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CHECK report for geneClassifiers on machv2

This page was generated on 2021-01-25 12:42:47 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE geneClassifiers PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 675/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneClassifiers 1.15.0
R Kuiper
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/geneClassifiers
Branch: master
Last Commit: 2b79514
Last Changed Date: 2020-10-27 11:21:25 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: geneClassifiers
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geneClassifiers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneClassifiers_1.15.0.tar.gz
StartedAt: 2021-01-25 00:49:00 -0500 (Mon, 25 Jan 2021)
EndedAt: 2021-01-25 00:49:52 -0500 (Mon, 25 Jan 2021)
EllapsedTime: 51.3 seconds
RetCode: 0
Status:  OK 
CheckDir: geneClassifiers.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geneClassifiers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneClassifiers_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/geneClassifiers.Rcheck’
* using R Under development (unstable) (2021-01-06 r79800)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneClassifiers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneClassifiers’ version ‘1.15.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘geneClassifiers’ 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 ... OK
* 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.13-bioc/meat/geneClassifiers.Rcheck/00check.log’
for details.



Installation output

geneClassifiers.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL geneClassifiers
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘geneClassifiers’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (geneClassifiers)

Tests output

geneClassifiers.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-01-06 r79800) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(geneClassifiers)
> 
> test_check("geneClassifiers")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
> 
> proc.time()
   user  system elapsed 
  4.845   0.213   5.038 

Example timings

geneClassifiers.Rcheck/geneClassifiers-Ex.timings

nameusersystemelapsed
bracket-methods0.0420.0090.050
dim-methods0.0160.0040.020
getBatchCorrection-methods0.4370.0170.455
getCitations-methods0.0030.0000.002
getClassifications-methods0.0350.0020.038
getClassifier-methods0.0020.0010.003
getDecisionBoundaries-methods0.0030.0010.003
getDescription-methods0.0010.0000.001
getEventChain-methods0.0010.0000.002
getIntercept-methods0.0030.0010.003
getMeans-methods0.0020.0020.004
getName-methods0.0030.0010.003
getNormalizationMethod-methods0.0600.0070.066
getProbeNames-methods0.0020.0010.003
getScores-methods0.0240.0030.028
getSds-methods0.0020.0020.004
getTargetValue-methods0.0150.0020.017
getTrainingData-methods0.0440.0010.045
getWeightingType-methods0.0320.0020.035
getWeights-methods0.0040.0020.006
runClassifier-methods0.0310.0020.034
setNormalizationMethod-methods0.0300.0030.033
showClassifierList-methods0.0300.0030.033