Package: PathoStat

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2019-10-16 05:22:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:30:35 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 456.6 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 20.632  0.226  20.891
* 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-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
 17.484   1.511  18.946 

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	20.632	0.226	20.891
Chisq_Test_Pam	0.004	0.001	0.004
Fisher_Test_Pam	0.005	0.000	0.005
GET_PAM	0.003	0.000	0.003
LOOAUC_simple_multiple_noplot_one_df	4.505	0.018	4.522
LOOAUC_simple_multiple_one_df	4.767	0.037	4.804
PathoStat-class	0.071	0.001	0.071
TranslateIdToTaxLevel	0.003	0.001	0.003
Wilcox_Test_df	0.012	0.002	0.015
findRAfromCount	0.221	0.003	0.224
findTaxonMat	0.172	0.010	0.182
findTaxonomy	0.176	0.008	0.184
findTaxonomy300	0.139	0.004	0.142
getShinyInput	0.000	0.000	0.001
getShinyInputCombat	0	0	0
getShinyInputOrig	0.000	0.000	0.001
getSignatureFromMultipleGlmnet	1.717	0.056	1.774
grepTid	0.001	0.000	0.001
loadPathoscopeReports	0.002	0.000	0.003
loadPstat	0.003	0.001	0.003
log2CPM	0.001	0.000	0.002
percent	0.001	0.000	0.001
phyloseq_to_edgeR	0.097	0.014	0.111
plotPCAPlotly	0.348	0.067	0.416
plotPCoAPlotly	0.274	0.045	0.321
readPathoscopeData	0.057	0.003	0.060
runPathoStat	0.096	0.001	0.098
savePstat	0.006	0.001	0.008
setShinyInput	0.000	0.001	0.001
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0.001	0.000	0.001
summarizeTable	0.004	0.001	0.005