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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4822
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4617
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4564
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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 lconway

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: 1.25.1

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_1.25.1.tar.gz

StartedAt: 2025-09-03 21:10:48 -0400 (Wed, 03 Sep 2025)

EndedAt: 2025-09-03 21:13:12 -0400 (Wed, 03 Sep 2025)

EllapsedTime: 144.0 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_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.25.1’
* 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 ... 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            26.309 17.832  22.663
assignDefaultMthds 25.006 13.391  20.362
* 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 ‘1.25.1’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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 (v1.25.1) 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

⠏ |          0 | 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                                    
⠙ |          2 | 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 | 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: 2.1 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 
  6.404   0.600   7.114

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

name	user	system	elapsed
Models	0.148	0.027	0.188
assay_funcs	0.495	0.051	0.550
assignDefaultMthds	25.006	13.391	20.362
buildAssayTab	0.014	0.003	0.018
config_funcs	0.007	0.004	0.012
deleteStudy	0	0	0
exportResultForToxpiGUI	0.341	0.046	0.389
exportResultTable	0.155	0.013	0.170
glComputeToxInd	0.311	0.024	0.336
glPlotPie	1.553	0.055	1.617
glPlotPieLogo	0.924	0.011	0.942
glPlotPosCtrl	1.210	0.032	1.251
glPlotPosCtrlMEC	0.524	0.044	0.573
glPlotStat	0.914	0.023	0.944
glPlotToxInd	0.633	0.026	0.666
gtoxAICProb	0.000	0.000	0.001
gtoxAddModel	0.455	0.011	0.471
gtoxCalcVmad	0.042	0.003	0.047
gtoxCode2CASN	0.001	0.000	0.001
gtoxFit	0.361	0.003	0.366
gtoxImportThermoDB	0.002	0.000	0.003
gtoxListFlds	0.007	0.001	0.008
gtoxLoadApid	0.013	0.003	0.016
gtoxLoadChem	0.060	0.010	0.071
gtoxLoadClib	0.007	0.001	0.009
gtoxLoadData	0.091	0.010	0.102
gtoxLoadVehicle	0.007	0.001	0.008
gtoxLoadVmad	0.008	0.002	0.010
gtoxLoadWaid	0.025	0.003	0.028
gtoxMakeAeidPlts	0.482	0.033	0.527
gtoxPlotErrBar	0.379	0.016	0.398
gtoxPlotFitc	0.281	0.004	0.286
gtoxPlotFits	0.172	0.014	0.186
gtoxPlotM4ID	0.663	0.055	0.722
gtoxPlotPie	0.191	0.013	0.206
gtoxPlotPieLgnd	0.007	0.001	0.008
gtoxPlotPlate	0.257	0.023	0.285
gtoxPlotWin	0.000	0.000	0.001
gtoxPrepOtpt	0.151	0.014	0.170
gtoxReport	0.000	0.000	0.001
gtoxRun	26.309	17.832	22.663
gtoxSetWllq	0.111	0.031	0.147
gtoxSubsetChid	0.133	0.020	0.155
gtoxWriteData	0.000	0.001	0.001
hill_utils	0.001	0.001	0.002
loadAnnot	0.000	0.001	0.001
lu	0.000	0.000	0.001
lw	0.000	0.001	0.000
mthd_funcs	0.018	0.004	0.022
prepareDatForDB	0.000	0.001	0.001
query_funcs	0.020	0.003	0.023
rgstr_funcs	0.288	0.030	0.323