PDF version of manual without hyperrefs or index

Found the following significant warnings:
  WARNING: installation-time patches will not be applied, could not get the patches index
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/slga/slga.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.