PMP S.A. R Support
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/GladiaTOX |
| git_branch: master |
| git_last_commit: f7f469b |
| git_last_commit_date: 2021-10-26 12:52:08 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:39 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 789/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GladiaTOX 1.11.0 (landing page) PMP S.A. R Support
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GladiaTOX |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GladiaTOX.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GladiaTOX_1.11.0.tar.gz |
| StartedAt: 2022-03-17 19:13:20 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:15:13 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 112.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GladiaTOX.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GladiaTOX_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GladiaTOX.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.11.0'
* 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 5.7Mb
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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
assignDefaultMthds 15.20 0.67 16.10
gtoxRun 14.72 0.44 15.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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
'D:/biocbuild/bbs-3.15-bioc/meat/GladiaTOX.Rcheck/00check.log'
for details.
GladiaTOX.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GladiaTOX
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (GladiaTOX)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'cellbaseR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MOSim' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TissueEnrich' is missing or broken
done
GladiaTOX.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 (v1.11.0) loaded with the following settings:
TCPL_DB: D:/biocbuild/bbs-3.15-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 [0.1s]
/ | 0 | getsplit
/ | 0 | getsplit
v | 1 | getsplit
/ | 0 | glComputeToxInd
- | 1 | glComputeToxInd
v | 1 | glComputeToxInd [0.2s]
/ | 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
v | 2 | Check assay endpoint table
/ | 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: 1.3 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
3.96 0.53 4.53
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.10 | 0.02 | 0.11 | |
| assay_funcs | 0.28 | 0.06 | 0.34 | |
| assignDefaultMthds | 15.20 | 0.67 | 16.10 | |
| buildAssayTab | 0.02 | 0.00 | 0.01 | |
| config_funcs | 0.01 | 0.00 | 0.02 | |
| deleteStudy | 0 | 0 | 0 | |
| exportResultForToxpiGUI | 0.25 | 0.00 | 0.25 | |
| exportResultTable | 0.11 | 0.02 | 0.12 | |
| glComputeToxInd | 0.19 | 0.04 | 0.24 | |
| glPlotPie | 1.50 | 0.02 | 1.51 | |
| glPlotPieLogo | 0.72 | 0.00 | 0.72 | |
| glPlotPosCtrl | 0.70 | 0.01 | 0.72 | |
| glPlotStat | 0.66 | 0.03 | 0.69 | |
| glPlotToxInd | 0.40 | 0.00 | 0.41 | |
| gtoxAICProb | 0 | 0 | 0 | |
| gtoxAddModel | 0.44 | 0.02 | 0.48 | |
| gtoxCalcVmad | 0.03 | 0.00 | 0.03 | |
| gtoxCode2CASN | 0 | 0 | 0 | |
| gtoxFit | 0.35 | 0.00 | 0.34 | |
| gtoxImportThermoDB | 0 | 0 | 0 | |
| gtoxListFlds | 0 | 0 | 0 | |
| gtoxLoadApid | 0.02 | 0.00 | 0.02 | |
| gtoxLoadChem | 0.04 | 0.00 | 0.04 | |
| gtoxLoadClib | 0 | 0 | 0 | |
| gtoxLoadData | 0.08 | 0.00 | 0.08 | |
| gtoxLoadVehicle | 0 | 0 | 0 | |
| gtoxLoadVmad | 0.02 | 0.00 | 0.01 | |
| gtoxLoadWaid | 0.01 | 0.00 | 0.02 | |
| gtoxMakeAeidPlts | 0.36 | 0.05 | 0.41 | |
| gtoxPlotErrBar | 0.33 | 0.01 | 0.34 | |
| gtoxPlotFitc | 0.23 | 0.00 | 0.24 | |
| gtoxPlotFits | 0.11 | 0.00 | 0.11 | |
| gtoxPlotM4ID | 0.50 | 0.03 | 0.53 | |
| gtoxPlotPie | 0.11 | 0.02 | 0.12 | |
| gtoxPlotPieLgnd | 0 | 0 | 0 | |
| gtoxPlotPlate | 0.16 | 0.02 | 0.18 | |
| gtoxPlotWin | 0 | 0 | 0 | |
| gtoxPrepOtpt | 0.06 | 0.03 | 0.09 | |
| gtoxReport | 0 | 0 | 0 | |
| gtoxRun | 14.72 | 0.44 | 15.22 | |
| gtoxSetWllq | 0.09 | 0.00 | 0.13 | |
| gtoxSubsetChid | 0.09 | 0.00 | 0.09 | |
| gtoxWriteData | 0 | 0 | 0 | |
| hill_utils | 0 | 0 | 0 | |
| loadAnnot | 0 | 0 | 0 | |
| lu | 0 | 0 | 0 | |
| lw | 0 | 0 | 0 | |
| mthd_funcs | 0.02 | 0.00 | 0.02 | |
| prepareDatForDB | 0 | 0 | 0 | |
| query_funcs | 0.02 | 0.00 | 0.01 | |
| rgstr_funcs | 0.17 | 0.05 | 0.22 | |