Multiple platform build/check report for BioC 3.7 - CHECK report for PathoStat on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PathoStat_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PathoStat.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.6.1’
* 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 ‘PathoStat’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Bootstrap_LOOCV_LR_AUC 36.691  0.166  37.217
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PathoStat
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PathoStat’ ...
** R
** data
** 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
* DONE (PathoStat)

Tests output


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(PathoStat)
> 
> test_check("PathoStat")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.576   0.653  13.299

Example timings

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	36.691	0.166	37.217
Chisq_Test_Pam	0.005	0.001	0.005
Fisher_Test_Pam	0.005	0.000	0.007
GET_PAM	0.003	0.001	0.004
LOOAUC_simple_multiple_noplot_one_df	4.002	0.010	4.049
LOOAUC_simple_multiple_one_df	4.061	0.016	4.104
TranslateIdToTaxLevel	0.005	0.001	0.005
Wilcox_Test_df	0.012	0.001	0.013
findRAfromCount	0.242	0.002	0.246
findTaxonMat	0.226	0.019	0.936
findTaxonomy	0.163	0.003	0.852
getShinyInput	0.000	0.000	0.001
getShinyInputCombat	0.001	0.000	0.001
getShinyInputOrig	0.001	0.000	0.001
getSignatureFromMultipleGlmnet	1.750	0.041	1.802
grepTid	0.001	0.000	0.002
loadPathoscopeReports	0.003	0.000	0.004
loadPstat	0.002	0.000	0.002
log2CPM	0.001	0.000	0.002
percent	0.001	0.001	0.001
phyloseq_to_edgeR	0.081	0.005	0.086
plotHeatmapColor	1.217	0.035	1.262
plotPCAPlotly	0.297	0.031	0.331
plotPCoAPlotly	0.246	0.019	0.268
readPathoscopeData	0.002	0.000	0.002
runPathoStat	0.100	0.002	0.101
savePstat	0.007	0.001	0.009
setShinyInput	0.002	0.000	0.002
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0.001	0.000	0.002
summarizeTable	0.005	0.000	0.006

CHECK report for PathoStat on merida2

Summary

Command output

Installation output

Tests output

Example timings