CRAN Rcpp dependency fixes

[dan-knight]

Description

This PR addresses time-sensitive CRAN requirements (detailed in #192). R CMD check passes locally and on CRAN (including Winbuilder).

Winbuilder Results

* using log directory 'd:/RCompile/CRANguest/R-devel/BoutrosLab.plotting.general.Rcheck'
* using R Under development (unstable) (2024-09-30 r87204 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'BoutrosLab.plotting.general/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BoutrosLab.plotting.general' version '7.1.2'
* checking CRAN incoming feasibility ... [11s] OK
* 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 'BoutrosLab.plotting.general' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... [28s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'create.scatterplot.Rd':
  \examples lines wider than 100 characters:
         # "s" connects points with the vertical segment first. "S" connects points with the horizontal segment first.

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  legend.grob.Rd: draw.key
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [10s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'test_plotting_functions.R'
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31s] OK
* checking PDF version of manual ... [27s] OK
* checking HTML version of manual ... [14s] OK
* DONE
Status: 2 NOTEs

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.

• This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the NEWS under the next release version or unreleased, and updated the date. I have also updated the version number in DESCRIPTION according to semantic versioning rules.

• Both R CMD build and R CMD check run successfully.

Testing Results

Case 1

# input code

Case 2

# input code

[whelena]

I'm assuming the CICD base warnings are unrelated to this PR and can be ignored?

[jarbet]

LGTM. Just need to fix the R CMD CHECK warnings?
https://github.com/uclahs-cds/package-BoutrosLab-plotting-general/actions/runs/10743054813/job/29796997774

[dan-knight]

LGTM. Just need to fix the R CMD CHECK warnings?

This one is a false positive in our CI/CD workflow that is unrelated to this change. It doesn't show up in CRAN's checks, so in the interest of submitting to CRAN, I think we can push this through as long as I make it a priority to fix our CI/CD issue after.