Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:36:50 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1199/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabolomicsWorkbenchR 1.12.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/metabolomicsWorkbenchR
git_branch: RELEASE_3_18
git_last_commit: 262a317
git_last_commit_date: 2023-10-24 11:25:05 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for metabolomicsWorkbenchR on palomino4


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: 1.12.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabolomicsWorkbenchR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings metabolomicsWorkbenchR_1.12.0.tar.gz
StartedAt: 2024-03-26 02:31:44 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 02:35:04 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 199.6 seconds
RetCode: 0
Status:   OK  
CheckDir: metabolomicsWorkbenchR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabolomicsWorkbenchR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings metabolomicsWorkbenchR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/metabolomicsWorkbenchR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metabolomicsWorkbenchR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metabolomicsWorkbenchR' version '1.12.0'
* 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 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/metabolomicsWorkbenchR.Rcheck/00check.log'
for details.



Installation output

metabolomicsWorkbenchR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL metabolomicsWorkbenchR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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)

Tests output

metabolomicsWorkbenchR.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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 
  20.51    0.82   21.40 

Example timings

metabolomicsWorkbenchR.Rcheck/metabolomicsWorkbenchR-Ex.timings

nameusersystemelapsed
check_pattern000
check_puts0.010.000.01
context000
context_inputs000
context_outputs000
do_query000
input_example000
input_item000
is_valid000
mw_base000
output_item000