Multiple platform build/check report for BioC 3.11 - CHECK report for GladiaTOX on machv2

Package: GladiaTOX

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2020-10-17 01:39:54 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 01:42:46 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 171.9 seconds

RetCode: 0

Status: OK

CheckDir: GladiaTOX.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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            38.066 16.228  28.061
assignDefaultMthds 34.456 10.949  24.218
* 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-3.11-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GladiaTOX
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 (v1.4.0) loaded with the following settings:
  TCPL_DB:    /Library/Frameworks/R.framework/Versions/4.0/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 [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 [0.5 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 
  8.161   0.504   8.699

name	user	system	elapsed
Models	0.219	0.036	0.270
assay_funcs	0.600	0.052	0.700
assignDefaultMthds	34.456	10.949	24.218
buildAssayTab	0.049	0.005	0.054
config_funcs	0.008	0.003	0.011
deleteStudy	0	0	0
exportResultForToxpiGUI	0.427	0.044	0.472
exportResultTable	0.215	0.013	0.228
glComputeToxInd	0.382	0.022	0.404
glPlotPie	2.491	0.054	2.551
glPlotPieLogo	1.216	0.014	1.237
glPlotPosCtrl	1.158	0.028	1.222
glPlotStat	1.073	0.022	1.099
glPlotToxInd	0.763	0.022	0.788
gtoxAICProb	0.001	0.001	0.002
gtoxAddModel	0.936	0.019	0.960
gtoxCalcVmad	0.045	0.003	0.048
gtoxCode2CASN	0.001	0.000	0.002
gtoxFit	0.745	0.008	0.757
gtoxImportThermoDB	0.001	0.000	0.001
gtoxListFlds	0.007	0.001	0.008
gtoxLoadApid	0.014	0.005	0.018
gtoxLoadChem	0.062	0.017	0.080
gtoxLoadClib	0.009	0.001	0.009
gtoxLoadData	0.090	0.009	0.099
gtoxLoadVehicle	0.006	0.001	0.006
gtoxLoadVmad	0.009	0.002	0.010
gtoxLoadWaid	0.033	0.004	0.037
gtoxMakeAeidPlts	0.665	0.032	0.699
gtoxPlotErrBar	0.477	0.017	0.493
gtoxPlotFitc	0.447	0.012	0.461
gtoxPlotFits	0.240	0.012	0.253
gtoxPlotM4ID	0.911	0.047	0.960
gtoxPlotPie	0.243	0.012	0.255
gtoxPlotPieLgnd	0.009	0.001	0.009
gtoxPlotPlate	0.305	0.018	0.323
gtoxPlotWin	0.000	0.001	0.001
gtoxPrepOtpt	0.195	0.011	0.226
gtoxReport	0.000	0.000	0.001
gtoxRun	38.066	16.228	28.061
gtoxSetWllq	0.152	0.040	0.192
gtoxSubsetChid	0.153	0.015	0.168
gtoxWriteData	0.000	0.001	0.001
hill_utils	0.002	0.002	0.003
loadAnnot	0.000	0.000	0.002
lu	0.001	0.001	0.000
lw	0.000	0.001	0.000
mthd_funcs	0.016	0.003	0.019
prepareDatForDB	0.000	0.000	0.001
query_funcs	0.023	0.003	0.026
rgstr_funcs	0.380	0.032	0.413

CHECK report for GladiaTOX on machv2

Summary

Command output

Installation output

Tests output

Example timings