PMP S.A. R Support
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GladiaTOX |
| Branch: RELEASE_3_9 |
| Last Commit: 996062e |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:05:07 -0400 (Wed, 16 Oct 2019).
| Package 683/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GladiaTOX 1.0.0 PMP S.A. R Support
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GladiaTOX |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GladiaTOX_1.0.0.tar.gz |
| StartedAt: 2019-10-16 03:16:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:20:38 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 233.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GladiaTOX_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GladiaTOX.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.0’
* 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 5.2Mb
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
assignDefaultMthds 52.266 28.438 40.916
gtoxRun 47.758 24.670 35.588
glPlotPie 10.468 3.789 4.707
glComputeToxInd 8.015 3.236 2.311
exportResultForToxpiGUI 6.981 3.462 2.100
exportResultTable 5.769 3.783 2.011
glPlotStat 5.900 2.192 2.053
glPlotToxInd 5.388 2.201 1.481
gtoxPlotM4ID 4.685 2.104 1.323
gtoxMakeAeidPlts 3.248 2.556 1.050
gtoxPlotErrBar 3.507 1.862 0.811
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GladiaTOX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 (v1.0.0) loaded with the following settings:
TCPL_DB: /Library/Frameworks/R.framework/Versions/3.6/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")
✔ | OK F W S | Context
⠏ | 0 | test_assignDefaultMthds
⠋ | 1 | test_assignDefaultMthds
✔ | 1 | test_assignDefaultMthds [1.3 s]
⠏ | 0 | test_exportResultTable
⠙ | 2 | test_exportResultTable
✔ | 2 | test_exportResultTable [1.1 s]
⠏ | 0 | getsplit
✖ | 0 1 | getsplit
────────────────────────────────────────────────────────────────────────────────
test_getsplit.R:4: error: getsplit:split word correctly
could not find function "getsplit"
1: expect_equal(getsplit("toto_tata", "_", 1), "toto") at testthat/test_getsplit.R:4
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | test_glComputeToxInd
⠋ | 0 1 | test_glComputeToxInd
✔ | 1 3 | test_glComputeToxInd [2.1 s]
────────────────────────────────────────────────────────────────────────────────
test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values
no non-missing arguments to min; returning Inf
test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values
no non-missing arguments to min; returning Inf
test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values
no non-missing arguments to max; returning -Inf
────────────────────────────────────────────────────────────────────────────────
⠏ | 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
⠋ | 1 | test_gtoxLoadAsid
✔ | 3 | test_gtoxLoadAsid [0.1 s]
⠏ | 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"
1: .handleSimpleError(function (e)
{
handled <<- TRUE
test_error <<- e
options(expressions = expressions_opt_new)
on.exit(options(expressions = expressions_opt), add = TRUE)
e$expectation_calls <- frame_calls(11, 2)
test_error <<- e
register_expectation(e)
e$handled <- TRUE
test_error <<- e
}, "could not find function \"is.odd\"", base::quote(is.odd(2))) at testthat/test_is.odd.R:2
2: eval(code, test_env)
────────────────────────────────────────────────────────────────────────────────
⠏ | 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"
1: .handleSimpleError(function (e)
{
handled <<- TRUE
test_error <<- e
options(expressions = expressions_opt_new)
on.exit(options(expressions = expressions_opt), add = TRUE)
e$expectation_calls <- frame_calls(11, 2)
test_error <<- e
register_expectation(e)
e$handled <- TRUE
test_error <<- e
}, "could not find function \"mc2_mthds\"", base::quote(mc2_mthds())) at testthat/test_mc2.R:2
2: eval(code, test_env)
────────────────────────────────────────────────────────────────────────────────
⠏ | 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"
1: expect_true("resp.log2" %in% names(mc3_mthds())) at testthat/test_mc3.R:2
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
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"
1: expect_true("bmad5" %in% names(mc5_mthds())) at testthat/test_mc5.R:2
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
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"
1: expect_true("pintool" %in% names(mc6_mthds())) at testthat/test_mc6.R:2
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
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"
1: expect_true("pval.zero" %in% names(sc1_mthds())) at testthat/test_sc1.R:2
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
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"
1: expect_true("bmad6" %in% names(sc2_mthds())) at testthat/test_sc2.R:2
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: "bmad6" %in% names(sc2_mthds())
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.9 s
OK: 23
Failed: 8
Warnings: 3
Skipped: 0
> test_check("GladiaTOX")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
35.169 16.534 13.358
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.445 | 0.033 | 0.505 | |
| assay_funcs | 0.768 | 0.133 | 0.903 | |
| assignDefaultMthds | 52.266 | 28.438 | 40.916 | |
| buildAssayTab | 0.107 | 0.041 | 0.149 | |
| config_funcs | 0.014 | 0.005 | 0.019 | |
| deleteStudy | 0.001 | 0.000 | 0.001 | |
| exportResultForToxpiGUI | 6.981 | 3.462 | 2.100 | |
| exportResultTable | 5.769 | 3.783 | 2.011 | |
| glComputeToxInd | 8.015 | 3.236 | 2.311 | |
| glPlotPie | 10.468 | 3.789 | 4.707 | |
| glPlotPieLogo | 1.608 | 0.011 | 1.620 | |
| glPlotPosCtrl | 3.459 | 1.084 | 1.645 | |
| glPlotStat | 5.900 | 2.192 | 2.053 | |
| glPlotToxInd | 5.388 | 2.201 | 1.481 | |
| gtoxAICProb | 0.002 | 0.000 | 0.003 | |
| gtoxAddModel | 0.754 | 0.029 | 0.783 | |
| gtoxCalcVmad | 0.064 | 0.018 | 0.059 | |
| gtoxCode2CASN | 0.005 | 0.004 | 0.002 | |
| gtoxFit | 1.044 | 0.317 | 0.751 | |
| gtoxImportThermoDB | 0.002 | 0.000 | 0.002 | |
| gtoxListFlds | 0.008 | 0.001 | 0.009 | |
| gtoxLoadApid | 0.015 | 0.005 | 0.020 | |
| gtoxLoadChem | 0.943 | 0.027 | 0.111 | |
| gtoxLoadClib | 0.022 | 0.015 | 0.007 | |
| gtoxLoadData | 0.507 | 0.391 | 0.169 | |
| gtoxLoadVehicle | 0.032 | 0.023 | 0.012 | |
| gtoxLoadVmad | 0.039 | 0.025 | 0.017 | |
| gtoxLoadWaid | 0.127 | 0.099 | 0.044 | |
| gtoxMakeAeidPlts | 3.248 | 2.556 | 1.050 | |
| gtoxPlotErrBar | 3.507 | 1.862 | 0.811 | |
| gtoxPlotFitc | 3.028 | 1.708 | 0.728 | |
| gtoxPlotFits | 1.055 | 0.831 | 0.330 | |
| gtoxPlotM4ID | 4.685 | 2.104 | 1.323 | |
| gtoxPlotPie | 1.005 | 0.694 | 0.401 | |
| gtoxPlotPieLgnd | 0.029 | 0.020 | 0.010 | |
| gtoxPlotPlate | 0.834 | 0.553 | 0.398 | |
| gtoxPlotWin | 0.002 | 0.002 | 0.000 | |
| gtoxPrepOtpt | 0.807 | 0.586 | 0.289 | |
| gtoxReport | 0.001 | 0.001 | 0.001 | |
| gtoxRun | 47.758 | 24.670 | 35.588 | |
| gtoxSetWllq | 0.186 | 0.056 | 0.247 | |
| gtoxSubsetChid | 1.340 | 0.043 | 0.298 | |
| gtoxWriteData | 0.001 | 0.000 | 0.001 | |
| hill_utils | 0.101 | 0.001 | 0.005 | |
| loadAnnot | 0.001 | 0.001 | 0.000 | |
| lu | 0.000 | 0.001 | 0.001 | |
| lw | 0 | 0 | 0 | |
| mthd_funcs | 0.428 | 0.007 | 0.044 | |
| prepareDatForDB | 0.000 | 0.000 | 0.001 | |
| query_funcs | 0.155 | 0.058 | 0.037 | |
| rgstr_funcs | 0.910 | 0.543 | 0.506 | |