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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GladiaTOX_1.6.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ 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 ‘GladiaTOX’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    sql   3.8Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
gtoxRun            34.522 18.223  27.295
assignDefaultMthds 32.705 11.725  23.627
* 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-3.12-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GladiaTOX
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GladiaTOX’ ...
** using staged installation
** R
** 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 (GladiaTOX)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(GladiaTOX)
Loading required package: data.table
GladiaTOX (v1.6.1) loaded with the following settings:
  TCPL_DB:    /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GladiaTOX/sql/gladiatoxdb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in gtox config file. See ?gtoxConf for more information.
> 
> options(testthat.junit.output_file="tests-out.xml")
> test_dir("testthat")
✔ |  OK F W S | Context

⠏ |   0       | assignDefaultMthds                                              
⠋ |   1       | assignDefaultMthds                                              
✔ |   1       | assignDefaultMthds [0.8 s]

⠏ |   0       | exportResultTable                                               
⠋ |   1       | exportResultTable                                               
⠙ |   2       | exportResultTable                                               
✔ |   2       | exportResultTable [0.4 s]

⠏ |   0       | getsplit                                                        
⠏ |   0       | getsplit                                                        
✔ |   1       | getsplit

⠏ |   0       | glComputeToxInd                                                 
⠋ |   1       | glComputeToxInd                                                 
✔ |   1       | glComputeToxInd [0.5 s]

⠏ |   0       | gtoxAICProb                                                     
✔ |   1       | gtoxAICProb

⠏ |   0       | gtoxCalcVmad                                                    
⠏ |   0       | Calculate Vmad                                                  
✔ |   1       | Calculate Vmad

⠏ |   0       | gtoxLoadAcid                                                    
⠏ |   0       | Check assay component table                                     
⠙ |   2       | Check assay component table                                     
✔ |   2       | Check assay component table [0.1 s]

⠏ |   0       | gtoxLoadAeid                                                    
⠏ |   0       | Check assay endpoint table                                      
⠙ |   2       | Check assay endpoint table                                      
✔ |   2       | Check assay endpoint table [0.1 s]

⠏ |   0       | gtoxLoadAid                                                     
✔ |   1       | gtoxLoadAid

⠏ |   0       | gtoxLoadApid                                                    
⠏ |   0       | Check assay plate table                                         
✔ |   2       | Check assay plate table

⠏ |   0       | gtoxLoadAsid                                                    
✔ |   3       | gtoxLoadAsid

⠏ |   0       | gtoxLoadChem                                                    
⠏ |   0       | Check assay chemical table                                      
✔ |   3       | Check assay chemical table

⠏ |   0       | gtoxLoadWaid                                                    
⠏ |   0       | Check assay well table                                          
✔ |   2       | Check assay well table

⠏ |   0       | is.odd                                                          
✔ |   2       | is.odd

⠏ |   0       | lu                                                              
✔ |   1       | lu

⠏ |   0       | lw                                                              
✔ |   1       | lw

⠏ |   0       | mc2                                                             
✔ |   1       | mc2

⠏ |   0       | mc3                                                             
✔ |   1       | mc3

⠏ |   0       | mc5                                                             
✔ |   1       | mc5

⠏ |   0       | mc6                                                             
✔ |   1       | mc6

⠏ |   0       | sc1                                                             
✔ |   1       | sc1

⠏ |   0       | sc2                                                             
✔ |   1       | sc2

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.4 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> test_check("GladiaTOX")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
  7.385   0.430   7.818