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CHECK report for ropls on malbec2

This page was generated on 2020-10-17 11:55:37 -0400 (Sat, 17 Oct 2020).

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 1526/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ropls 1.20.0
Etienne A. Thevenot
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ropls
Branch: RELEASE_3_11
Last Commit: d56916b
Last Changed Date: 2020-04-27 14:50:05 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ropls
Version: 1.20.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ropls.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ropls_1.20.0.tar.gz
StartedAt: 2020-10-17 04:58:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:59:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 70.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ropls.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ropls.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ropls_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ropls.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 5.572  0.132   5.704
* 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-3.11-bioc/meat/ropls.Rcheck/00check.log’
for details.



Installation output

ropls.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ropls
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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
checkW4M0.1560.0120.169
coef0.5020.0320.533
fitted0.9890.0040.993
fromW4M0.1140.0000.114
getEset0.5090.0040.514
getLoadingMN0.5040.0000.504
getMset5.5720.1325.704
getPcaVarVn0.0830.0040.087
getScoreMN0.4970.0040.501
getSubsetVi0.0490.0080.057
getSummaryDF0.5180.0000.518
getVipVn0.5170.0000.517
getWeightMN0.980.000.98
opls-class1.8210.0521.872
opls4.4100.0124.423
oplsMultiDataSet-class000
plot3.0880.0003.089
predict0.050.000.05
print0.5150.0000.516
residuals0.3600.0040.362
ropls-package2.1450.0042.149
show0.5110.0000.510
tested0.0480.0000.049
toW4M0.1070.0000.107
view0.5300.0040.534