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This page was generated on 2022-06-27 11:09:55 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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: 2022-06-26 13:55:11 -0400 (Sun, 26 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

Summary

Package: funtooNorm
Version: 1.20.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings funtooNorm_1.20.0.tar.gz
StartedAt: 2022-06-26 19:55:59 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:02:17 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 378.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings funtooNorm_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/funtooNorm.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.20.0’
* 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          19.607  0.440  20.048
getNormM            18.451  0.180  18.630
plotValidationGraph 18.105  0.076  18.181
getNormBeta         17.610  0.188  17.798
getSnpM             17.202  0.184  17.386
fromRGChannelSet    13.619  0.512  14.132
getRawBeta           5.796  0.168   5.963
getGRanges           5.540  0.076   5.616
* checking PDF version of manual ... OK
* DONE

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



Installation output

funtooNorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL funtooNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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-class0.0010.0000.001
agreement0.0020.0000.001
fromRGChannelSet13.619 0.51214.132
funtooNorm19.607 0.44020.048
getGRanges5.5400.0765.616
getNormBeta17.610 0.18817.798
getNormM18.451 0.18018.630
getRawBeta5.7960.1685.963
getSnpM17.202 0.18417.386
plotValidationGraph18.105 0.07618.181
show-SampleSet-method4.370.024.39