PDF package man building by R CMD Rd2pdf doesn't grab <name>-package.Rd help file

Package development
, ,
1

After building an R package using devtools and roxygen2 in RStudio, I often try to build the pdf package manual (using R CMD Rd2pdf with package tinytex installed), essentially an alphabetical listing of individual help pages. However, this almost always fails to include the <pkgname>-package.Rd documentation file for the whole package in the resulting pdf document. (It should appear as the first 'entry' of the doc.)

Example:

  1. In RStudio, select File Menu > New Project... > New Directory > New Package.

  2. Choose a name in 'Package name' field, and a path for the new package in 'Create project as subdirectory of:' field. Check 'Open in new session', and click 'Create Project'. I named my project 'myThemes'.

  3. In Tools Menu > Project Options > Build Tools, check 'Generate documentation with Roxygen', and select all the features in the 'Configure...' Roxygen options dialog.

  4. Delete the files R/hello.R, man/hello.Rd, and NAMESPACE files in the project. I did this through the Files pane.

  5. Edit the DESCRIPTION file as follows:

Package: myThemes
Type: Package
Title: Themes for ggplot
Version: 0.0.1
Authors@R: c(
    person(
      "Jane", "Doe",
      email = "jane@example.com",
      role = c("aut", "cre")
    )
  )
Description: Supplemental themes for use in ggplot.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: grid, ggplot2
ImportFrom: 
    grid unit
    ggplot2 element_line element_rect element_text theme theme_bw
Config/Needs/roxygen: list(markdown = TRUE) 
RoxygenNote: 7.3.2
  1. Create the following R/myThemes-package.R file:
#' @name
#' myThemes-package
#'
#' @title
#' Themes for ggplot
#'
#' @aliases
#' myThemes myThemes-package
#'
#' @description
#' Supplemental themes for use in ggplot.
#'
#' @references
#' Wickham, Hadley (July 2010). "ggplot2: Elegant Graphics for Data Analysis". Journal of
#' Statistical Software. 35 (1).
#'
#' Wickham, H. (2016). \emph{ggplot2: Elegant Graphics for Data Analysis, 2nd ed}.
#' Springer-Verlag, New York. ISBN 978-3-319-24277-4
#'
#' "Extending ggplot2" vignette
#' (\code{https://cran.r-project.org/web/packages/ggplot2/vignettes/extending-ggplot2.html})
#'
#' @seealso \code{\link[ggplot2]{theme}}
#'
#' @importFrom ggplot2 element_line element_rect element_text theme theme_bw
#' @importFrom grid unit
#'
#' @keywords internal
"_PACKAGE"
  1. Create the following R/theme_min.R file:
#' @name
#' theme_min
#'
#' @aliases
#' theme_min
#'
#' @title
#' A customized ggplot theme.
#'
#' @description
#' A customized ggplot theme, based on 'ggplot2'::\code{theme_bw}.
#'
#' @details
#' This is a custom 'ggplot2'::\code{theme}.  Its main features include center aligning of all
#' labels, a lightening of plot backgrounds, and lightening of grid lines.  Its main design goal
#' is to maximize the data to ink ratio.
#'
#' @usage
#' theme_min(base_size = 11, base_family = "", completeQ = FALSE)
#'
#' @param base_size
#' base font size
#'
#' @param base_family
#' base font family
#'
#' @param completeQ
#' logical: provides the explicit \code{complete} argument to \code{theme}.  This may be helpful
#' when using other packages which use 'ggplot2'.
#'
#' @return
#' The function returns a list of theme parameters, but is normally called for its side effect
#' of setting the theme of a ggplot object.
#'
#' @seealso 'ggplot2'::\code{theme_bw}
#'
#' @examples
#' \dontrun{theme_min()}

#' @export
theme_min <- function(base_size = 11, base_family = "", completeQ = FALSE)  {

  ggplot2::theme_bw(base_size = base_size, base_family = base_family) +

    ggplot2::theme(
        panel.grid.major   = ggplot2::element_line(colour = "grey90"),
        panel.grid.minor   = ggplot2::element_line(colour = "grey96", size = 0.25),
        panel.spacing      = grid::unit(0, "lines"),
        legend.title.align = 0.5,
        legend.key         = ggplot2::element_rect(fill = 0, colour = "white"),
        legend.position    = 'right',
        strip.background   = ggplot2::element_rect(fill = 0, colour = "grey40"),
        strip.text.x       = ggplot2::element_text(hjust = 0.5, color = "black", size = 12),
        strip.text.y       = ggplot2::element_text(hjust = 0.5, color = "black", size = 12),
        plot.subtitle      = ggplot2::element_text(hjust = 0.5),
        plot.title         = ggplot2::element_text(hjust = 0.5),
        complete           = completeQ )
}

  1. At this point, running devtools::check() at the R console of the project resulted in only one note, regarding the presence of a .DS_Store file, an artifact of the Macintosh operating system. This note can later be addressed via the .Rbuildignore file. Of importance is that two .Rd files now exist in the 'man/' directory, corresponding to the two .R files in 'R/'.

  2. Run system(paste(shQuote(file.path(R.home("bin"), "R")), "CMD", "Rd2pdf", shQuote(getwd()))) at the R console of the project. The R console yields the following (forgive the LaTeX mess):

myThemes> system(paste(shQuote(file.path(R.home("bin"), "R")), "CMD", "Rd2pdf", shQuote(getwd())))
Hmm ... looks like a package
Converting Rd files to LaTeX 
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2024) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2024-06-01> patch level 2
L3 programming layer <2024-09-10>
(./Rd2.tex
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/book.cls
Document Class: book 2024/02/08 v1.4n Standard LaTeX document class
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/ifthen.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/iftex/iftex.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/longtable.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/bm.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/alltt.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/verbatim.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/url/url.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/textcomp.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amstext.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amsfonts.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amssymb.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/eucal.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/fontenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/times.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/color.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-def/pdftex.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hyperref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hycolor/hycolor.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/nameref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/refcount/refcount.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/stringenc/stringenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/pd1enc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/intcalc/intcalc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/puenc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bitset/bitset.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hpdftex.def (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file Rd2.idx
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file Rd2.aux.
No file Rd2.toc.
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsa.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsb.fd)
[1{/Users/<name>/Library/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pdftex.map}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/base/8r.enc}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}]
No file Rd2.ind.

[2] (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )</Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (2 pages, 64006 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.17 [TeX Live 2024] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (1 entries accepted, 0 rejected).
Sorting entries...done (0 comparisons).
Generating output file Rd2.ind....done (5 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2024) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2024-06-01> patch level 2
L3 programming layer <2024-09-10>
(./Rd2.tex
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/book.cls
Document Class: book 2024/02/08 v1.4n Standard LaTeX document class
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/ifthen.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/iftex/iftex.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/longtable.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/bm.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/alltt.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/verbatim.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/url/url.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/textcomp.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amstext.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amsfonts.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amssymb.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/eucal.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/fontenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/times.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/color.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-def/pdftex.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hyperref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hycolor/hycolor.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/nameref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/refcount/refcount.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/stringenc/stringenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/pd1enc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/intcalc/intcalc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/puenc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bitset/bitset.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hpdftex.def (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file Rd2.idx
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.aux) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.out) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.out) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.toc (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsa.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsb.fd)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
[1{/Users/<name>/Library/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pdftex.map}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/base/8r.enc}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}] (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.ind
[2]

[3]) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )</Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (3 pages, 64613 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.17 [TeX Live 2024] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (1 entries accepted, 0 rejected).
Sorting entries...done (0 comparisons).
Generating output file Rd2.ind....done (5 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2024) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2024-06-01> patch level 2
L3 programming layer <2024-09-10>
(./Rd2.tex
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/book.cls
Document Class: book 2024/02/08 v1.4n Standard LaTeX document class
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/ifthen.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/iftex/iftex.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/longtable.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/bm.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/alltt.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/tools/verbatim.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/url/url.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/textcomp.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amstext.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amsfonts.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/amssymb.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/eucal.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/fontenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/times.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/color.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics-def/pdftex.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hyperref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hycolor/hycolor.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/nameref.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/refcount/refcount.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/stringenc/stringenc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/pd1enc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/intcalc/intcalc.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/puenc.def) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bitset/bitset.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/hyperref/hpdftex.def (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/Users/<name>/Library/TinyTeX/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file Rd2.idx
(/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.aux) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.out) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.out) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.toc (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsa.fd) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsb.fd)) (/Users/<name>/Library/TinyTeX/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
[1{/Users/<name>/Library/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pdftex.map}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/base/8r.enc}{/Users/<name>/Library/TinyTeX/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}] (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.ind
[2]

[3]) (/Users/<name>/<path>/myThemes/.Rd2pdf51197/Rd2.aux) )</Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></Users/<name>/Library/TinyTeX/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (3 pages, 65071 bytes).
Transcript written on Rd2.log.
Saving output to ‘myThemes.pdf’ ...
Done
myThemes>
  1. The resulting pdf manual file is attached. Note its building did not grab the man/myThemes-package.Rd file.

myThemes.pdf (63.5 KB)

I am somewhat suspicious of the fact that there is a temp file called Rd2.tex (with no known filename prepended) generated, but otherwise have no idea why this happens. Any guidance welcome.

RStudio 2024.12.0+467 "Kousa Dogwood" 
Release (cf37a3e5488c937207f992226d255be71f5e3f41, 2024-12-11) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) 
AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2024.12.0+467 
Chrome/126.0.6478.234 Electron/31.7.6 Safari/537.36, 
Quarto 1.6.40 (/Applications/quarto/bin/quarto)

myThemes> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.4.2    tools_4.4.2       rstudioapi_0.17.1 <private>_0.0.2     tinytex_0.54     
 [6] extrafont_0.19    extrafontdb_1.0   xfun_0.50         xtable_1.8-4      Rttf2pt1_1.3.12  
myThemes>