Package: PathoStat

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathoStat_1.4.1.tar.gz

StartedAt: 2018-04-12 07:26:42 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:32:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 323.7 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 --no-vignettes --timings PathoStat_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PathoStat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 loading without being on the library search path ... 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 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
loadPathoscopeReports 5.650  0.832   6.577
runPathoStat          4.337  0.279   5.007
createPathoStat       1.324  0.019  18.307
* 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

* installing *source* package ‘PathoStat’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PathoStat)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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")
   inline R code fragments

label: unnamed-chunk-1 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-2 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 12
 $ fig.height: num 8

/usr/local/bin/pandoc +RTS -K512m -RTS pathostat_report.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /Users/biocbuild/bbs-3.6-bioc/meat/PathoStat.Rcheck/tests/testthat/PathoStat_report.html --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 2 --template PathoStat.html --highlight-style pygments --css /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css --mathjax 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.737   0.694  41.234 

name	user	system	elapsed
coreOTU	0.055	0.002	0.060
coreOTUModule	0.001	0.000	0.001
coreOTUModuleUI	0.176	0.004	0.184
coreOTUNormalize	0.065	0.001	0.067
coreOTUQuantile	0.027	0.002	0.028
createPathoStat	1.324	0.019	18.307
findRAfromCount	0.146	0.002	0.153
findTaxonLevel	0.060	0.001	0.542
findTaxonMat	0.167	0.003	2.801
findTaxonomy	0.147	0.002	2.775
getShinyInput	0.001	0.001	0.001
getShinyInputCombat	0	0	0
getShinyInputOrig	0.000	0.000	0.001
grepTid	0	0	0
loadPathoscopeReports	5.650	0.832	6.577
loadPstat	0.002	0.000	0.003
log2CPM	0.030	0.001	0.031
pathostat	0.388	0.001	0.395
plotConfRegion	1.183	0.011	1.219
readPathoscopeData	0.065	0.005	0.072
runPathoStat	4.337	0.279	5.007
savePstat	0.007	0.001	0.008
setShinyInput	0.001	0.000	0.000
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0	0	0
sizeNormalize	0.031	0.001	0.033