Each of the provided template Rmd setups from vitae
do this. The current output below is from the vitae::hyndman
template.
It looks like it might be the UTF-8 error as the bibtex file does use french accents, and opening the .bib file in notepad++ does show it to be encoded as ANSI. I'm not well versed with reading LaTeX logs, however.
Any advice on correcting this? I can provde any other requested files. As noted my (only) latex install is tinytex and I have tried reinstalling it to see if that corrects this.
My session info:
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 bookdown_0.16 crayon_1.3.4 assertthat_0.2.1 digest_0.6.23 dplyr_0.8.3
[7] R6_2.4.1 magrittr_1.5 evaluate_0.14 pillar_1.4.2 blogdown_0.17 rlang_0.4.2
[13] rstudioapi_0.10 rmarkdown_1.18 tools_3.6.1 glue_1.3.1 purrr_0.3.3 tinytex_0.17
[19] xfun_0.11 yaml_2.2.0 compiler_3.6.1 pkgconfig_2.0.3 htmltools_0.4.0 vitae_0.2.0
[25] tidyselect_0.2.5 knitr_1.26 tibble_2.1.3
My markdown log:
processing file: test.Rmd
|........ | 11%
inline R code fragments
|................ | 22%
label: setup (with options)
List of 1
$ include: logi FALSE
|....................... | 33%
ordinary text without R code
|............................... | 44%
label: unnamed-chunk-1
|....................................... | 56%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-2
|...................................................... | 78%
ordinary text without R code
|.............................................................. | 89%
label: unnamed-chunk-3
Writing 12 Bibtex entries ... OK
Results written to file 'curie.bib'
|......................................................................| 100%
ordinary text without R code
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.tex --self-contained --table-of-contents --toc-depth 2 --template "C:\Users\Brandon\Documents\R\win-library\3.6\vitae\rmarkdown\templates\hyndman\resources\hyndmantemplate.tex" --number-sections --highlight-style tango --pdf-engine pdflatex --biblatex --lua-filter "C:/Users/Brandon/Documents/R/win-library/3.6/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter "C:/Users/Brandon/Documents/R/win-library/3.6/rmarkdown/rmd/lua/latex-div.lua" --wrap preserve --variable tables=yes --standalone --include-in-header "C:\Users\Brandon\AppData\Local\Temp\RtmpgjpeHg\cv-header43e01a7a18fc.tex"
output file: test.knit.md
INFO - This is Biber 2.13
INFO - Logfile is 'test.blg'
INFO - Reading 'test.bcf'
INFO - Found 12 citekeys in bib section 0
INFO - Processing section 0
INFO - Globbing data source 'curie.bib'
INFO - Globbed data source 'curie.bib' to curie.bib
INFO - Looking for bibtex format file 'curie.bib' for section 0
Can't decode ill-formed UTF-8 octet sequence <E9> at C:\Users\Brandon\AppData\Local\Temp\par-4272616e646f6e\cache-b43718b0be759cc5a59e3532d115b4e299925ade\inc\lib/File/Slurper.pm line 63.
Error: Failed to build the bibliography via biber
In addition: Warning message:
In RefManageR::as.BibEntry(.) :
rownames of data.frame not meaningful for creating keys
Execution halted
Warning message:
Package biblatex Warning: '\DeclareSortingScheme' is deprecated.
(biblatex) Please use '\DeclareSortingTemplate'.
LaTeX Warning: Empty bibliography on input line 289.
LaTeX Warning: Citation '1' undefined on input line 302.
LaTeX Warning: Citation '2' undefined on input line 302.
LaTeX Warning: Citation '3' undefined on input line 302.
LaTeX Warning: Citation '4' undefined on input line 302.
LaTeX Warning: Citation '5' undefined on input line 302.
LaTeX Warning: Citation '6' undefined on input line 302.
LaTeX Warning: Citation '7' undefined on input line 302.
LaTeX Warning: Citation '8' undefined on input line 302.
LaTeX Warning: Citation '9' undefined on input line 302.
LaTeX Warning: Citation '10' undefined on input line 302.
LaTeX Warning: Citation '11' undefined on input line 302.
LaTeX Warning: Citation '12' undefined on input line 302.
Package rerunfilecheck Warning: File `test.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfile [... truncated]
My LaTeX log file is here.
Just to be certain:
This error is produced on each of the example templates files included by the vitae
package. More on this can be found on the github page for vitae
here.
I am producing this error without modifying the templates.