Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).

CHECK results for GladiaTOX on tokay2

To the developers/maintainers of the GladiaTOX package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 773/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GladiaTOX 1.8.0  (landing page)
PMP S.A. R Support
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GladiaTOX
git_branch: RELEASE_3_13
git_last_commit: 53cee0f
git_last_commit_date: 2021-05-19 12:43:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GladiaTOX
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GladiaTOX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GladiaTOX_1.8.0.tar.gz
StartedAt: 2021-10-14 23:51:33 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:54:54 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 201.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GladiaTOX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GladiaTOX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GladiaTOX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GladiaTOX.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GladiaTOX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GladiaTOX' version '1.8.0'
* 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 whether package 'GladiaTOX' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
assignDefaultMthds 17.35   0.89   20.57
gtoxRun            17.63   0.44   18.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
gtoxRun            17.20   0.46   17.66
assignDefaultMthds 16.69   0.56   17.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/GladiaTOX.Rcheck/00check.log'
for details.



Installation output

GladiaTOX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GladiaTOX_1.8.0.tar.gz && rm -rf GladiaTOX.buildbin-libdir && mkdir GladiaTOX.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GladiaTOX.buildbin-libdir GladiaTOX_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GladiaTOX_1.8.0.zip && rm GladiaTOX_1.8.0.tar.gz GladiaTOX_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 43 2074k   43  892k    0     0  1785k      0  0:00:01 --:--:--  0:00:01 1784k
100 2074k  100 2074k    0     0  2606k      0 --:--:-- --:--:-- --:--:-- 2606k

install for i386

* installing *source* package 'GladiaTOX' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GladiaTOX'
    finding HTML links ... done
    MC2_Methods                             html  
    MC3_Methods                             html  
    MC5_Methods                             html  
    MC6_Methods                             html  
    Models                                  html  
    SC1_Methods                             html  
    SC2_Methods                             html  
    assay_funcs                             html  
    assignDefaultMthds                      html  
    blineShift                              html  
    buildAssayTab                           html  
    config_funcs                            html  
    deleteStudy                             html  
    exportResultForToxpiGUI                 html  
    exportResultTable                       html  
    flareFunc                               html  
    glComputeToxInd                         html  
    glPlotPie                               html  
    glPlotPieLogo                           html  
    glPlotPosCtrl                           html  
    glPlotStat                              html  
    glPlotToxInd                            html  
    gtoxAICProb                             html  
    gtoxAddModel                            html  
    gtoxAppend                              html  
    gtoxCalcVmad                            html  
    gtoxCascade                             html  
    gtoxCode2CASN                           html  
    gtoxDelete                              html  
    gtoxFit                                 html  
    gtoxImportThermoDB                      html  
    gtoxListFlds                            html  
    gtoxLoadApid                            html  
    gtoxLoadChem                            html  
    gtoxLoadClib                            html  
    gtoxLoadData                            html  
    finding level-2 HTML links ... done

    gtoxLoadUnit                            html  
    gtoxLoadVehicle                         html  
    gtoxLoadVmad                            html  
    gtoxLoadWaid                            html  
    gtoxMakeAeidPlts                        html  
    gtoxPlotErrBar                          html  
    gtoxPlotFitc                            html  
    gtoxPlotFits                            html  
    gtoxPlotM4ID                            html  
    gtoxPlotPie                             html  
    gtoxPlotPieLgnd                         html  
    gtoxPlotPlate                           html  
    gtoxPlotWin                             html  
    gtoxPrepOtpt                            html  
    gtoxReport                              html  
    gtoxRun                                 html  
    gtoxSetWllq                             html  
    gtoxSubsetChid                          html  
    gtoxWriteData                           html  
    hill_utils                              html  
    interlaceFunc                           html  
    is.odd                                  html  
    loadAnnot                               html  
    lu                                      html  
    lw                                      html  
    mc1                                     html  
    mc2                                     html  
    mc3                                     html  
    mc4                                     html  
    mc5                                     html  
    mc6                                     html  
    mthd_funcs                              html  
    prepareDatForDB                         html  
    query_funcs                             html  
    registerMthd                            html  
    rgstr_funcs                             html  
    sc1                                     html  
    sc2                                     html  
    sink_reset                              html  
** 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

install for x64

* installing *source* package 'GladiaTOX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GladiaTOX' as GladiaTOX_1.8.0.zip
* DONE (GladiaTOX)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GladiaTOX' successfully unpacked and MD5 sums checked

Tests output

GladiaTOX.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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 (v1.8.0) loaded with the following settings:
  TCPL_DB:    C:/Users/biocbuild/bbs-3.13-bioc/R/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")
v | F W S  OK | Context

/ |         0 | assignDefaultMthds                                              
- |         1 | assignDefaultMthds                                              
v |         1 | assignDefaultMthds [0.5s]

/ |         0 | exportResultTable                                               
\ |         2 | exportResultTable                                               
v |         2 | exportResultTable [0.2s]

/ |         0 | getsplit                                                        
/ |         0 | getsplit                                                        
v |         1 | getsplit

/ |         0 | glComputeToxInd                                                 
- |         1 | glComputeToxInd                                                 
v |         1 | glComputeToxInd [0.3s]

/ |         0 | gtoxAICProb                                                     
v |         1 | gtoxAICProb

/ |         0 | gtoxCalcVmad                                                    
/ |         0 | Calculate Vmad                                                  
v |         1 | Calculate Vmad

/ |         0 | gtoxLoadAcid                                                    
/ |         0 | Check assay component table                                     
\ |         2 | Check assay component table                                     
v |         2 | Check assay component table [0.1s]

/ |         0 | gtoxLoadAeid                                                    
/ |         0 | Check assay endpoint table                                      
\ |         2 | Check assay endpoint table                                      
v |         2 | Check assay endpoint table [0.1s]

/ |         0 | gtoxLoadAid                                                     
v |         1 | gtoxLoadAid

/ |         0 | gtoxLoadApid                                                    
/ |         0 | Check assay plate table                                         
v |         2 | Check assay plate table

/ |         0 | gtoxLoadAsid                                                    
v |         3 | gtoxLoadAsid

/ |         0 | gtoxLoadChem                                                    
/ |         0 | Check assay chemical table                                      
v |         3 | Check assay chemical table

/ |         0 | gtoxLoadWaid                                                    
/ |         0 | Check assay well table                                          
v |         2 | Check assay well table

/ |         0 | is.odd                                                          
v |         2 | is.odd

/ |         0 | lu                                                              
v |         1 | lu

/ |         0 | lw                                                              
v |         1 | lw

/ |         0 | mc2                                                             
v |         1 | mc2

/ |         0 | mc3                                                             
v |         1 | mc3

/ |         0 | mc5                                                             
v |         1 | mc5

/ |         0 | mc6                                                             
v |         1 | mc6

/ |         0 | sc1                                                             
v |         1 | sc1

/ |         0 | sc2                                                             
v |         1 | sc2

== Results =====================================================================
Duration: 1.7 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 
   5.48    0.42    5.89 

GladiaTOX.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 (v1.8.0) loaded with the following settings:
  TCPL_DB:    C:/Users/biocbuild/bbs-3.13-bioc/R/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")
v | F W S  OK | Context

/ |         0 | assignDefaultMthds                                              
- |         1 | assignDefaultMthds                                              
v |         1 | assignDefaultMthds [0.6s]

/ |         0 | exportResultTable                                               
\ |         2 | exportResultTable                                               
v |         2 | exportResultTable [0.2s]

/ |         0 | getsplit                                                        
/ |         0 | getsplit                                                        
v |         1 | getsplit

/ |         0 | glComputeToxInd                                                 
- |         1 | glComputeToxInd                                                 
v |         1 | glComputeToxInd [0.3s]

/ |         0 | gtoxAICProb                                                     
v |         1 | gtoxAICProb

/ |         0 | gtoxCalcVmad                                                    
/ |         0 | Calculate Vmad                                                  
v |         1 | Calculate Vmad

/ |         0 | gtoxLoadAcid                                                    
/ |         0 | Check assay component table                                     
v |         2 | Check assay component table

/ |         0 | gtoxLoadAeid                                                    
/ |         0 | Check assay endpoint table                                      
\ |         2 | Check assay endpoint table                                      
v |         2 | Check assay endpoint table [0.1s]

/ |         0 | gtoxLoadAid                                                     
v |         1 | gtoxLoadAid

/ |         0 | gtoxLoadApid                                                    
/ |         0 | Check assay plate table                                         
v |         2 | Check assay plate table

/ |         0 | gtoxLoadAsid                                                    
v |         3 | gtoxLoadAsid

/ |         0 | gtoxLoadChem                                                    
/ |         0 | Check assay chemical table                                      
v |         3 | Check assay chemical table

/ |         0 | gtoxLoadWaid                                                    
/ |         0 | Check assay well table                                          
v |         2 | Check assay well table

/ |         0 | is.odd                                                          
v |         2 | is.odd

/ |         0 | lu                                                              
v |         1 | lu

/ |         0 | lw                                                              
v |         1 | lw

/ |         0 | mc2                                                             
v |         1 | mc2

/ |         0 | mc3                                                             
v |         1 | mc3

/ |         0 | mc5                                                             
v |         1 | mc5

/ |         0 | mc6                                                             
v |         1 | mc6

/ |         0 | sc1                                                             
v |         1 | sc1

/ |         0 | sc2                                                             
v |         1 | sc2

== Results =====================================================================
Duration: 1.6 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 
   5.50    0.45    5.95 

Example timings

GladiaTOX.Rcheck/examples_i386/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.220.030.75
assay_funcs0.450.080.60
assignDefaultMthds17.35 0.8920.57
buildAssayTab0.080.000.12
config_funcs0.010.000.02
deleteStudy000
exportResultForToxpiGUI0.450.060.56
exportResultTable0.180.020.19
glComputeToxInd0.340.000.34
glPlotPie1.750.011.77
glPlotPieLogo0.640.000.64
glPlotPosCtrl0.580.020.59
glPlotStat0.830.000.82
glPlotToxInd0.50.00.5
gtoxAICProb0.010.000.02
gtoxAddModel0.720.000.72
gtoxCalcVmad0.030.000.03
gtoxCode2CASN000
gtoxFit0.410.000.41
gtoxImportThermoDB000
gtoxListFlds000
gtoxLoadApid0.010.000.01
gtoxLoadChem0.040.000.03
gtoxLoadClib0.010.000.02
gtoxLoadData0.080.000.08
gtoxLoadVehicle000
gtoxLoadVmad000
gtoxLoadWaid0.030.000.03
gtoxMakeAeidPlts0.490.040.51
gtoxPlotErrBar0.250.000.25
gtoxPlotFitc0.420.010.47
gtoxPlotFits0.150.020.17
gtoxPlotM4ID0.580.000.58
gtoxPlotPie0.140.000.14
gtoxPlotPieLgnd000
gtoxPlotPlate0.210.010.22
gtoxPlotWin000
gtoxPrepOtpt0.100.000.11
gtoxReport000
gtoxRun17.63 0.4418.05
gtoxSetWllq0.080.000.08
gtoxSubsetChid0.110.000.11
gtoxWriteData000
hill_utils000
loadAnnot000
lu000
lw000
mthd_funcs0.010.000.01
prepareDatForDB000
query_funcs0.030.000.03
rgstr_funcs0.330.030.36

GladiaTOX.Rcheck/examples_x64/GladiaTOX-Ex.timings

nameusersystemelapsed
Models0.160.050.21
assay_funcs0.440.050.48
assignDefaultMthds16.69 0.5617.23
buildAssayTab0.010.000.02
config_funcs000
deleteStudy000
exportResultForToxpiGUI0.230.030.27
exportResultTable0.140.000.14
glComputeToxInd0.220.020.23
glPlotPie1.640.031.67
glPlotPieLogo0.690.000.69
glPlotPosCtrl0.610.030.64
glPlotStat0.610.010.63
glPlotToxInd0.410.020.42
gtoxAICProb000
gtoxAddModel0.470.000.47
gtoxCalcVmad0.020.000.02
gtoxCode2CASN000
gtoxFit0.340.000.34
gtoxImportThermoDB000
gtoxListFlds0.020.000.02
gtoxLoadApid000
gtoxLoadChem0.030.000.03
gtoxLoadClib0.010.000.02
gtoxLoadData0.050.000.04
gtoxLoadVehicle0.020.000.02
gtoxLoadVmad000
gtoxLoadWaid0.010.000.01
gtoxMakeAeidPlts0.470.020.49
gtoxPlotErrBar0.280.010.30
gtoxPlotFitc0.270.000.26
gtoxPlotFits0.120.000.13
gtoxPlotM4ID0.450.020.46
gtoxPlotPie0.150.000.15
gtoxPlotPieLgnd000
gtoxPlotPlate0.170.000.17
gtoxPlotWin000
gtoxPrepOtpt0.100.010.11
gtoxReport000
gtoxRun17.20 0.4617.66
gtoxSetWllq0.050.010.06
gtoxSubsetChid0.110.020.13
gtoxWriteData000
hill_utils000
loadAnnot000
lu000
lw000
mthd_funcs0.010.000.01
prepareDatForDB000
query_funcs0.020.000.02
rgstr_funcs0.180.030.22