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CHECK report for MCbiclust on malbec2

This page was generated on 2020-10-17 11:55:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MCbiclust PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1008/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MCbiclust 1.12.0
Robert Bentham
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MCbiclust
Branch: RELEASE_3_11
Last Commit: 864f992
Last Changed Date: 2020-04-27 15:05:04 -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: MCbiclust
Version: 1.12.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MCbiclust_1.12.0.tar.gz
StartedAt: 2020-10-17 02:51:51 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:57:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 319.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MCbiclust.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MCbiclust_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MCbiclust.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 ‘MCbiclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MCbiclust’ version ‘1.12.0’
* 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 ‘MCbiclust’ 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 ... 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
SilhouetteClustGroups 30.370  0.562  31.402
CVPlot                17.060  0.112  17.171
PointScoreCalc        12.257  0.615  13.353
ThresholdBic           9.137  0.288   9.894
CVEval                 9.001  0.155   9.611
PC1VecFun              8.007  0.211   8.699
SampleSort             6.303  0.474   7.263
GOEnrichmentAnalysis   6.546  0.028   6.575
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

MCbiclust.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MCbiclust
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MCbiclust’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** 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 (MCbiclust)

Tests output

MCbiclust.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(MCbiclust)


> 
> test_check("MCbiclust")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 75.148   0.915  76.544 

Example timings

MCbiclust.Rcheck/MCbiclust-Ex.timings

nameusersystemelapsed
CVEval9.0010.1559.611
CVPlot17.060 0.11217.171
CorScoreCalc3.0280.0443.072
FindSeed3.3110.0243.334
GOEnrichmentAnalysis6.5460.0286.575
HclustGenesHiCor2.3580.0242.382
PC1VecFun8.0070.2118.699
PointScoreCalc12.257 0.61513.353
SampleSort6.3030.4747.263
SilhouetteClustGroups30.370 0.56231.402
ThresholdBic9.1370.2889.894