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CHECK report for ropls on merida1

This page was generated on 2021-05-06 12:36:33 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ropls package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1568/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ropls 1.22.0  (landing page)
Etienne A. Thevenot
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ropls
Branch: RELEASE_3_12
Last Commit: 78847f9
Last Changed Date: 2020-10-27 11:06:35 -0400 (Tue, 27 Oct 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: ropls
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ropls_1.22.0.tar.gz
StartedAt: 2021-05-06 05:39:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:41:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 89.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ropls.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ropls_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ropls.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ropls/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ropls’ version ‘1.22.0’
* package encoding: UTF-8
* 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 ‘ropls’ 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
getMset 6.719  0.213   6.948
opls    4.831  0.156   5.001
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/ropls.Rcheck/00check.log’
for details.



Installation output

ropls.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ropls
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ropls’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘opls’ 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 (ropls)

Tests output


Example timings

ropls.Rcheck/ropls-Ex.timings

nameusersystemelapsed
checkW4M0.1880.0170.205
coef0.8330.1110.946
fitted1.3400.0591.403
fromW4M0.1410.0040.146
getEset0.6920.0600.759
getLoadingMN0.6790.0560.738
getMset6.7190.2136.948
getPcaVarVn0.1220.0070.130
getScoreMN0.7560.0450.802
getSubsetVi0.0820.0060.098
getSummaryDF0.7140.0260.742
getVipVn0.7360.0360.774
getWeightMN1.1630.0421.209
opls-class2.3670.1072.502
opls4.8310.1565.001
oplsMultiDataSet-class000
plot4.3100.1094.440
predict0.0820.0080.090
print0.8050.0370.880
residuals0.4430.0120.456
ropls-package3.0250.0943.126
show0.7550.0260.784
tested0.0800.0040.084
toW4M0.1530.0050.158
view0.6320.0750.712