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CHECK report for MiChip on merida1

This page was generated on 2019-04-16 11:55:05 -0400 (Tue, 16 Apr 2019).

Package 953/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiChip 1.36.0
Jonathon Blake
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MiChip
Branch: RELEASE_3_8
Last Commit: bec77ef
Last Changed Date: 2018-10-30 11:41:45 -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: MiChip
Version: 1.36.0
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_1.36.0.tar.gz
StartedAt: 2019-04-16 01:15:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:16:23 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 33.6 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_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MiChip.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.36.0’
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘MiChip’ ...
** 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
* DONE (MiChip)

Tests output


Example timings

MiChip.Rcheck/MiChip-Ex.timings

nameusersystemelapsed
boxplotData0.0000.0010.000
boxplotDataNoFile000
correctForFlags0.0000.0010.000
myForgivingMedian000
naOmitMedian000
normalizePerChipMedian000
outputAnnotatedDataMatrix000
panelCor0.0010.0010.000
parseRawData0.0000.0000.001
plotIntensitiesScatter0.0000.0010.000
removeUnwantedRows000
returnAnnotatedDataMatrix0.0000.0010.001
setIntensityCutoff0.0010.0000.000
standardRemoveRows0.0000.0010.000
summarizeIntensitiesAsMedian000
workedExampleMedianNormalize2.3390.0812.657
workedExampleNotNormalizedData0.0000.0010.000