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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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

Package 884/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.24.0  (landing page)
PMP S.A. R Support
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: RELEASE_3_21
git_last_commit: e015dfd
git_last_commit_date: 2025-04-15 11:46:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GladiaTOX on kjohnson3

To the developers/maintainers of the GladiaTOX package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GladiaTOX
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2025-04-21 19:39:26 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 19:40:11 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 45.6 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GladiaTOX’ can be installed ... OK
* checking installed package size ... INFO
  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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gtoxLoadData.Rd: data.table
  gtoxLoadUnit.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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            7.353  6.153   6.901
assignDefaultMthds 6.232  3.552   5.210
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-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/4.5-arm64/Resources/library’
* installing *source* package ‘GladiaTOX’ ...
** this is package ‘GladiaTOX’ version ‘1.24.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 (v1.24.0) loaded with the following settings:
  TCPL_DB:    /Library/Frameworks/R.framework/Versions/4.5-arm64/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 | exportResultTable                                              
✔ |          2 | exportResultTable

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

⠏ |          0 | glComputeToxInd                                                
✔ |          1 | glComputeToxInd

⠏ |          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

⠏ |          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 ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> test_check("GladiaTOX")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
  2.270   0.190   2.064 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.0380.0070.048
assay_funcs0.1080.0130.121
assignDefaultMthds6.2323.5525.210
buildAssayTab0.0070.0020.009
config_funcs0.0020.0010.003
deleteStudy000
exportResultForToxpiGUI0.1010.0230.124
exportResultTable0.0420.0030.046
glComputeToxInd0.0830.0080.091
glPlotPie0.6680.0250.415
glPlotPieLogo0.2230.0020.227
glPlotPosCtrl0.4790.0160.265
glPlotPosCtrlMEC0.1170.0110.115
glPlotStat0.2730.0070.280
glPlotToxInd0.2520.0120.176
gtoxAICProb0.0010.0010.000
gtoxAddModel0.2840.0090.182
gtoxCalcVmad0.0130.0020.014
gtoxCode2CASN0.0010.0000.000
gtoxFit0.1360.0010.137
gtoxImportThermoDB0.0000.0000.001
gtoxListFlds0.0020.0000.002
gtoxLoadApid0.0020.0000.003
gtoxLoadChem0.0170.0030.021
gtoxLoadClib0.0020.0010.002
gtoxLoadData0.0220.0030.025
gtoxLoadVehicle0.0020.0000.002
gtoxLoadVmad0.0020.0000.002
gtoxLoadWaid0.0080.0010.008
gtoxMakeAeidPlts0.1270.0100.137
gtoxPlotErrBar0.1500.0070.107
gtoxPlotFitc0.1680.0060.087
gtoxPlotFits0.0810.0060.043
gtoxPlotM4ID0.1650.0150.165
gtoxPlotPie0.0370.0030.041
gtoxPlotPieLgnd0.0020.0010.003
gtoxPlotPlate0.0600.0050.066
gtoxPlotWin000
gtoxPrepOtpt0.0640.0060.044
gtoxReport000
gtoxRun7.3536.1536.901
gtoxSetWllq0.0240.0120.037
gtoxSubsetChid0.0310.0100.041
gtoxWriteData000
hill_utils0.0010.0000.000
loadAnnot000
lu000
lw000
mthd_funcs0.0040.0010.006
prepareDatForDB000
query_funcs0.0040.0010.006
rgstr_funcs0.0870.0190.106