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This page was generated on 2022-06-24 12:07:28 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 funtooNorm on merida1


To the developers/maintainers of the funtooNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/funtooNorm.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 711/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.20.0  (landing page)
Kathleen Klein
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/funtooNorm
git_branch: RELEASE_3_15
git_last_commit: cac6b4f
git_last_commit_date: 2022-04-26 11:38:31 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: funtooNorm
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings funtooNorm_1.20.0.tar.gz
StartedAt: 2022-06-24 02:58:04 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 03:10:34 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 749.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings funtooNorm_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/funtooNorm.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.20.0’
* 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 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MyEndnoteLibrary.bib’, ‘funtooNorm.Rmd’, ‘funtooNorm.pdf’,
    ‘validationcurvesPCRlow.jpg’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/funtooNorm.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
funtooNorm            41.250  1.107  44.994
getNormM              39.650  0.671  41.029
plotValidationGraph   39.112  0.530  40.259
getNormBeta           38.709  0.863  42.616
getSnpM               37.380  0.685  39.490
fromRGChannelSet      18.909  0.772  20.087
getGRanges             9.640  0.329  10.407
getRawBeta             8.094  0.297   9.265
show-SampleSet-method  7.396  0.230   7.766
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/funtooNorm.Rcheck/00check.log’
for details.



Installation output

funtooNorm.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-class0.0020.0000.003
agreement0.0020.0010.002
fromRGChannelSet18.909 0.77220.087
funtooNorm41.250 1.10744.994
getGRanges 9.640 0.32910.407
getNormBeta38.709 0.86342.616
getNormM39.650 0.67141.029
getRawBeta8.0940.2979.265
getSnpM37.380 0.68539.490
plotValidationGraph39.112 0.53040.259
show-SampleSet-method7.3960.2307.766