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This page was generated on 2024-06-25 11:37 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 852/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.21.0  (landing page)
PMP S.A. R Support
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: devel
git_last_commit: 57ecf15
git_last_commit_date: 2024-04-30 11:14:59 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GladiaTOX on nebbiolo2

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: 1.21.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GladiaTOX_1.21.0.tar.gz
StartedAt: 2024-06-24 23:26:50 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 23:31:45 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 295.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GladiaTOX_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘1.21.0’
* 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 ... NOTE
  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 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            17.607  9.523  13.428
assignDefaultMthds 16.117  7.030  11.913
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.


Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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 RC (2024-04-16 r86468) -- "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 (v1.21.0) loaded with the following settings:
  TCPL_DB:    /home/biocbuild/bbs-3.20-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 
  5.133   0.296   5.408 

Example timings

GladiaTOX.Rcheck/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.1180.0120.141
assay_funcs0.3310.0480.380
assignDefaultMthds16.117 7.03011.913
buildAssayTab0.0330.0040.038
config_funcs0.0030.0030.007
deleteStudy000
exportResultForToxpiGUI0.2380.0430.281
exportResultTable0.1290.0050.133
glComputeToxInd0.2330.0390.271
glPlotPie1.2610.0161.264
glPlotPieLogo0.7240.0280.752
glPlotPosCtrl0.8590.0050.813
glPlotPosCtrlMEC0.3580.0000.358
glPlotStat0.7270.0150.742
glPlotToxInd0.4870.0120.484
gtoxAICProb0.0010.0000.000
gtoxAddModel0.4430.0080.451
gtoxCalcVmad0.0210.0040.026
gtoxCode2CASN0.0000.0000.001
gtoxFit0.3230.0000.323
gtoxImportThermoDB0.0000.0000.001
gtoxListFlds0.0050.0000.005
gtoxLoadApid0.0010.0080.008
gtoxLoadChem0.0610.0040.065
gtoxLoadClib0.0050.0000.006
gtoxLoadData0.070.000.07
gtoxLoadVehicle0.0070.0000.006
gtoxLoadVmad0.0080.0000.007
gtoxLoadWaid0.0210.0000.021
gtoxMakeAeidPlts0.3490.0120.361
gtoxPlotErrBar0.3020.0240.312
gtoxPlotFitc0.2290.0000.230
gtoxPlotFits0.1090.0040.114
gtoxPlotM4ID0.4740.0200.494
gtoxPlotPie0.1350.0080.143
gtoxPlotPieLgnd0.0060.0000.006
gtoxPlotPlate0.1860.0040.190
gtoxPlotWin000
gtoxPrepOtpt0.1740.0000.134
gtoxReport000
gtoxRun17.607 9.52313.428
gtoxSetWllq0.0800.0040.084
gtoxSubsetChid0.0870.0120.099
gtoxWriteData0.0010.0000.000
hill_utils0.0000.0000.001
loadAnnot000
lu000
lw000
mthd_funcs0.0130.0000.013
prepareDatForDB000
query_funcs0.0140.0000.014
rgstr_funcs0.2360.0240.260