##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabolomicsWorkbenchR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metabolomicsWorkbenchR_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/metabolomicsWorkbenchR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metabolomicsWorkbenchR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metabolomicsWorkbenchR' version '1.5.0'
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL metabolomicsWorkbenchR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'metabolomicsWorkbenchR' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metabolomicsWorkbenchR'
    finding HTML links ... done
    check_pattern                           html  
    check_puts                              html  
    context                                 html  
    context_inputs                          html  
    context_outputs                         html  
    do_query                                html  
    input_example                           html  
    input_item                              html  
    is_valid                                html  
    metabolomicsWorkbenchR                  html  
    mw_base                                 html  
    output_item                             html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'networkBMA' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'phenoTest' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  16.37    0.40   16.76