Closed llrs closed 3 years ago
Thanks @llrs !
I pushed a fix to remove the warning.
About the system2()
error, I can't reproduce with the default template. I don't know where it comes from.
Do you have a traceback for this error ?
Also noted that this format is not tested on test/testit/test-formats.R
It is tested here: https://github.com/rstudio/rticles/blob/e894ed5f44caeef4a333fedaef4a5df7e60884d6/tests/testit/test-formats.R#L51
Sorry my mistake. This might not be related to rticles and I also missed the joss reference on the file.
When I click the Knitr button I see this:
processing file: Untitled.Rmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
/usr/lib/rstudio/bin/pandoc/pandoc +RTS -K512m -RTS Untitled.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output Untitled.tex --lua-filter /home/lrevilla/R/x86_64-pc-linux-gnu-library/3.6/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/lrevilla/R/x86_64-pc-linux-gnu-library/3.6/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --template /home/lrevilla/R/x86_64-pc-linux-gnu-library/3.6/rticles/rmarkdown/templates/joss/resources/template.tex --highlight-style tango --pdf-engine pdflatex -V logo_path=/home/lrevilla/R/x86_64-pc-linux-gnu-library/3.6/rticles/rmarkdown/templates/joss/resources/JOSS-logo.png -V 'journal_name=Journal of Open Source Software' -V graphics=true --citeproc
output file: Untitled.knit.md
! LaTeX Error: File `biblatex.sty' not found.
! Emergency stop.
<read *>
Error: LaTeX failed to compile Untitled.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Untitled.log for more info.
In addition: Warning message:
In citation_package_arg(citation_package) :
citation_package = 'none' was deprecated; please use 'default' instead.
Execution halted
However if I use
knitr::knitr("Untitled/Untitled.Rmd") the untitled.md (joss article) file can be created without errors.
I had to install texlive-xetex texlive-bibtex-extra biber
and then the knitr button on rstudio worked! Thanks!!
I had to install texlive-xetex texlive-bibtex-extra biber and then the knitr button on rstudio worked! Thanks!!
Oh it seems you are using texlive so tinytex should have installed the missing packages automatically. Unless your user don't have writing right to the directory.
When you have this type of error ! LaTeX Error: File
biblatex.sty' not found.`, you can find the missing package using
> tinytex::parse_packages(text = "! LaTeX Error: File `biblatex.sty' not found.")
tlmgr search --file --global "/biblatex.sty"
[1] "biblatex"
or
> tinytex::parse_packages(file= "biblatex.sty")
tlmgr search --file --global "/biblatex.sty"
[1] "biblatex
Then with TeX Live and tinytex, you can install with tinytex::tlmgr_install()
.
Note that tinytex::parse_install
will do both: detection then installation.
I tried with tinytex::parse_packages but I got the following message:
tlmgr search --file --global '/biblatex.sty'
TLPDB: not a directory, not loading: /home/lrevilla/texmf
tlmgr: running in usermode, did you call `tlmgr init-usertree'?
Warning messages:
1: In system2("tlmgr", args, ...) :
running command ''tlmgr' search --file --global '/biblatex.sty'' had status 2
2: In parse_packages(...) :
Failed to find a package that contains biblatex.sty
After calling tlmgr init-usertree
on a different terminal (not Rstudio terminal):
tlmgr search --file --global '/biblatex.sty'
/usr/bin/tlmgr: unexpected return value from verify_checksum: -5
Warning messages:
1: In system2("tlmgr", args, ...) :
running command ''tlmgr' search --file --global '/biblatex.sty'' had status 1
2: In parse_packages(...) :
Failed to find a package that contains biblatex.sty
Anyway thanks for the support and the quick fix of the warning
Ok I guess it does not work the same on all texlive
installation. You may be using your system installation and not a user enabled one.
It works great with TinyteX distribution though if your are interested : https://tinytex.yihui.org/
This old thread has been automatically locked. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary.
Many thanks for providing templates for journals! Quite useful as I had created my own version of .Rmd for a submission.
I just installed rticles from CRAN for an article in JOSS. However, using the template for rticles::joss_article without touching anything I get an error:
The error seems to be on: https://github.com/rstudio/rticles/blob/3340e40084f4bb7c9a336e3943afc90bb7741d7a/R/joss_article.R#L34
Also noted that this format is not tested on test/testit/test-formats.R
Session info
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