Multiple platform build/check report for BioC 3.22 - CHECK results for GladiaTOX on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4668
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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 merida1

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: 1.26.0

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_1.26.0.tar.gz

StartedAt: 2025-12-05 05:26:39 -0500 (Fri, 05 Dec 2025)

EndedAt: 2025-12-05 05:31:45 -0500 (Fri, 05 Dec 2025)

EllapsedTime: 306.0 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ version ‘1.26.0’
* 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            49.484 24.368  42.027
assignDefaultMthds 48.194 19.421  41.101
* 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-3.22-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-x86_64/Resources/library’
* installing *source* package ‘GladiaTOX’ ...
** this is package ‘GladiaTOX’ version ‘1.26.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 (v1.26.0) loaded with the following settings:
  TCPL_DB:    /Library/Frameworks/R.framework/Versions/4.5-x86_64/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 [1.8s]

⠏ |          0 | exportResultTable                                              
⠋ |          1 | exportResultTable                                              
⠙ |          2 | exportResultTable                                              
✔ |          2 | exportResultTable

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

⠏ |          0 | glComputeToxInd                                                
⠋ |          1 | glComputeToxInd                                                
✔ |          1 | glComputeToxInd

⠏ |          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                                    
✔ |          2 | Check assay component table

⠏ |          0 | gtoxLoadAeid                                                   
⠏ |          0 | Check assay endpoint table                                     
⠋ |          1 | Check assay endpoint table                                     
⠙ |          2 | Check assay endpoint table                                     
✔ |          2 | Check assay endpoint table

⠏ |          0 | gtoxLoadAid                                                    
⠋ |          1 | gtoxLoadAid                                                    
✔ |          1 | gtoxLoadAid

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

⠏ |          0 | gtoxLoadAsid                                                   
⠋ |          1 | gtoxLoadAsid                                                   
✔ |          3 | gtoxLoadAsid

⠏ |          0 | gtoxLoadChem                                                   
⠏ |          0 | Check assay chemical table                                     
⠙ |          2 | Check assay chemical table                                     
✔ |          3 | Check assay chemical table

⠏ |          0 | gtoxLoadWaid                                                   
⠏ |          0 | Check assay well table                                         
⠙ |          2 | 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: 4.8 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 
 13.162   1.072  15.802

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

name	user	system	elapsed
Models	0.269	0.028	0.364
assay_funcs	0.823	0.079	1.035
assignDefaultMthds	48.194	19.421	41.101
buildAssayTab	0.032	0.006	0.039
config_funcs	0.014	0.007	0.020
deleteStudy	0.000	0.001	0.001
exportResultForToxpiGUI	0.652	0.093	0.856
exportResultTable	0.311	0.020	0.386
glComputeToxInd	0.589	0.041	0.727
glPlotPie	4.174	0.185	4.968
glPlotPieLogo	2.087	0.026	2.400
glPlotPosCtrl	2.453	0.051	2.888
glPlotPosCtrlMEC	0.838	0.071	1.059
glPlotStat	2.695	0.040	3.149
glPlotToxInd	1.383	0.043	1.662
gtoxAICProb	0.002	0.002	0.006
gtoxAddModel	1.191	0.039	1.429
gtoxCalcVmad	0.056	0.007	0.071
gtoxCode2CASN	0.001	0.000	0.002
gtoxFit	0.923	0.010	1.084
gtoxImportThermoDB	0.001	0.002	0.004
gtoxListFlds	0.010	0.001	0.011
gtoxLoadApid	0.018	0.007	0.029
gtoxLoadChem	0.132	0.030	0.183
gtoxLoadClib	0.018	0.002	0.027
gtoxLoadData	0.156	0.022	0.196
gtoxLoadVehicle	0.011	0.002	0.016
gtoxLoadVmad	0.014	0.004	0.021
gtoxLoadWaid	0.046	0.008	0.066
gtoxMakeAeidPlts	0.740	0.059	0.902
gtoxPlotErrBar	0.660	0.031	0.803
gtoxPlotFitc	0.569	0.017	0.683
gtoxPlotFits	0.269	0.024	0.337
gtoxPlotM4ID	1.104	0.092	1.363
gtoxPlotPie	0.309	0.024	0.381
gtoxPlotPieLgnd	0.011	0.002	0.015
gtoxPlotPlate	0.387	0.038	0.477
gtoxPlotWin	0.001	0.001	0.002
gtoxPrepOtpt	0.286	0.021	0.350
gtoxReport	0.000	0.001	0.001
gtoxRun	49.484	24.368	42.027
gtoxSetWllq	0.193	0.064	0.277
gtoxSubsetChid	0.197	0.039	0.263
gtoxWriteData	0.001	0.002	0.002
hill_utils	0.001	0.002	0.006
loadAnnot	0.000	0.001	0.001
lu	0.001	0.001	0.001
lw	0.000	0.000	0.001
mthd_funcs	0.029	0.009	0.041
prepareDatForDB	0.000	0.002	0.002
query_funcs	0.034	0.009	0.048
rgstr_funcs	0.549	0.102	0.726