Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:20 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MiChip on machv2


To the developers/maintainers of the MiChip package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/MiChip.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1140/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiChip 1.48.0  (landing page)
Jonathon Blake
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MiChip
git_branch: RELEASE_3_14
git_last_commit: 26cc5a6
git_last_commit_date: 2021-10-26 11:54:28 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MiChip
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MiChip.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MiChip_1.48.0.tar.gz
StartedAt: 2022-04-12 15:25:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:26:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 43.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MiChip.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MiChip.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MiChip_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MiChip.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MiChip/DESCRIPTION’ ... OK
* this is package ‘MiChip’ version ‘1.48.0’
* 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-3.14-bioc/meat/MiChip.Rcheck/00check.log’
for details.



Installation output

MiChip.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MiChip
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
boxplotData000
boxplotDataNoFile0.0000.0000.001
correctForFlags0.0000.0000.001
myForgivingMedian0.0000.0000.001
naOmitMedian000
normalizePerChipMedian0.0000.0010.000
outputAnnotatedDataMatrix0.0000.0000.001
panelCor0.0000.0000.001
parseRawData0.0000.0000.001
plotIntensitiesScatter000
removeUnwantedRows0.0000.0010.000
returnAnnotatedDataMatrix000
setIntensityCutoff000
standardRemoveRows000
summarizeIntensitiesAsMedian000
workedExampleMedianNormalize2.1110.0942.255
workedExampleNotNormalizedData0.0000.0000.001