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This page was generated on 2024-05-04 11:36:37 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 876/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.20.0  (landing page)
PMP S.A. R Support
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: RELEASE_3_19
git_last_commit: 00e131d
git_last_commit_date: 2024-04-30 11:14:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for GladiaTOX on nebbiolo1


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: 1.20.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GladiaTOX_1.20.0.tar.gz
StartedAt: 2024-05-03 23:44:17 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:49:22 -0400 (Fri, 03 May 2024)
EllapsedTime: 304.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GladiaTOX_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ version ‘1.20.0’
* 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 ... OK
* 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 loading without being on the library search path ... 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 ... 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            18.750 11.535  15.082
assignDefaultMthds 15.971  6.868  11.732
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.


Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 (v1.20.0) loaded with the following settings:
  TCPL_DB:    /home/biocbuild/bbs-3.19-bioc/R/site-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

⠏ |          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: 1.5 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 
  5.071   0.261   5.311 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.0950.0440.143
assay_funcs0.350.040.39
assignDefaultMthds15.971 6.86811.732
buildAssayTab0.0340.0040.038
config_funcs0.0050.0020.008
deleteStudy000
exportResultForToxpiGUI0.2820.0160.299
exportResultTable0.1330.0000.133
glComputeToxInd0.2350.0280.262
glPlotPie1.2660.0381.293
glPlotPieLogo0.6850.0050.691
glPlotPosCtrl0.8270.0410.842
glPlotPosCtrlMEC0.3370.0200.358
glPlotStat0.7020.0230.726
glPlotToxInd0.4680.0160.478
gtoxAICProb0.0010.0000.001
gtoxAddModel0.4350.0000.434
gtoxCalcVmad0.0280.0000.028
gtoxCode2CASN0.0010.0000.001
gtoxFit0.3130.0030.316
gtoxImportThermoDB0.0010.0000.001
gtoxListFlds0.0050.0010.005
gtoxLoadApid0.0060.0030.010
gtoxLoadChem0.0510.0120.063
gtoxLoadClib0.0050.0010.006
gtoxLoadData0.0640.0070.072
gtoxLoadVehicle0.0060.0000.006
gtoxLoadVmad0.0080.0000.008
gtoxLoadWaid0.0180.0030.021
gtoxMakeAeidPlts0.3290.0000.328
gtoxPlotErrBar0.3010.0250.320
gtoxPlotFitc0.2300.0080.239
gtoxPlotFits0.1190.0080.127
gtoxPlotM4ID0.4800.0240.505
gtoxPlotPie0.1300.0120.141
gtoxPlotPieLgnd0.0060.0000.006
gtoxPlotPlate0.1830.0120.195
gtoxPlotWin000
gtoxPrepOtpt0.1350.0190.123
gtoxReport000
gtoxRun18.75011.53515.082
gtoxSetWllq0.0870.0160.104
gtoxSubsetChid0.1130.0240.137
gtoxWriteData0.0000.0000.001
hill_utils0.0000.0010.001
loadAnnot000
lu000
lw0.0000.0000.001
mthd_funcs0.0170.0010.018
prepareDatForDB0.0000.0000.001
query_funcs0.0180.0000.018
rgstr_funcs0.2770.0560.333