Fix conditional usage of suggested packages (fs, ggalign)

[Copilot]

CRAN check failures due to unconditional usage of packages in Suggests. Per Writing R Extensions, suggested packages must be used conditionally with requireNamespace() checks.

Changes

• R/03-accessors.R: Wrapped fs::is_file() calls with requireNamespace("fs", quietly = TRUE) checks
• R/02-pipeline.R: Added conditional checks for all fs:: functions with base R fallbacks:
  • fs::path_temp() → tempdir()
  • fs::dir_create() → dir.create(..., recursive = TRUE, showWarnings = FALSE)
  • fs::path() → file.path() with paste0() for extensions
  • Removed fs from rlang::check_installed() since fallbacks are provided
• R/04-show.R: Wrapped ggalign::align_plots() with conditional check, falling back to list(plots = valid_plots) when unavailable

Example

Before:

fs::dir_create(md_path)  # Error if fs not installed

After:

if (requireNamespace("fs", quietly = TRUE)) {
  fs::dir_create(md_path)
} else {
  dir.create(md_path, showWarnings = FALSE, recursive = TRUE)
}

Both ggalign::alignpatches objects and the fallback list provide consistent $plots accessor for tests.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>package check issue</issue_title>
<issue_description>Packages in Suggests should be used conditionally: see 'Writing R Extensions'

   if (requireNamespace("rgl", quietly = TRUE)) {
      rgl::plot3d(...)
   } else {
      ## do something else not involving rgl.
   }

Current check issue:

* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/bregr.Rcheck’
* using R Under development (unstable) (2026-01-16 r89305)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bregr/DESCRIPTION’ ... OK
* this is package ‘bregr’ version ‘1.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘qs’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bregr’ can be installed ... [24s/31s] 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ... [39s/43s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bregr-Ex.R’ failed
The error most likely occurred in:

> ### Name: accessors
> ### Title: Accessor functions for 'breg' objects
> ### Aliases: accessors br_get_data br_get_y br_get_x br_get_n_x br_get_x2
> ###   br_get_n_x2 br_get_group_by br_get_config br_get_models br_get_model
> ###   br_get_model_names br_rename_models br_get_results
> 
> ### ** Examples
> 
> m <- br_pipeline(mtcars,
+   y = "mpg",
+   x = colnames(mtcars)[2:4],
+   x2 = "vs",
+   method = "gaussian"
+ )
Error in loadNamespace(x) : there is no package called ‘fs’
Calls: br_pipeline ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [129s/154s]
 [130s/154s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bregr)
  Welcome to 'bregr' package!
  =======================================================================
  You are using bregr version 1.3.1
  
  Project home : https://github.com/WangLabCSU/bregr
  Documentation: https://wanglabcsu.github.io/bregr/
  Cite as      : https://doi.org/10.1002/mdr2.70028
    Wang, S., Peng, Y., Shu, C., Wang, C., Yang, Y., Zhao, Y., Cui, Y., Hu, D. and Zhou, J.-G. (2025),
    bregr: An R Package for Streamlined Batch Processing and Visualization of Biomedical Regression Models. Med Research.
  =======================================================================
                   
  > 
  > test_check("bregr")
  filtered variables: "x2" and "x3"
  filtered variables: "x2"
  Pre-filtering...

</details>



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- Fixes WangLabCSU/bregr#61

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