Package: PathoStat

Version: 1.12.0

Command: /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_1.12.0.tar.gz

StartedAt: 2020-04-15 04:26:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:33:14 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 375.9 seconds

RetCode: 0

Status:  OK

CheckDir: PathoStat.Rcheck

Warnings: 0

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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/PathoStat.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 ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.12.0’
* 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 ‘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 ... NOTE
Namespaces in Imports field not imported from:
  ‘ComplexHeatmap’ ‘RColorBrewer’
  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 or elapsed time > 5s
                         user system elapsed
Bootstrap_LOOCV_LR_AUC 19.226  0.247  19.618
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/PathoStat.Rcheck/00check.log’
for details.

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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/3.6/Resources/library’
* installing *source* package ‘PathoStat’ ...
** using staged installation
** 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 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 (PathoStat)

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(PathoStat)
> 
> test_check("PathoStat")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 14.356   0.749  15.238 

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	19.226	0.247	19.618
Chisq_Test_Pam	0.005	0.000	0.005
Fisher_Test_Pam	0.007	0.000	0.007
GET_PAM	0.004	0.000	0.004
LOOAUC_simple_multiple_noplot_one_df	3.886	0.042	3.967
LOOAUC_simple_multiple_one_df	3.911	0.021	3.957
PathoStat-class	0.058	0.001	0.059
TranslateIdToTaxLevel	0.002	0.000	0.002
Wilcox_Test_df	0.015	0.001	0.017
findRAfromCount	0.241	0.001	0.245
findTaxonMat	0.135	0.004	0.141
findTaxonomy	0.142	0.003	0.146
findTaxonomy300	0.148	0.002	0.150
getShinyInput	0.001	0.000	0.000
getShinyInputCombat	0.000	0.001	0.001
getShinyInputOrig	0	0	0
getSignatureFromMultipleGlmnet	1.540	0.031	1.579
grepTid	0.000	0.000	0.001
loadPathoscopeReports	0.001	0.000	0.002
loadPstat	0.002	0.001	0.002
log2CPM	0.001	0.000	0.001
percent	0.000	0.000	0.001
phyloseq_to_edgeR	0.099	0.011	0.109
plotPCAPlotly	0.278	0.031	0.312
plotPCoAPlotly	0.200	0.017	0.220
readPathoscopeData	0.074	0.002	0.077
runPathoStat	0.159	0.001	0.162
savePstat	0.006	0.000	0.006
setShinyInput	0.000	0.000	0.001
setShinyInputCombat	0	0	0
setShinyInputOrig	0.000	0.000	0.001
summarizeTable	0.003	0.000	0.004