Package: PathoStat

Version: 1.9.4

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_1.9.4.tar.gz

StartedAt: 2019-04-09 02:44:21 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:50:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 361.5 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_1.9.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.4’
* 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 35.074  0.137  35.526
* 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’ ...
** 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)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
 13.594   0.688  14.350 

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	35.074	0.137	35.526
Chisq_Test_Pam	0.004	0.000	0.004
Fisher_Test_Pam	0.006	0.000	0.006
GET_PAM	0.003	0.000	0.003
LOOAUC_simple_multiple_noplot_one_df	4.101	0.009	4.139
LOOAUC_simple_multiple_one_df	4.000	0.014	4.060
PathoStat-class	0.077	0.000	0.079
TranslateIdToTaxLevel	0.003	0.000	0.004
Wilcox_Test_df	0.017	0.001	0.019
findRAfromCount	0.197	0.001	0.205
findTaxonMat	0.339	0.020	1.099
findTaxonomy	0.278	0.006	0.952
findTaxonomy300	0.287	0.008	0.954
getShinyInput	0.001	0.000	0.001
getShinyInputCombat	0	0	0
getShinyInputOrig	0.000	0.001	0.000
getSignatureFromMultipleGlmnet	1.817	0.035	1.863
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	0	0
phyloseq_to_edgeR	0.079	0.005	0.083
plotPCAPlotly	0.260	0.032	0.299
plotPCoAPlotly	0.237	0.024	0.263
readPathoscopeData	0.067	0.003	0.069
runPathoStat	0.110	0.002	0.113
savePstat	0.004	0.000	0.006
setShinyInput	0.001	0.000	0.001
setShinyInputCombat	0	0	0
setShinyInputOrig	0	0	0
summarizeTable	0.004	0.000	0.004