3: LaTeX Warning: You have requested document class `pinp',
but the document class provides `widetext'.
LaTeX Warning: You have requested document class `pinp',
but the document class provides `pnasresearcharticle'.
and indeed
edd@rob:~/git/pinp(master)$ grep Provides inst/rmarkdown/templates/pdf/skeleton/pinp.cls
\ProvidesClass{pinp}[2017-Sep-12, based on pnas-new 28/02/2015, v1.2]
\ProvidesPackage{widetext}
\ProvidesPackage{pnasresearcharticle}[2016/02/28 v1.2 PNAS two column research article style]
edd@rob:~/git/pinp(master)$
Compiling a pinp document I see
and indeed
The second and third need to be commented out.