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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).

CHECK results for funtooNorm on tokay2

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 681/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.16.0  (landing page)
Kathleen Klein
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/funtooNorm
git_branch: RELEASE_3_13
git_last_commit: 3256fea
git_last_commit_date: 2021-05-19 12:25:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: funtooNorm
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:funtooNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings funtooNorm_1.16.0.tar.gz
StartedAt: 2021-10-14 23:20:55 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:29:59 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 544.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:funtooNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings funtooNorm_1.16.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/funtooNorm.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.16.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getNormBeta         15.19   0.67   15.86
plotValidationGraph 15.56   0.19   15.75
funtooNorm          13.83   1.28   15.11
getSnpM             12.03   0.47   12.51
getNormM            11.11   0.52   11.62
fromRGChannelSet     8.94   0.68    9.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plotValidationGraph 18.52   0.30   18.83
getSnpM             13.36   0.59   13.95
getNormBeta         12.74   0.82   13.54
funtooNorm          12.52   0.70   13.22
getNormM            11.74   0.54   12.28
fromRGChannelSet     9.11   0.38    9.48
getRawBeta           5.50   0.35    5.84
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/funtooNorm.Rcheck/00check.log'
for details.



Installation output

funtooNorm.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/funtooNorm_1.16.0.tar.gz && rm -rf funtooNorm.buildbin-libdir && mkdir funtooNorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=funtooNorm.buildbin-libdir funtooNorm_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL funtooNorm_1.16.0.zip && rm funtooNorm_1.16.0.tar.gz funtooNorm_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 2508k    7  180k    0     0   607k      0  0:00:04 --:--:--  0:00:04  608k
100 2508k  100 2508k    0     0  2650k      0 --:--:-- --:--:-- --:--:-- 2651k

install for i386

* 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

install for x64

* installing *source* package 'funtooNorm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'funtooNorm' as funtooNorm_1.16.0.zip
* DONE (funtooNorm)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'funtooNorm' successfully unpacked and MD5 sums checked

Tests output


Example timings

funtooNorm.Rcheck/examples_i386/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class000
agreement000
fromRGChannelSet8.940.689.64
funtooNorm13.83 1.2815.11
getGRanges4.250.374.62
getNormBeta15.19 0.6715.86
getNormM11.11 0.5211.62
getRawBeta3.140.203.35
getSnpM12.03 0.4712.51
plotValidationGraph15.56 0.1915.75
show-SampleSet-method2.490.272.75

funtooNorm.Rcheck/examples_x64/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class000
agreement000
fromRGChannelSet9.110.389.48
funtooNorm12.52 0.7013.22
getGRanges4.280.374.66
getNormBeta12.74 0.8213.54
getNormM11.74 0.5412.28
getRawBeta5.500.355.84
getSnpM13.36 0.5913.95
plotValidationGraph18.52 0.3018.83
show-SampleSet-method3.000.253.25