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

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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.

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### Running command:
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###   /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)

name	user	system	elapsed
boxplotData	0.000	0.000	0.001
boxplotDataNoFile	0.000	0.000	0.001
correctForFlags	0	0	0
myForgivingMedian	0.001	0.000	0.000
naOmitMedian	0	0	0
normalizePerChipMedian	0.000	0.001	0.000
outputAnnotatedDataMatrix	0.001	0.000	0.001
panelCor	0.000	0.000	0.001
parseRawData	0.001	0.000	0.001
plotIntensitiesScatter	0.000	0.000	0.001
removeUnwantedRows	0.000	0.000	0.001
returnAnnotatedDataMatrix	0	0	0
setIntensityCutoff	0	0	0
standardRemoveRows	0.001	0.000	0.001
summarizeIntensitiesAsMedian	0.000	0.000	0.001
workedExampleMedianNormalize	2.554	0.233	2.835
workedExampleNotNormalizedData	0.000	0.001	0.000