Multiple platform build/check report for BioC 3.20 - CHECK results for metabolomicsWorkbenchR on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for metabolomicsWorkbenchR on merida1

To the developers/maintainers of the metabolomicsWorkbenchR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metabolomicsWorkbenchR.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.

raw results

Summary

Package: metabolomicsWorkbenchR

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabolomicsWorkbenchR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabolomicsWorkbenchR_1.16.0.tar.gz

StartedAt: 2024-12-20 05:42:13 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 05:48:09 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 355.4 seconds

RetCode: 0

Status: OK

CheckDir: metabolomicsWorkbenchR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabolomicsWorkbenchR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabolomicsWorkbenchR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metabolomicsWorkbenchR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabolomicsWorkbenchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabolomicsWorkbenchR’ version ‘1.16.0’
* 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 ... NOTE
Found the following non-portable file paths:
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/data.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/factors.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/summary.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes/summary.json
  metabolomicsWorkbenchR/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010/summary.json
  metabolomicsWorkbenchR/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored
  metabolomicsWorkbenchR/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes
  metabolomicsWorkbenchR/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010
  metabolomicsWorkbenchR/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 code 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 ... 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-3.20-bioc/meat/metabolomicsWorkbenchR.Rcheck/00check.log’
for details.

Installation output

metabolomicsWorkbenchR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabolomicsWorkbenchR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

metabolomicsWorkbenchR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 31.943   1.381  33.834

Example timings

metabolomicsWorkbenchR.Rcheck/metabolomicsWorkbenchR-Ex.timings

name	user	system	elapsed
check_pattern	0.002	0.000	0.003
check_puts	0.037	0.004	0.041
context	0.001	0.001	0.002
context_inputs	0.001	0.000	0.002
context_outputs	0.001	0.001	0.001
do_query	0.001	0.001	0.000
input_example	0.000	0.000	0.001
input_item	0.001	0.001	0.002
is_valid	0.001	0.000	0.001
mw_base	0.000	0.001	0.001
output_item	0.001	0.002	0.003