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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metabolomicsWorkbenchR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metabolomicsWorkbenchR_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metabolomicsWorkbenchR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘metabolomicsWorkbenchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabolomicsWorkbenchR’ version ‘1.9.0’
* package encoding: UTF-8
* 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 ‘metabolomicsWorkbenchR’ can be installed ... OK
* checking installed package size ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘Introduction_to_metabolomicsWorkbenchR.Rmd’ using ‘UTF-8’... OK
  ‘example_using_structToolbox.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_metabolomicsWorkbenchR.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/metabolomicsWorkbenchR.Rcheck/vign_test/metabolomicsWorkbenchR/vignettes/Introduction_to_metabolomicsWorkbenchR_files/figure-html/unnamed-chunk-4-1.png" but not available.
Killed
--- re-building ‘example_using_structToolbox.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/metabolomicsWorkbenchR.Rcheck/vign_test/metabolomicsWorkbenchR/vignettes/example_using_structToolbox_files/figure-html/unnamed-chunk-7-1.png" but not available.
--- finished re-building ‘example_using_structToolbox.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_metabolomicsWorkbenchR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/metabolomicsWorkbenchR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metabolomicsWorkbenchR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘metabolomicsWorkbenchR’ ...
** using staged installation
** R
** 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 (metabolomicsWorkbenchR)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(metabolomicsWorkbenchR)
> 
> test_check("metabolomicsWorkbenchR")
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/exactmass/PC(34:1)/M+H"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/datatable"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/datatable"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/datatable"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_data"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary"
[1] "TEST mode"
[1] "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors"
[1] "TEST mode"
A Metabolomics Workbench "input_item"

Name:	"study_id"

Exact pattern matching:
	"^ST[0-9]{6}$"

Partial pattern matching:
	"^S(T[0-9]{0,6})?$"

Examples: 
	"ST000001"
	"ST"

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 119 ]
> 
> proc.time()
   user  system elapsed 
 19.664   0.538  20.466