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CHECK report for OSAT on merida1

This page was generated on 2021-02-22 12:44:14 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the OSAT package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1281/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.38.0
Li Yan
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/OSAT
Branch: RELEASE_3_12
Last Commit: dead1e7
Last Changed Date: 2020-10-27 10:46:15 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OSAT_1.38.0.tar.gz
StartedAt: 2021-02-22 04:39:11 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 04:39:51 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 39.8 seconds
RetCode: 0
Status:   OK  
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OSAT_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/OSAT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OSAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OSAT’ version ‘1.38.0’
* 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 ‘OSAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
assign.sample.to.container: no visible global function definition for
  ‘head’
barplot.gExperimentSetup: no visible global function definition for
  ‘layout’
barplot.gExperimentSetup: no visible global function definition for
  ‘barplot’
barplot.gExperimentSetup: no visible global function definition for
  ‘gray’
barplot.gExperimentSetup: no visible global function definition for
  ‘points’
barplot.gExperimentSetup: no visible global function definition for
  ‘mtext’
multi.barplot: no visible global function definition for ‘layout’
multi.barplot: no visible global function definition for ‘barplot’
multi.barplot: no visible global function definition for ‘gray’
multi.barplot: no visible global function definition for ‘mtext’
show,gAssembly: no visible global function definition for ‘head’
show,gAssembly: no visible global function definition for ‘tail’
show,gContainer: no visible global function definition for ‘head’
show,gContainer: no visible global function definition for ‘tail’
show,gExperimentSetup: no visible global function definition for ‘head’
show,gExperimentSetup: no visible global function definition for ‘tail’
show,gPlate: no visible global function definition for ‘head’
show,gPlate: no visible global function definition for ‘tail’
show,gSample: no visible global function definition for ‘head’
show,gSample: no visible global function definition for ‘tail’
Undefined global functions or variables:
  barplot gray head layout mtext points tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "barplot", "layout", "mtext", "points")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/OSAT.Rcheck/00check.log’
for details.



Installation output

OSAT.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OSAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘OSAT’ ...
** using staged installation
** R
** data
** 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 (OSAT)

Tests output


Example timings

OSAT.Rcheck/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.0110.0020.013
BeadPlate-class0.0120.0010.013
MSAroboticPlate-class0.3520.0180.371
QC1.6110.0251.637
create.optimized.setup1.2900.0151.306
example.setup0.0490.0100.060
gContainer-class0.0260.0020.029
gExperimentSetup-class0.0700.0030.073
gSample-class0.0140.0010.015
gSlide-class0.0370.0010.038
get.experiment.setup1.3680.0111.380
multi.barplot0.0250.0030.027
multi.chisq.test0.0130.0020.015
optimal.block1.8600.0091.871
optimal.shuffle1.3940.0211.416