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This page was generated on 2022-04-13 12:08:05 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GladiaTOX on machv2


To the developers/maintainers of the GladiaTOX package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GladiaTOX.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 786/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.10.3  (landing page)
PMP S.A. R Support
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: RELEASE_3_14
git_last_commit: f196e41
git_last_commit_date: 2022-04-07 07:56:03 -0400 (Thu, 07 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GladiaTOX
Version: 1.10.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GladiaTOX_1.10.3.tar.gz
StartedAt: 2022-04-12 13:52:31 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:55:28 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 176.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GladiaTOX_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.3’
* 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 ... NOTE
glCheckInput: no visible global function definition for ‘read.csv’
glLoadInput: no visible global function definition for ‘read.csv’
glPlotPosCtrlMEC: no visible binding for global variable ‘aenm_wrap’
glPlotPosCtrlMEC: no visible binding for global variable ‘modl_acc’
Undefined global functions or variables:
  aenm_wrap modl_acc read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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            38.492 16.771  28.524
assignDefaultMthds 34.942 11.638  24.570
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.



Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

GladiaTOX.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 (v1.10.3) loaded with the following settings:
  TCPL_DB:    /Library/Frameworks/R.framework/Versions/4.1/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")
✔ | F W S  OK | Context

⠏ |         0 | assignDefaultMthds                                              
⠋ |         1 | assignDefaultMthds                                              
✔ |         1 | assignDefaultMthds [0.9s]

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

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

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

⠏ |         0 | gtoxAICProb                                                     
✔ |         1 | gtoxAICProb

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

⠏ |         0 | gtoxLoadAcid                                                    
⠏ |         0 | Check assay component table                                     
⠋ |         1 | Check assay component table                                     
✔ |         2 | Check assay component table [0.2s]

⠏ |         0 | gtoxLoadAeid                                                    
⠏ |         0 | Check assay endpoint table                                      
⠙ |         2 | Check assay endpoint table                                      
✔ |         2 | Check assay endpoint table [0.2s]

⠏ |         0 | gtoxLoadAid                                                     
✔ |         1 | gtoxLoadAid

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

⠏ |         0 | gtoxLoadAsid                                                    
⠹ |         3 | gtoxLoadAsid                                                    
✔ |         3 | gtoxLoadAsid [0.1s]

⠏ |         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: 2.8 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 
  9.027   0.539   9.555 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.1870.0300.258
assay_funcs0.6110.0520.666
assignDefaultMthds34.94211.63824.570
buildAssayTab0.0630.0060.068
config_funcs0.0080.0030.012
deleteStudy0.0000.0000.001
exportResultForToxpiGUI0.5730.0650.668
exportResultTable0.1880.0110.200
glComputeToxInd0.4530.0260.480
glPlotPie2.8250.0682.895
glPlotPieLogo1.1790.0071.188
glPlotPosCtrl1.1150.0261.143
glPlotPosCtrlMEC0.7320.0460.778
glPlotStat1.1310.0151.147
glPlotToxInd0.7070.0220.730
gtoxAICProb0.0010.0010.001
gtoxAddModel0.9300.0170.948
gtoxCalcVmad0.0460.0040.049
gtoxCode2CASN0.0010.0010.002
gtoxFit0.6780.0030.683
gtoxImportThermoDB0.0010.0010.002
gtoxListFlds0.0080.0010.009
gtoxLoadApid0.0120.0040.016
gtoxLoadChem0.0800.0180.098
gtoxLoadClib0.0080.0010.010
gtoxLoadData0.1070.0120.118
gtoxLoadVehicle0.0080.0020.010
gtoxLoadVmad0.0110.0020.013
gtoxLoadWaid0.0370.0050.041
gtoxMakeAeidPlts0.6190.0300.650
gtoxPlotErrBar0.3980.0120.411
gtoxPlotFitc0.4280.0040.433
gtoxPlotFits0.2060.0120.218
gtoxPlotM4ID0.8640.0460.911
gtoxPlotPie0.2000.0110.211
gtoxPlotPieLgnd0.0070.0010.007
gtoxPlotPlate0.3270.0200.348
gtoxPlotWin000
gtoxPrepOtpt0.1990.0120.211
gtoxReport0.0000.0000.001
gtoxRun38.49216.77128.524
gtoxSetWllq0.1650.0470.214
gtoxSubsetChid0.1700.0180.189
gtoxWriteData0.0000.0010.001
hill_utils0.0010.0010.002
loadAnnot0.0000.0010.001
lu000
lw0.0000.0010.000
mthd_funcs0.0170.0040.020
prepareDatForDB0.0000.0010.001
query_funcs0.0240.0040.028
rgstr_funcs0.3210.0290.352