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CHECK report for OmicsMarkeR on merida1

This page was generated on 2020-04-15 12:41:45 -0400 (Wed, 15 Apr 2020).

Package 1181/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsMarkeR 1.18.0
Charles E. Determan Jr.
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/OmicsMarkeR
Branch: RELEASE_3_10
Last Commit: 76b46b7
Last Changed Date: 2019-10-29 13:09:16 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: OmicsMarkeR
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OmicsMarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmicsMarkeR_1.18.0.tar.gz
StartedAt: 2020-04-15 04:19:31 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:24:06 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 274.8 seconds
RetCode: 0
Status:  OK 
CheckDir: OmicsMarkeR.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:OmicsMarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmicsMarkeR_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.18.0’
* 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 ‘OmicsMarkeR’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          15.756  0.331  16.216
feature.table       13.449  0.484  14.017
perm.features       12.996  0.425  13.503
performance.metrics 12.909  0.338  13.345
fs.stability        12.719  0.397  13.212
predictNewClasses   12.044  0.524  12.660
* 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

OmicsMarkeR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OmicsMarkeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘OmicsMarkeR’ ...
** using staged installation
** R
** inst
** 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 (OmicsMarkeR)

Tests output

OmicsMarkeR.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(OmicsMarkeR)
> 
> test_check("OmicsMarkeR")
solo last variable══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 100 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 79.332   2.031  82.319 

Example timings

OmicsMarkeR.Rcheck/OmicsMarkeR-Ex.timings

nameusersystemelapsed
RPT0.0040.0010.006
aggregation0.0070.0010.009
canberra0.0020.0000.002
canberra_stability0.0020.0000.002
create.corr.matrix0.0070.0020.009
create.discr.matrix0.0050.0010.005
create.random.matrix0.0180.0020.020
denovo.grid0.0140.0020.016
feature.table13.449 0.48414.017
fit.only.model4.4180.3414.790
fs.ensembl.stability000
fs.stability12.719 0.39713.212
jaccard0.0010.0010.002
kuncheva0.0010.0000.002
modelList0.0030.0010.003
ochiai0.0010.0000.001
pairwise.model.stability0.0130.0010.013
pairwise.stability0.0050.0000.006
params0.0030.0010.002
performance.metrics12.909 0.33813.345
perm.class15.756 0.33116.216
perm.features12.996 0.42513.503
pof0.0000.0000.001
predictNewClasses12.044 0.52412.660
sorensen0.0010.0000.001
spearman0.0010.0000.001
svmrfeFeatureRanking0.1070.0020.109
svmrfeFeatureRankingForMulticlass0.1590.0010.160