| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:00 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 | ||||
| Package 864/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GladiaTOX 1.18.0 (landing page) PMP S.A. R Support
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the GladiaTOX package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GladiaTOX |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GladiaTOX_1.18.0.tar.gz |
| StartedAt: 2024-04-15 23:19:26 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 23:24:22 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 296.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GladiaTOX.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GladiaTOX.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GladiaTOX_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GladiaTOX.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GladiaTOX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GladiaTOX’ version ‘1.18.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 19.779 11.773 15.709
assignDefaultMthds 15.954 6.410 11.603
* 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 ...
‘GladiaTOX.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘GladiaTOX.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/GladiaTOX.Rcheck/vign_test/GladiaTOX/vignettes/GladiaTOX_files/figure-html/logo-1.png" but not available.
Quitting from lines at lines 231-234 [unnamed-chunk-15] (GladiaTOX.Rmd)
Error: processing vignette 'GladiaTOX.Rmd' failed with diagnostics:
Join results in 26880 rows; more than 23040 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.
--- failed re-building ‘GladiaTOX.Rmd’
SUMMARY: processing the following file failed:
‘GladiaTOX.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/GladiaTOX.Rcheck/00check.log’
for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GladiaTOX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 (v1.18.0) loaded with the following settings:
TCPL_DB: /home/biocbuild/bbs-3.18-bioc/R/site-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 | exportResultTable
⠙ | 2 | exportResultTable
✔ | 2 | exportResultTable
⠏ | 0 | getsplit
⠏ | 0 | getsplit
✔ | 1 | getsplit
⠏ | 0 | glComputeToxInd
⠋ | 1 | glComputeToxInd
✔ | 1 | glComputeToxInd
⠏ | 0 | gtoxAICProb
✔ | 1 | gtoxAICProb
⠏ | 0 | gtoxCalcVmad
⠏ | 0 | Calculate Vmad
✔ | 1 | Calculate Vmad
⠏ | 0 | gtoxLoadAcid
⠏ | 0 | Check assay component table
✔ | 2 | Check assay component table
⠏ | 0 | gtoxLoadAeid
⠏ | 0 | Check assay endpoint table
✔ | 2 | Check assay endpoint table
⠏ | 0 | gtoxLoadAid
✔ | 1 | gtoxLoadAid
⠏ | 0 | gtoxLoadApid
⠏ | 0 | Check assay plate table
✔ | 2 | Check assay plate table
⠏ | 0 | gtoxLoadAsid
✔ | 3 | gtoxLoadAsid
⠏ | 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: 1.6 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
5.222 0.157 5.357
GladiaTOX.Rcheck/GladiaTOX-Ex.timings
| name | user | system | elapsed | |
| Models | 0.098 | 0.020 | 0.129 | |
| assay_funcs | 0.292 | 0.052 | 0.344 | |
| assignDefaultMthds | 15.954 | 6.410 | 11.603 | |
| buildAssayTab | 0.033 | 0.005 | 0.038 | |
| config_funcs | 0.007 | 0.000 | 0.007 | |
| deleteStudy | 0 | 0 | 0 | |
| exportResultForToxpiGUI | 0.281 | 0.011 | 0.292 | |
| exportResultTable | 0.117 | 0.008 | 0.125 | |
| glComputeToxInd | 0.242 | 0.011 | 0.251 | |
| glPlotPie | 1.313 | 0.044 | 1.330 | |
| glPlotPieLogo | 0.72 | 0.00 | 0.72 | |
| glPlotPosCtrl | 0.862 | 0.011 | 0.820 | |
| glPlotPosCtrlMEC | 0.348 | 0.004 | 0.353 | |
| glPlotStat | 0.774 | 0.008 | 0.782 | |
| glPlotToxInd | 0.509 | 0.004 | 0.498 | |
| gtoxAICProb | 0.001 | 0.000 | 0.000 | |
| gtoxAddModel | 0.439 | 0.000 | 0.440 | |
| gtoxCalcVmad | 0.027 | 0.000 | 0.027 | |
| gtoxCode2CASN | 0.001 | 0.000 | 0.001 | |
| gtoxFit | 0.323 | 0.000 | 0.324 | |
| gtoxImportThermoDB | 0.001 | 0.000 | 0.001 | |
| gtoxListFlds | 0.006 | 0.000 | 0.005 | |
| gtoxLoadApid | 0.009 | 0.000 | 0.009 | |
| gtoxLoadChem | 0.050 | 0.004 | 0.054 | |
| gtoxLoadClib | 0.005 | 0.000 | 0.006 | |
| gtoxLoadData | 0.079 | 0.008 | 0.087 | |
| gtoxLoadVehicle | 0.006 | 0.000 | 0.006 | |
| gtoxLoadVmad | 0.007 | 0.000 | 0.007 | |
| gtoxLoadWaid | 0.027 | 0.000 | 0.027 | |
| gtoxMakeAeidPlts | 0.339 | 0.004 | 0.343 | |
| gtoxPlotErrBar | 0.294 | 0.024 | 0.304 | |
| gtoxPlotFitc | 0.235 | 0.016 | 0.251 | |
| gtoxPlotFits | 0.116 | 0.000 | 0.116 | |
| gtoxPlotM4ID | 0.480 | 0.016 | 0.495 | |
| gtoxPlotPie | 0.127 | 0.004 | 0.130 | |
| gtoxPlotPieLgnd | 0.005 | 0.000 | 0.006 | |
| gtoxPlotPlate | 0.218 | 0.004 | 0.222 | |
| gtoxPlotWin | 0 | 0 | 0 | |
| gtoxPrepOtpt | 0.166 | 0.004 | 0.136 | |
| gtoxReport | 0.000 | 0.000 | 0.001 | |
| gtoxRun | 19.779 | 11.773 | 15.709 | |
| gtoxSetWllq | 0.085 | 0.023 | 0.110 | |
| gtoxSubsetChid | 0.111 | 0.008 | 0.119 | |
| gtoxWriteData | 0 | 0 | 0 | |
| hill_utils | 0.001 | 0.000 | 0.001 | |
| loadAnnot | 0 | 0 | 0 | |
| lu | 0 | 0 | 0 | |
| lw | 0.000 | 0.000 | 0.001 | |
| mthd_funcs | 0.018 | 0.000 | 0.018 | |
| prepareDatForDB | 0 | 0 | 0 | |
| query_funcs | 0.014 | 0.004 | 0.018 | |
| rgstr_funcs | 0.249 | 0.019 | 0.269 | |