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CHECK report for GladiaTOX on malbec1

This page was generated on 2021-05-06 12:27:46 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GladiaTOX package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 746/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.6.1  (landing page)
PMP S.A. R Support
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GladiaTOX
Branch: RELEASE_3_12
Last Commit: 364144b
Last Changed Date: 2020-11-13 04:08:48 -0400 (Fri, 13 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GladiaTOX
Version: 1.6.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GladiaTOX_1.6.1.tar.gz
StartedAt: 2021-05-06 02:04:40 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:06:43 -0400 (Thu, 06 May 2021)
EllapsedTime: 122.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GladiaTOX_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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            27.728  7.952  18.411
assignDefaultMthds 25.740  5.772  16.828
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.



Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)

Tests output

GladiaTOX.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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:    /home/biocbuild/bbs-3.12-bioc/R/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 [0.5 s]

⠏ |   0       | exportResultTable                                               
⠋ |   1       | exportResultTable                                               
⠙ |   2       | exportResultTable                                               
✔ |   2       | exportResultTable [0.3 s]

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

⠏ |   0       | glComputeToxInd                                                 
⠋ |   1       | glComputeToxInd                                                 
✔ |   1       | glComputeToxInd [0.3 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

⠏ |   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 [0.1 s]

⠏ |   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: 1.9 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 
  6.156   0.200   6.373 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.1960.0120.560
assay_funcs0.5720.0240.595
assignDefaultMthds25.740 5.77216.828
buildAssayTab0.0560.0000.069
config_funcs0.0080.0000.009
deleteStudy000
exportResultForToxpiGUI0.4480.0280.476
exportResultTable0.1400.0040.141
glComputeToxInd0.3000.0120.314
glPlotPie2.0480.0242.073
glPlotPieLogo1.1640.0001.234
glPlotPosCtrl1.0000.0080.995
glPlotStat0.6600.0000.659
glPlotToxInd0.4960.0040.497
gtoxAICProb0.0000.0000.001
gtoxAddModel0.5320.0080.537
gtoxCalcVmad0.0240.0000.027
gtoxCode2CASN0.0000.0000.001
gtoxFit0.3600.0000.362
gtoxImportThermoDB0.0000.0000.001
gtoxListFlds0.0040.0000.004
gtoxLoadApid0.0080.0000.007
gtoxLoadChem0.0320.0080.039
gtoxLoadClib0.0040.0000.005
gtoxLoadData0.0680.0000.066
gtoxLoadVehicle0.0040.0000.005
gtoxLoadVmad0.0080.0000.006
gtoxLoadWaid0.0160.0000.018
gtoxMakeAeidPlts0.4320.0120.442
gtoxPlotErrBar0.3240.0040.326
gtoxPlotFitc0.3440.0080.354
gtoxPlotFits0.1240.0000.121
gtoxPlotM4ID0.5000.0000.501
gtoxPlotPie0.1480.0040.154
gtoxPlotPieLgnd0.0040.0000.006
gtoxPlotPlate0.1920.0080.202
gtoxPlotWin0.0000.0000.001
gtoxPrepOtpt0.1640.0040.148
gtoxReport000
gtoxRun27.728 7.95218.411
gtoxSetWllq0.1160.0160.132
gtoxSubsetChid0.1440.0200.164
gtoxWriteData000
hill_utils0.0040.0000.001
loadAnnot000
lu000
lw000
mthd_funcs0.0160.0000.013
prepareDatForDB0.0000.0000.001
query_funcs0.0080.0040.014
rgstr_funcs0.3120.0040.319