W4MRUtils
Useful Functions for Harmonized W4M Tool Development
Description
Provides a set of utility function to prevent the spread of utility scripts in W4M (Workflow4Metabolomics) tools, and centralize them in a single package. To note, some are meant to be replaced by the use of dedicated packages in the future, like the parse_args() function: it is here only to prepare the ground for more global changes in W4M scripts and tools. This package is used by part of the W4M Galaxy modules, some of them being available on the community-maintained GitHub repository for Metabolomics' Galaxy tools <https://github.com/workflow4metabolomics/tools-metabolomics>. See Delporte et al (2025) <doi:10.1002/cpz1.70095> for more details.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 30, 2026
ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Apr 18, 2026
examples
Running examples in ‘W4MRUtils-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optparse_parameters
> ### Title: optparse_parameters - parse easily the command line parameters
> ##
...[truncated]...
boolean",
+ "FALSE",
+ "--a-character",
+ "FALSE",
+ "--a-list",
+ "1.5,2,3",
+ "--a-char-list",
+ "1.5,2,3",
+ "--a-int-list",
+ "1.5,2,3"
+ )
+ )
Usage: %prog [options]
NA: error: "FALSE" is not a valid option
examples
Running examples in ‘W4MRUtils-Ex.R’ failed The error most likely occurred in: > ### Name: optparse_parameters > ### Title: optparse_parameters - parse easily the command line parameters > ### Aliases: optparse_parameters > > ### ** Examples > > ...[truncated]... boolean", + "FALSE", + "--a-character", + "FALSE", + "--a-list", + "1.5,2,3", + "--a-char-list", + "1.5,2,3", + "--a-int-list", + "1.5,2,3" + ) + ) Usage: %prog [options] NA: error: "FALSE" is not a valid option
examples
Running examples in ‘W4MRUtils-Ex.R’ failed The error most likely occurred in: > ### Name: optparse_parameters > ### Title: optparse_parameters - parse easily the command line parameters > ### Aliases: optparse_parameters > > ### ** Examples > > ...[truncated]... boolean", + "FALSE", + "--a-character", + "FALSE", + "--a-list", + "1.5,2,3", + "--a-char-list", + "1.5,2,3", + "--a-int-list", + "1.5,2,3" + ) + ) Usage: %prog [options] NA: error: "FALSE" is not a valid option
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Code
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