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CHECK report for funtooNorm on malbec1

This page was generated on 2021-05-06 12:27:39 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the funtooNorm package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 655/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.14.0  (landing page)
Kathleen Klein
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/funtooNorm
Branch: RELEASE_3_12
Last Commit: 66254f5
Last Changed Date: 2020-10-27 11:20:49 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: funtooNorm
Version: 1.14.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings funtooNorm_1.14.0.tar.gz
StartedAt: 2021-05-06 01:41:18 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:48:40 -0400 (Thu, 06 May 2021)
EllapsedTime: 442.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings funtooNorm_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/funtooNorm.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘funtooNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘funtooNorm’ version ‘1.14.0’
* 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 ‘funtooNorm’ 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 ... WARNING
Documented arguments not in \usage in documentation object 'show,SampleSet-method':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotValidationGraph 24.940  0.120  25.108
getSnpM             17.964  0.096  18.088
getNormM            17.724  0.044  17.807
getNormBeta         16.356  0.092  16.490
funtooNorm          15.968  0.160  16.160
fromRGChannelSet    12.736  0.480  14.251
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/funtooNorm.Rcheck/00check.log’
for details.



Installation output

funtooNorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL funtooNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘funtooNorm’ ...
** 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 (funtooNorm)

Tests output


Example timings

funtooNorm.Rcheck/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class0.0040.0000.002
agreement0.0040.0000.003
fromRGChannelSet12.736 0.48014.251
funtooNorm15.968 0.16016.160
getGRanges4.7560.0124.782
getNormBeta16.356 0.09216.490
getNormM17.724 0.04417.807
getRawBeta4.0760.0404.120
getSnpM17.964 0.09618.088
plotValidationGraph24.940 0.12025.108
show-SampleSet-method4.7640.0044.776