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This page was generated on 2023-04-12 11:05:35 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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 823/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.14.0  (landing page)
PMP S.A. R Support
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: RELEASE_3_16
git_last_commit: b80ea3c
git_last_commit_date: 2022-11-01 11:19:57 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GladiaTOX
Version: 1.14.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GladiaTOX.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GladiaTOX_1.14.0.tar.gz
StartedAt: 2023-04-11 02:00:53 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 02:03:04 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 130.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GladiaTOX.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GladiaTOX_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/GladiaTOX.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.14.0'
* 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 whether package 'GladiaTOX' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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            18.66   0.67   19.58
assignDefaultMthds 17.81   0.89   18.95
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/GladiaTOX.Rcheck/00check.log'
for details.



Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 (v1.14.0) loaded with the following settings:
  TCPL_DB:    F:/biocbuild/bbs-3.16-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")
✔ | F W S  OK | Context

⠏ |         0 | assignDefaultMthds                                              
⠋ |         1 | assignDefaultMthds                                              
✔ |         1 | assignDefaultMthds [0.6s]

⠏ |         0 | exportResultTable                                               
⠙ |         2 | exportResultTable                                               
✔ |         2 | exportResultTable [0.2s]

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

⠏ |         0 | glComputeToxInd                                                 
⠋ |         1 | glComputeToxInd                                                 
✔ |         1 | glComputeToxInd [0.4s]

⠏ |         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 [0.1s]

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

⠏ |         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: 1.8 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 
   5.35    0.65    6.14 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.140.000.14
assay_funcs0.470.010.49
assignDefaultMthds17.81 0.8918.95
buildAssayTab0.020.000.02
config_funcs0.010.000.01
deleteStudy000
exportResultForToxpiGUI0.280.050.33
exportResultTable0.140.000.14
glComputeToxInd0.30.00.3
glPlotPie1.910.061.97
glPlotPieLogo0.830.020.89
glPlotPosCtrl0.780.010.80
glPlotPosCtrlMEC0.340.070.40
glPlotStat0.770.030.80
glPlotToxInd0.570.040.62
gtoxAICProb000
gtoxAddModel0.430.020.44
gtoxCalcVmad0.010.020.03
gtoxCode2CASN000
gtoxFit0.310.000.31
gtoxImportThermoDB000
gtoxListFlds000
gtoxLoadApid0.020.000.02
gtoxLoadChem0.050.000.05
gtoxLoadClib000
gtoxLoadData0.040.010.07
gtoxLoadVehicle0.020.000.01
gtoxLoadVmad000
gtoxLoadWaid0.020.000.02
gtoxMakeAeidPlts0.450.030.48
gtoxPlotErrBar0.370.030.41
gtoxPlotFitc0.280.000.28
gtoxPlotFits0.150.020.15
gtoxPlotM4ID0.620.010.65
gtoxPlotPie0.170.020.18
gtoxPlotPieLgnd0.020.000.02
gtoxPlotPlate0.190.020.20
gtoxPlotWin000
gtoxPrepOtpt0.120.000.14
gtoxReport000
gtoxRun18.66 0.6719.58
gtoxSetWllq0.090.020.11
gtoxSubsetChid0.110.000.10
gtoxWriteData000
hill_utils000
loadAnnot000
lu000
lw000
mthd_funcs0.020.000.02
prepareDatForDB000
query_funcs0.000.010.02
rgstr_funcs0.230.050.28