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This page was generated on 2022-03-18 11:07:33 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 692/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.19.0  (landing page)
Kathleen Klein
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/funtooNorm
git_branch: master
git_last_commit: 00aa869
git_last_commit_date: 2021-11-23 15:54:41 -0400 (Tue, 23 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: funtooNorm
Version: 1.19.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:funtooNorm.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings funtooNorm_1.19.0.tar.gz
StartedAt: 2022-03-17 19:08:15 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:13:33 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 317.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:funtooNorm.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings funtooNorm_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/funtooNorm.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'funtooNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'funtooNorm' version '1.19.0'
* 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 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 16.09   0.81   16.90
getNormM            13.17   1.44   14.61
getSnpM             12.84   1.70   14.55
funtooNorm          12.27   1.80   14.08
getNormBeta         11.36   1.39   12.75
fromRGChannelSet    10.30   1.15   11.46
getRawBeta           5.97   0.84    6.81
getGRanges           4.48   0.94    5.42
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/funtooNorm.Rcheck/00check.log'
for details.



Installation output

funtooNorm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL funtooNorm
###
##############################################################################
##############################################################################


* installing to library 'D:/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
  converting help for package 'funtooNorm'
    finding HTML links ... done
    SampleSet-class                         html  
    agreement                               html  
    fromGenStudFiles                        html  
    fromRGChannelSet                        html  
    funtooNorm-package                      html  
    funtooNorm                              html  
    getGRanges                              html  
    getNormBeta                             html  
    getNormM                                html  
    getRawBeta                              html  
    getSnpM                                 html  
    plotValidationGraph                     html  
    show-SampleSet-method                   html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ssPATHS' is missing or broken
 done

Tests output


Example timings

funtooNorm.Rcheck/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class0.020.000.01
agreement000
fromRGChannelSet10.30 1.1511.46
funtooNorm12.27 1.8014.08
getGRanges4.480.945.42
getNormBeta11.36 1.3912.75
getNormM13.17 1.4414.61
getRawBeta5.970.846.81
getSnpM12.84 1.7014.55
plotValidationGraph16.09 0.8116.90
show-SampleSet-method3.160.833.98