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CHECK report for biosigner on malbec1

This page was generated on 2020-08-10 11:42:07 -0400 (Mon, 10 Aug 2020).

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 176/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.17.0
Philippe Rinaudo , Etienne Thevenot
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/biosigner
Branch: master
Last Commit: a227d42
Last Changed Date: 2020-04-27 14:55:12 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biosigner
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2020-08-10 02:01:59 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 02:05:22 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 203.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: biosigner.Rcheck
Warnings: 1

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_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/biosigner.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.17.0’
* 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 ‘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 ... WARNING
Documented arguments not in \usage in documentation object 'getMset,biosignMultiDataSet-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 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 55.780  0.356  56.248
plot    48.172  0.056  48.305
getMset 42.892  0.052  43.019
* 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, 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-class3.2720.0363.312
biosign55.780 0.35656.248
biosignMultiDataSet-class000
biosigner-package2.9720.0042.984
getAccuracyMN2.4680.0162.484
getEset2.8400.0002.841
getMset42.892 0.05243.019
getSignatureLs3.6560.0043.667
plot48.172 0.05648.305
predict2.7080.0082.718
show2.6560.0042.662