Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:05 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 786/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GladiaTOX 1.10.3 (landing page) PMP S.A. R Support
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GladiaTOX |
Version: 1.10.3 |
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_1.10.3.tar.gz |
StartedAt: 2022-04-12 13:52:31 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 13:55:28 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 176.5 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_1.10.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GladiaTOX.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GladiaTOX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GladiaTOX’ version ‘1.10.3’ * 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 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 ... 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 38.492 16.771 28.524 assignDefaultMthds 34.942 11.638 24.570 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.14-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/4.1/Resources/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)
GladiaTOX.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 (v1.10.3) loaded with the following settings: TCPL_DB: /Library/Frameworks/R.framework/Versions/4.1/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 [0.9s] ⠏ | 0 | exportResultTable ⠙ | 2 | exportResultTable ✔ | 2 | exportResultTable [0.3s] ⠏ | 0 | getsplit ⠏ | 0 | getsplit ✔ | 1 | getsplit ⠏ | 0 | glComputeToxInd ⠋ | 1 | glComputeToxInd ✔ | 1 | glComputeToxInd [0.5s] ⠏ | 0 | gtoxAICProb ✔ | 1 | gtoxAICProb ⠏ | 0 | gtoxCalcVmad ⠏ | 0 | Calculate Vmad ✔ | 1 | Calculate Vmad ⠏ | 0 | gtoxLoadAcid ⠏ | 0 | Check assay component table ⠋ | 1 | Check assay component table ✔ | 2 | Check assay component table [0.2s] ⠏ | 0 | gtoxLoadAeid ⠏ | 0 | Check assay endpoint table ⠙ | 2 | Check assay endpoint table ✔ | 2 | Check assay endpoint table [0.2s] ⠏ | 0 | gtoxLoadAid ✔ | 1 | gtoxLoadAid ⠏ | 0 | gtoxLoadApid ⠏ | 0 | Check assay plate table ✔ | 2 | Check assay plate table ⠏ | 0 | gtoxLoadAsid ⠹ | 3 | gtoxLoadAsid ✔ | 3 | gtoxLoadAsid [0.1s] ⠏ | 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: 2.8 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 9.027 0.539 9.555
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
name | user | system | elapsed | |
Models | 0.187 | 0.030 | 0.258 | |
assay_funcs | 0.611 | 0.052 | 0.666 | |
assignDefaultMthds | 34.942 | 11.638 | 24.570 | |
buildAssayTab | 0.063 | 0.006 | 0.068 | |
config_funcs | 0.008 | 0.003 | 0.012 | |
deleteStudy | 0.000 | 0.000 | 0.001 | |
exportResultForToxpiGUI | 0.573 | 0.065 | 0.668 | |
exportResultTable | 0.188 | 0.011 | 0.200 | |
glComputeToxInd | 0.453 | 0.026 | 0.480 | |
glPlotPie | 2.825 | 0.068 | 2.895 | |
glPlotPieLogo | 1.179 | 0.007 | 1.188 | |
glPlotPosCtrl | 1.115 | 0.026 | 1.143 | |
glPlotPosCtrlMEC | 0.732 | 0.046 | 0.778 | |
glPlotStat | 1.131 | 0.015 | 1.147 | |
glPlotToxInd | 0.707 | 0.022 | 0.730 | |
gtoxAICProb | 0.001 | 0.001 | 0.001 | |
gtoxAddModel | 0.930 | 0.017 | 0.948 | |
gtoxCalcVmad | 0.046 | 0.004 | 0.049 | |
gtoxCode2CASN | 0.001 | 0.001 | 0.002 | |
gtoxFit | 0.678 | 0.003 | 0.683 | |
gtoxImportThermoDB | 0.001 | 0.001 | 0.002 | |
gtoxListFlds | 0.008 | 0.001 | 0.009 | |
gtoxLoadApid | 0.012 | 0.004 | 0.016 | |
gtoxLoadChem | 0.080 | 0.018 | 0.098 | |
gtoxLoadClib | 0.008 | 0.001 | 0.010 | |
gtoxLoadData | 0.107 | 0.012 | 0.118 | |
gtoxLoadVehicle | 0.008 | 0.002 | 0.010 | |
gtoxLoadVmad | 0.011 | 0.002 | 0.013 | |
gtoxLoadWaid | 0.037 | 0.005 | 0.041 | |
gtoxMakeAeidPlts | 0.619 | 0.030 | 0.650 | |
gtoxPlotErrBar | 0.398 | 0.012 | 0.411 | |
gtoxPlotFitc | 0.428 | 0.004 | 0.433 | |
gtoxPlotFits | 0.206 | 0.012 | 0.218 | |
gtoxPlotM4ID | 0.864 | 0.046 | 0.911 | |
gtoxPlotPie | 0.200 | 0.011 | 0.211 | |
gtoxPlotPieLgnd | 0.007 | 0.001 | 0.007 | |
gtoxPlotPlate | 0.327 | 0.020 | 0.348 | |
gtoxPlotWin | 0 | 0 | 0 | |
gtoxPrepOtpt | 0.199 | 0.012 | 0.211 | |
gtoxReport | 0.000 | 0.000 | 0.001 | |
gtoxRun | 38.492 | 16.771 | 28.524 | |
gtoxSetWllq | 0.165 | 0.047 | 0.214 | |
gtoxSubsetChid | 0.170 | 0.018 | 0.189 | |
gtoxWriteData | 0.000 | 0.001 | 0.001 | |
hill_utils | 0.001 | 0.001 | 0.002 | |
loadAnnot | 0.000 | 0.001 | 0.001 | |
lu | 0 | 0 | 0 | |
lw | 0.000 | 0.001 | 0.000 | |
mthd_funcs | 0.017 | 0.004 | 0.020 | |
prepareDatForDB | 0.000 | 0.001 | 0.001 | |
query_funcs | 0.024 | 0.004 | 0.028 | |
rgstr_funcs | 0.321 | 0.029 | 0.352 | |