fix: stabilize CI by trimming fragile check dependencies

[sghng]

Summary

• install only hard dependencies in CI
• keep the vignette build working by explicitly installing knitr and rmarkdown
• remove deprecated Rcpp:::LdFlags() usage from the package Makevars files

Why

Recent failures were not caused by GDINA test regressions. CI was failing because:

• optional suggested packages could fail during installation on old R versions
• R-devel warns on the deprecated Rcpp:::LdFlags() pattern
• the package build still needs knitr and rmarkdown because the repo includes a vignette

Validation

• R CMD INSTALL .
• _R_CHECK_FORCE_SUGGESTS_=false R CMD check . --no-manual
• local check reaches Running 'testthat.R' OK

[sghng]

@Wenchao-Ma Done! The CI checks are now fixed.

[Wenchao-Ma]

Thank you for fixing this!