Unable to Compile Bookdown Source for "Efficient R Programming" into PDF - r

Question

I am trying to compile the PDF version of Efficient R Programming using RStudio on my Windows 7 machine. Using the instructions here I was able to compile the HTML version, but the code for the PDF version fails. After running the code below (which seems to work at first), I got the warning messages below:
## For pdf
bookdown::render_book("index.Rmd", output_format = bookdown::pdf_book())
output file: _main.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS _main.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output _main.tex --table-of-contents --toc-depth 2 --template "C:\R\R-3.4.4\library\rmarkdown\rmd\latex\default-1.17.0.2.tex" --number-sections --highlight-style tango --latex-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes" --variable tables=yes --standalone --filter pandoc-citeproc
Error: Failed to compile _main.tex.
In addition: Warning messages:
1: In file.remove("voc_voyages.xlsx") :
cannot remove file 'voc_voyages.xlsx', reason 'No such file or directory'
2: In connection_release(conn#ptr) :
There are 1 result in use. The connection will be released when they are closed
3: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'benchmarkme'
4: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'benchmarkme' from package DESCRIPTION file
5: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'bookdown'
6: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'bookdown' from package DESCRIPTION file
7: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'efficient'
8: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'efficient' from package DESCRIPTION file
9: running command '"pdflatex" -halt-on-error -interaction=batchmode "_main.tex"' had status 127
Please delete _main.Rmd after you finish debugging the error.
I found this discussion of MikTeX vs tinytex. I then installed tinytex and now get this (slightly different) error:
## For pdf
bookdown::render_book("index.Rmd", output_format = bookdown::pdf_book())
label: unnamed-chunk-235
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label: unnamed-chunk-236
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label: unnamed-chunk-237 (with options)
List of 1
$ message: logi FALSE
Attaching package: 'Matrix'
The following object is masked from 'package:tidyr':
expand
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label: unnamed-chunk-239 (with options)
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$ type : chr "rmdnote"
$ engine: chr "block"
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$ results: chr "hide"
$ indent : chr " "
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label: 7-4 (with options)
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$ echo : logi FALSE
$ out.width: chr "100%"
$ fig.cap : chr "Code profiling of the optimised code."
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$ eval: logi FALSE
$ echo: logi FALSE
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label: unnamed-chunk-242 (with options)
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$ echo: language 1:2
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$ type : chr "rmdnote"
$ engine: chr "block"
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label: unnamed-chunk-244 (with options)
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$ eval: logi FALSE
$ tidy: logi FALSE
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$ eval: logi FALSE
$ echo: language c(1, 3)
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$ eval: logi FALSE
$ echo: language 2:3
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$ eval: logi FALSE
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$ eval: logi FALSE
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$ type : chr "rmdtip"
$ engine: chr "block"
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$ echo: logi FALSE
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label: unnamed-chunk-252 (with options)
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$ results: chr "hide"
|.................................................. | 76%
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label: 7-5 (with options)
List of 7
$ echo : logi FALSE
$ fig.cap : chr "Downloads per day from the RStudio CRAN mirror of packages that provide R interfaces to other languages."
$ warning : logi FALSE
$ fig.width : num 6
$ fig.height: num 4
$ out.width : chr "70%"
$ fig.align : chr "center"
inline R code fragments
|.................................................. | 77%
label: test_cpp (with options)
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$ eval : logi FALSE
$ results: chr "hide"
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label: unnamed-chunk-253
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$ eval : logi FALSE
$ tidy : logi FALSE
$ engine: chr "Rcpp"
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$ tidy: logi FALSE
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$ type : chr "rmdnote"
$ engine: chr "block"
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$ echo: logi FALSE
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label: unnamed-chunk-259 (with options)
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$ eval : logi FALSE
$ engine: chr "Rcpp"
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$ eval : logi FALSE
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$ eval : logi FALSE
$ engine: chr "Rcpp"
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$ type : chr "rmdnote"
$ engine: chr "block"
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label: unnamed-chunk-263 (with options)
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$ engine: chr "Rcpp"
Building shared library for Rcpp code chunk...
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$ eval : logi FALSE
$ engine: chr "Rcpp"
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$ eval : logi FALSE
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$ engine: chr "Rcpp"
$ indent: chr " "
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List of 3
$ cache: logi TRUE
$ echo : language -1
$ eval : logi FALSE
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label: 7-6 (with options)
List of 7
$ fig.width : num 6
$ fig.height: num 4
$ echo : num 2
$ fig.cap : chr "Comparison of mean functions."
$ cache : logi TRUE
$ fig.pos : chr "t"
$ out.width : chr "70%"
|..................................................... | 82%
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label: unnamed-chunk-271 (with options)
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$ eval : logi FALSE
$ tidy : logi FALSE
$ engine: chr "Rcpp"
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$ indent: chr " "
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$ results: chr "hide"
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$ fig.cap : chr "Three DIMM slots on a computer motherboard used for increasing the amount of available RAM. Credit: Wikimedia.org"
$ echo : logi FALSE
$ out.width: chr "100%"
|........................................................ | 86%
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$ fig.cap: chr "A standard 2.5\" hard drive, found in most laptops. Credit: https://en.wikipedia.org/wiki/Hard\\_disk\\_drive"
$ echo : logi FALSE
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$ results: chr "hide"
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$ echo : logi FALSE
$ fig.width : num 6
$ fig.height: num 4
$ fig.cap : chr "CPU clock speed. The data for this figure was collected from web-forum and wikipedia. It is intended to indicat"| __truncated__
$ out.width : chr "70%"
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|......................................................... | 88%
label: 8-4 (with options)
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$ echo : logi FALSE
$ fig.width : num 6
$ fig.height: num 4
$ fig.cap : chr "CPU benchmarks from the R package, **benchmarkme**. Each point represents an individual CPU result."
$ fig.keep : chr "last"
$ out.width : chr "70%"
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$ include: logi FALSE
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$ type : chr "rmdwarning"
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$ results: chr "hide"
$ message: logi FALSE
Attaching package: 'lubridate'
The following objects are masked from 'package:data.table':
hour, isoweek, mday, minute, month, quarter, second, wday,
week, yday, year
The following object is masked from 'package:base':
date
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$ echo : language 2:5
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$ fig.cap : chr "The Git tab in RStudio"
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tweaking fortunes
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output file: _main.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS _main.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output _main.tex --table-of-contents --toc-depth 2 --template "C:\R\R-3.4.4\library\rmarkdown\rmd\latex\default-1.17.0.2.tex" --number-sections --highlight-style tango --latex-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes" --variable tables=yes --standalone --filter pandoc-citeproc
Output created: _book/_main.pdf
Error in tools::file_path_as_absolute(output_file) :
file '_book/_main.pdf' does not exist
In addition: Warning messages:
1: In file.remove("voc_voyages.xlsx") :
cannot remove file 'voc_voyages.xlsx', reason 'No such file or directory'
2: In connection_release(conn#ptr) :
There are 1 result in use. The connection will be released when they are closed
3: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'benchmarkme'
4: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'benchmarkme' from package DESCRIPTION file
5: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'bookdown'
6: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'bookdown' from package DESCRIPTION file
7: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
no date field in DESCRIPTION file of package 'efficient'
8: In citation(pkg, auto = if (pkg == "base") NULL else TRUE) :
could not determine year for 'efficient' from package DESCRIPTION file
9: running command '"pdflatex" -halt-on-error -interaction=batchmode "_main.tex"' had status 1
10: In readLines(logfile) : incomplete final line found on '_main.log'
Please delete _main.Rmd after you finish debugging the error.
Based on the comment from #jaySf below, I ran this code, but still got the same error:
remove.packages("rmarkdown")
install.packages("devtools")
library(devtools)
install_version("rmarkdown", version = "1.8")
## For pdf
bookdown::render_book("index.Rmd", output_format = bookdown::pdf_book())
Any suggestions would be appreciated. Thanks.