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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1218/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiChip 1.54.0  (landing page)
Jonathon Blake
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MiChip
git_branch: RELEASE_3_17
git_last_commit: 4240339
git_last_commit_date: 2023-04-25 09:49:20 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MiChip on kjohnson2


To the developers/maintainers of the MiChip package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MiChip
Version: 1.54.0
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_1.54.0.tar.gz
StartedAt: 2023-10-18 07:09:41 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 07:10:35 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 54.5 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_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MiChip.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MiChip/DESCRIPTION’ ... OK
* this is package ‘MiChip’ version ‘1.54.0’
* 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-3.17-bioc-mac-arm64/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
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
boxplotData0.0000.0010.000
boxplotDataNoFile0.0000.0010.001
correctForFlags000
myForgivingMedian0.0000.0010.000
naOmitMedian000
normalizePerChipMedian000
outputAnnotatedDataMatrix000
panelCor0.0000.0000.001
parseRawData000
plotIntensitiesScatter000
removeUnwantedRows000
returnAnnotatedDataMatrix000
setIntensityCutoff000
standardRemoveRows000
summarizeIntensitiesAsMedian000
workedExampleMedianNormalize1.6490.0752.615
workedExampleNotNormalizedData000