystemelapsed
boxplotData0.0000.0000.001
boxplotDataNoFile0.0000.0000.001
correctForFlags000
myForgivingMedian0.0010.0000.000
naOmitMedian000
normalizePerChipMedian0.0000.0010.000
outputAnnotatedDataMatrix0.0010.0000.001
panelCor0.0000.0000.001
parseRawData0.0010.0000.001
plotIntensitiesScatter0.0000.0000.001
removeUnwantedRows0.0000.0000.001
returnAnnotatedDataMatrix000
setIntensityCutoff000
standardRemoveRows0.0010.0000.001
summarizeIntensitiesAsMedian0.0000.0000.001
workedExampleMedianNormalize2.5540.2332.835
workedExampleNotNormalizedData0.0000.0010.000