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CHECK report for biosigner on malbec1

This page was generated on 2021-05-06 12:27:00 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the biosigner package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 186/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.18.2  (landing page)
Philippe Rinaudo , Etienne Thevenot
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/biosigner
Branch: RELEASE_3_12
Last Commit: 8a38d87
Last Changed Date: 2020-11-21 15:47:20 -0400 (Sat, 21 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: biosigner
Version: 1.18.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biosigner_1.18.2.tar.gz
StartedAt: 2021-05-05 23:30:20 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:34:04 -0400 (Wed, 05 May 2021)
EllapsedTime: 224.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biosigner.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biosigner_1.18.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/biosigner.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 ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.18.2’
* 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 ‘biosigner’ 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 ... NOTE
Namespace in Imports field not imported from: ‘MultiDataSet’
  All declared Imports should be used.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
biosign 66.264  0.352  73.980
plot    49.272  0.020  49.370
getMset 38.292  0.028  38.366
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/biosigner.Rcheck/00check.log’
for details.



Installation output

biosigner.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL biosigner
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘biosigner’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘biosign’ with signature ‘x="MultiDataSet"’: no definition for class “MultiDataSet”
** 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 (biosigner)

Tests output


Example timings

biosigner.Rcheck/biosigner-Ex.timings

nameusersystemelapsed
biosign-class3.8280.0484.045
biosign66.264 0.35273.980
biosignMultiDataSet-class000
biosigner-package4.4000.0124.425
getAccuracyMN3.7360.0044.736
getEset3.8280.0083.986
getMset38.292 0.02838.366
getSignatureLs2.7640.0002.768
plot49.272 0.02049.370
predict3.7880.0043.799
show2.7080.0082.717