PMP S.A. R Support
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GladiaTOX |
| Branch: RELEASE_3_10 |
| Last Commit: 2715ef9 |
| Last Changed Date: 2019-10-29 13:11:41 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:45 -0400 (Wed, 15 Apr 2020).
| Package 709/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GladiaTOX 1.2.0 PMP S.A. R Support
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GladiaTOX |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GladiaTOX_1.2.0.tar.gz |
| StartedAt: 2020-04-15 06:33:49 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:51:11 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1042.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GladiaTOX_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GladiaTOX.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 or elapsed time > 5s
user system elapsed
glPlotStat 559.680 2.488 93.440
exportResultForToxpiGUI 558.628 2.728 123.306
glComputeToxInd 502.188 2.516 99.214
glPlotToxInd 462.520 1.556 73.177
glPlotPie 418.696 2.296 81.869
exportResultTable 389.164 2.020 69.423
gtoxMakeAeidPlts 48.836 0.240 8.546
assignDefaultMthds 37.056 5.932 22.796
gtoxRun 31.420 7.328 17.497
gtoxPlotM4ID 34.092 0.180 5.978
gtoxPlotFitc 27.432 0.120 4.176
gtoxPlotErrBar 25.644 0.080 3.904
gtoxPlotPie 15.064 0.064 2.424
gtoxSubsetChid 13.000 0.052 2.153
gtoxPlotFits 12.512 0.052 2.036
gtoxPrepOtpt 6.600 0.032 1.245
glPlotPosCtrl 6.424 0.024 1.997
* 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-3.10-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GladiaTOX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 (v1.2.0) loaded with the following settings:
TCPL_DB: /home/biocbuild/bbs-3.10-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 [66.9 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 [103.7 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 [0.1 s]
⠏ | 0 | Check assay endpoint table
⠙ | 2 | Check assay endpoint table
✔ | 2 | Check assay endpoint table [0.1 s]
⠏ | 0 | test_gtoxLoadAid
⠋ | 1 | test_gtoxLoadAid
✔ | 1 | test_gtoxLoadAid [0.2 s]
⠏ | 0 | Check assay plate table
✔ | 2 | Check assay plate table
⠏ | 0 | test_gtoxLoadAsid
✔ | 3 | test_gtoxLoadAsid
⠏ | 0 | Check assay chemical table
⠋ | 1 | Check assay chemical table
⠹ | 3 | Check assay chemical table
✔ | 3 | Check assay chemical table [0.6 s]
⠏ | 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: 173.0 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
1863.992 8.840 360.582
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.176 | 0.004 | 0.248 | |
| assay_funcs | 0.592 | 0.024 | 0.617 | |
| assignDefaultMthds | 37.056 | 5.932 | 22.796 | |
| buildAssayTab | 0.060 | 0.004 | 0.082 | |
| config_funcs | 0.008 | 0.000 | 0.009 | |
| deleteStudy | 0 | 0 | 0 | |
| exportResultForToxpiGUI | 558.628 | 2.728 | 123.306 | |
| exportResultTable | 389.164 | 2.020 | 69.423 | |
| glComputeToxInd | 502.188 | 2.516 | 99.214 | |
| glPlotPie | 418.696 | 2.296 | 81.869 | |
| glPlotPieLogo | 1.100 | 0.004 | 1.107 | |
| glPlotPosCtrl | 6.424 | 0.024 | 1.997 | |
| glPlotStat | 559.680 | 2.488 | 93.440 | |
| glPlotToxInd | 462.520 | 1.556 | 73.177 | |
| gtoxAICProb | 0 | 0 | 0 | |
| gtoxAddModel | 0.492 | 0.004 | 0.496 | |
| gtoxCalcVmad | 0.280 | 0.004 | 0.098 | |
| gtoxCode2CASN | 0.004 | 0.000 | 0.002 | |
| gtoxFit | 0.340 | 0.000 | 0.341 | |
| gtoxImportThermoDB | 0.000 | 0.000 | 0.001 | |
| gtoxListFlds | 0.004 | 0.000 | 0.006 | |
| gtoxLoadApid | 0.008 | 0.000 | 0.007 | |
| gtoxLoadChem | 1.992 | 0.008 | 0.427 | |
| gtoxLoadClib | 0.008 | 0.000 | 0.007 | |
| gtoxLoadData | 1.692 | 0.012 | 0.399 | |
| gtoxLoadVehicle | 0.008 | 0.000 | 0.008 | |
| gtoxLoadVmad | 0.012 | 0.000 | 0.009 | |
| gtoxLoadWaid | 0.588 | 0.004 | 0.107 | |
| gtoxMakeAeidPlts | 48.836 | 0.240 | 8.546 | |
| gtoxPlotErrBar | 25.644 | 0.080 | 3.904 | |
| gtoxPlotFitc | 27.432 | 0.120 | 4.176 | |
| gtoxPlotFits | 12.512 | 0.052 | 2.036 | |
| gtoxPlotM4ID | 34.092 | 0.180 | 5.978 | |
| gtoxPlotPie | 15.064 | 0.064 | 2.424 | |
| gtoxPlotPieLgnd | 0.008 | 0.000 | 0.006 | |
| gtoxPlotPlate | 2.384 | 0.012 | 0.571 | |
| gtoxPlotWin | 0.004 | 0.000 | 0.000 | |
| gtoxPrepOtpt | 6.600 | 0.032 | 1.245 | |
| gtoxReport | 0 | 0 | 0 | |
| gtoxRun | 31.420 | 7.328 | 17.497 | |
| gtoxSetWllq | 0.116 | 0.008 | 0.123 | |
| gtoxSubsetChid | 13.000 | 0.052 | 2.153 | |
| gtoxWriteData | 0.004 | 0.000 | 0.000 | |
| hill_utils | 0 | 0 | 0 | |
| loadAnnot | 0 | 0 | 0 | |
| lu | 0 | 0 | 0 | |
| lw | 0 | 0 | 0 | |
| mthd_funcs | 0.080 | 0.000 | 0.022 | |
| prepareDatForDB | 0 | 0 | 0 | |
| query_funcs | 0.012 | 0.000 | 0.011 | |
| rgstr_funcs | 0.496 | 0.012 | 0.247 | |