PMP S.A. R Support
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GladiaTOX |
| Branch: RELEASE_3_11 |
| Last Commit: 79c3bfd |
| Last Changed Date: 2020-04-27 15:27:17 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:52 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GladiaTOX PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 737/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GladiaTOX 1.4.0 PMP S.A. R Support
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.4.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GladiaTOX_1.4.0.tar.gz |
| StartedAt: 2020-10-17 01:50:14 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:52:28 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 134.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GladiaTOX_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 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
gtoxRun 27.712 8.672 18.505
assignDefaultMthds 25.384 5.859 16.363
* 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
‘/home/biocbuild/bbs-3.11-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GladiaTOX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 (v1.4.0) loaded with the following settings:
TCPL_DB: /home/biocbuild/bbs-3.11-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")
✔ | OK F W S | Context
⠏ | 0 | test_assignDefaultMthds
⠋ | 1 | test_assignDefaultMthds
✔ | 1 | test_assignDefaultMthds [0.9 s]
⠏ | 0 | test_exportResultTable
⠙ | 2 | test_exportResultTable
✔ | 2 | test_exportResultTable [0.3 s]
⠏ | 0 | getsplit
✖ | 0 1 | getsplit
────────────────────────────────────────────────────────────────────────────────
test_getsplit.R:4: error: getsplit:split word correctly
could not find function "getsplit"
Backtrace:
1. testthat::expect_equal(getsplit("toto_tata", "_", 1), "toto") test_getsplit.R:4:4
2. testthat::quasi_label(enquo(object), label, arg = "object")
3. rlang::eval_bare(expr, quo_get_env(quo))
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_glComputeToxInd
⠋ | 1 | test_glComputeToxInd
✔ | 1 | test_glComputeToxInd [0.4 s]
⠏ | 0 | test_gtoxAICProb
✔ | 1 | test_gtoxAICProb
⠏ | 0 | Calculate Vmad
✔ | 1 | Calculate Vmad
⠏ | 0 | Check assay component table
⠙ | 2 | Check assay component table
✔ | 2 | Check assay component table [0.2 s]
⠏ | 0 | Check assay endpoint table
⠙ | 2 | Check assay endpoint table
✔ | 2 | Check assay endpoint table [0.2 s]
⠏ | 0 | test_gtoxLoadAid
✔ | 1 | test_gtoxLoadAid
⠏ | 0 | Check assay plate table
✔ | 2 | Check assay plate table
⠏ | 0 | test_gtoxLoadAsid
✔ | 3 | test_gtoxLoadAsid
⠏ | 0 | Check assay chemical table
✔ | 3 | Check assay chemical table
⠏ | 0 | Check assay well table
✔ | 2 | Check assay well table
⠏ | 0 | test_is.odd
✖ | 0 1 | test_is.odd
────────────────────────────────────────────────────────────────────────────────
test_is.odd.R:2: error: is.odd:has the expected behavior
could not find function "is.odd"
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_lu
✔ | 1 | test_lu
⠏ | 0 | test_lw
✔ | 1 | test_lw
⠏ | 0 | test_mc2
✖ | 0 1 | test_mc2
────────────────────────────────────────────────────────────────────────────────
test_mc2.R:2: error: mc2_mthds:returns log10 among the list of mc2 functions
could not find function "mc2_mthds"
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_mc3
✖ | 0 1 | test_mc3
────────────────────────────────────────────────────────────────────────────────
test_mc3.R:2: error: mc3:returns resp.log2 among the list of mc2 functions
could not find function "mc3_mthds"
Backtrace:
1. testthat::expect_true("resp.log2" %in% names(mc3_mthds())) test_mc3.R:2:4
4. "resp.log2" %in% names(mc3_mthds())
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_mc5
✖ | 0 1 | test_mc5
────────────────────────────────────────────────────────────────────────────────
test_mc5.R:2: error: mc5:returns bmad5 among the list of mc2 functions
could not find function "mc5_mthds"
Backtrace:
1. testthat::expect_true("bmad5" %in% names(mc5_mthds())) test_mc5.R:2:4
4. "bmad5" %in% names(mc5_mthds())
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_mc6
✖ | 0 1 | test_mc6
────────────────────────────────────────────────────────────────────────────────
test_mc6.R:2: error: mc6:returns pintool among the list of mc2 functions
could not find function "mc6_mthds"
Backtrace:
1. testthat::expect_true("pintool" %in% names(mc6_mthds())) test_mc6.R:2:4
4. "pintool" %in% names(mc6_mthds())
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_sc1
✖ | 0 1 | test_sc1
────────────────────────────────────────────────────────────────────────────────
test_sc1.R:2: error: sc1:returns pval.zero among the list of sc1 functions
could not find function "sc1_mthds"
Backtrace:
1. testthat::expect_true("pval.zero" %in% names(sc1_mthds())) test_sc1.R:2:4
4. "pval.zero" %in% names(sc1_mthds())
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_sc2
✖ | 0 1 | test_sc2
────────────────────────────────────────────────────────────────────────────────
test_sc2.R:2: error: sc2:returns pval.zero among the list of sc2 functions
could not find function "sc2_mthds"
Backtrace:
1. testthat::expect_true("bmad6" %in% names(sc2_mthds())) test_sc2.R:2:4
4. "bmad6" %in% names(sc2_mthds())
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.7 s
OK: 23
Failed: 8
Warnings: 0
Skipped: 0
> test_check("GladiaTOX")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.496 0.256 7.704
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.159 | 0.036 | 2.025 | |
| assay_funcs | 0.387 | 0.016 | 0.403 | |
| assignDefaultMthds | 25.384 | 5.859 | 16.363 | |
| buildAssayTab | 0.062 | 0.007 | 0.252 | |
| config_funcs | 0.011 | 0.000 | 0.012 | |
| deleteStudy | 0 | 0 | 0 | |
| exportResultForToxpiGUI | 0.437 | 0.015 | 0.452 | |
| exportResultTable | 0.140 | 0.005 | 0.145 | |
| glComputeToxInd | 0.320 | 0.014 | 0.297 | |
| glPlotPie | 1.564 | 0.024 | 1.586 | |
| glPlotPieLogo | 0.834 | 0.000 | 0.988 | |
| glPlotPosCtrl | 0.729 | 0.005 | 0.674 | |
| glPlotStat | 0.829 | 0.008 | 0.836 | |
| glPlotToxInd | 0.571 | 0.003 | 0.527 | |
| gtoxAICProb | 0.001 | 0.000 | 0.001 | |
| gtoxAddModel | 0.533 | 0.004 | 0.537 | |
| gtoxCalcVmad | 0.028 | 0.000 | 0.028 | |
| gtoxCode2CASN | 0.001 | 0.000 | 0.001 | |
| gtoxFit | 0.385 | 0.000 | 0.385 | |
| gtoxImportThermoDB | 0 | 0 | 0 | |
| gtoxListFlds | 0.004 | 0.000 | 0.004 | |
| gtoxLoadApid | 0.004 | 0.004 | 0.007 | |
| gtoxLoadChem | 0.034 | 0.008 | 0.042 | |
| gtoxLoadClib | 0.007 | 0.000 | 0.007 | |
| gtoxLoadData | 0.095 | 0.004 | 0.099 | |
| gtoxLoadVehicle | 0.006 | 0.000 | 0.006 | |
| gtoxLoadVmad | 0.005 | 0.000 | 0.005 | |
| gtoxLoadWaid | 0.017 | 0.000 | 0.017 | |
| gtoxMakeAeidPlts | 0.606 | 0.008 | 0.614 | |
| gtoxPlotErrBar | 0.472 | 0.014 | 0.381 | |
| gtoxPlotFitc | 0.280 | 0.004 | 0.283 | |
| gtoxPlotFits | 0.139 | 0.008 | 0.147 | |
| gtoxPlotM4ID | 0.571 | 0.008 | 0.579 | |
| gtoxPlotPie | 0.210 | 0.004 | 0.215 | |
| gtoxPlotPieLgnd | 0.002 | 0.004 | 0.007 | |
| gtoxPlotPlate | 0.195 | 0.000 | 0.194 | |
| gtoxPlotWin | 0.001 | 0.000 | 0.000 | |
| gtoxPrepOtpt | 0.196 | 0.002 | 0.122 | |
| gtoxReport | 0 | 0 | 0 | |
| gtoxRun | 27.712 | 8.672 | 18.505 | |
| gtoxSetWllq | 0.121 | 0.008 | 0.129 | |
| gtoxSubsetChid | 0.131 | 0.008 | 0.139 | |
| gtoxWriteData | 0 | 0 | 0 | |
| hill_utils | 0.001 | 0.000 | 0.001 | |
| 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 | 0.017 | 0.004 | 0.021 | |
| rgstr_funcs | 0.337 | 0.024 | 0.361 | |