PMP S.A. R Support
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GladiaTOX |
| git_branch: devel |
| git_last_commit: ab512db |
| git_last_commit_date: 2025-10-29 10:52:17 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 880/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GladiaTOX 1.27.0 (landing page) PMP S.A. R Support
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
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. |
| Package: GladiaTOX |
| Version: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2025-11-12 19:00:23 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 19:01:16 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 53.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GladiaTOX.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ version ‘1.27.0’
* 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 6.909 4.690 6.524
assignDefaultMthds 7.149 4.254 6.427
* 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-3.23-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GladiaTOX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘GladiaTOX’ ... ** this is package ‘GladiaTOX’ version ‘1.27.0’ ** 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)
GladiaTOX.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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 (v1.27.0) loaded with the following settings:
TCPL_DB: /Library/Frameworks/R.framework/Versions/4.6-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
2.150 0.209 2.488
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.044 | 0.005 | 0.051 | |
| assay_funcs | 0.121 | 0.017 | 0.162 | |
| assignDefaultMthds | 7.149 | 4.254 | 6.427 | |
| buildAssayTab | 0.007 | 0.002 | 0.010 | |
| config_funcs | 0.002 | 0.002 | 0.003 | |
| deleteStudy | 0 | 0 | 0 | |
| exportResultForToxpiGUI | 0.092 | 0.019 | 0.130 | |
| exportResultTable | 0.045 | 0.004 | 0.050 | |
| glComputeToxInd | 0.089 | 0.008 | 0.105 | |
| glPlotPie | 0.699 | 0.031 | 0.774 | |
| glPlotPieLogo | 0.273 | 0.006 | 0.307 | |
| glPlotPosCtrl | 0.331 | 0.011 | 0.425 | |
| glPlotPosCtrlMEC | 0.136 | 0.013 | 0.154 | |
| glPlotStat | 0.357 | 0.006 | 0.374 | |
| glPlotToxInd | 0.191 | 0.008 | 0.210 | |
| gtoxAICProb | 0.000 | 0.000 | 0.001 | |
| gtoxAddModel | 0.151 | 0.005 | 0.161 | |
| gtoxCalcVmad | 0.008 | 0.001 | 0.009 | |
| gtoxCode2CASN | 0.001 | 0.000 | 0.000 | |
| gtoxFit | 0.114 | 0.001 | 0.120 | |
| gtoxImportThermoDB | 0.001 | 0.000 | 0.001 | |
| gtoxListFlds | 0.002 | 0.001 | 0.003 | |
| gtoxLoadApid | 0.003 | 0.001 | 0.004 | |
| gtoxLoadChem | 0.018 | 0.004 | 0.024 | |
| gtoxLoadClib | 0.001 | 0.000 | 0.001 | |
| gtoxLoadData | 0.025 | 0.004 | 0.031 | |
| gtoxLoadVehicle | 0.006 | 0.001 | 0.006 | |
| gtoxLoadVmad | 0.003 | 0.001 | 0.004 | |
| gtoxLoadWaid | 0.009 | 0.001 | 0.010 | |
| gtoxMakeAeidPlts | 0.110 | 0.012 | 0.127 | |
| gtoxPlotErrBar | 0.098 | 0.008 | 0.110 | |
| gtoxPlotFitc | 0.217 | 0.003 | 0.241 | |
| gtoxPlotFits | 0.044 | 0.005 | 0.057 | |
| gtoxPlotM4ID | 0.160 | 0.019 | 0.188 | |
| gtoxPlotPie | 0.040 | 0.004 | 0.048 | |
| gtoxPlotPieLgnd | 0.003 | 0.000 | 0.009 | |
| gtoxPlotPlate | 0.059 | 0.007 | 0.069 | |
| gtoxPlotWin | 0 | 0 | 0 | |
| gtoxPrepOtpt | 0.046 | 0.007 | 0.163 | |
| gtoxReport | 0 | 0 | 0 | |
| gtoxRun | 6.909 | 4.690 | 6.524 | |
| gtoxSetWllq | 0.029 | 0.012 | 0.045 | |
| gtoxSubsetChid | 0.035 | 0.017 | 0.052 | |
| gtoxWriteData | 0.000 | 0.001 | 0.000 | |
| hill_utils | 0.000 | 0.000 | 0.001 | |
| loadAnnot | 0 | 0 | 0 | |
| lu | 0 | 0 | 0 | |
| lw | 0 | 0 | 0 | |
| mthd_funcs | 0.005 | 0.001 | 0.006 | |
| prepareDatForDB | 0 | 0 | 0 | |
| query_funcs | 0.005 | 0.002 | 0.006 | |
| rgstr_funcs | 0.074 | 0.020 | 0.094 | |