Unable to knit the joss_article template

[llrs]

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:

1: In citation_package_arg(citation_package) :
  citation_package = 'none' was deprecated; please use 'default' instead.
2: In system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
  error in running command
Execution halted

The error seems to be on:

rticles/R/joss_article.R

Line 34 in 3340e40

citation_package = "none",

Also noted that this format is not tested on test/testit/test-formats.R

Session info

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Madrid               
 date     2021-04-21                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 audio         0.1-7   2020-03-09 [1] CRAN (R 3.6.3)
 beepr       * 1.3     2018-06-04 [1] CRAN (R 3.6.0)
 cachem        1.0.4   2021-02-13 [1] CRAN (R 3.6.3)
 callr         3.6.0   2021-03-28 [1] CRAN (R 3.6.3)
 cli           2.4.0   2021-04-05 [1] CRAN (R 3.6.3)
 covr        * 3.5.1   2020-09-16 [1] CRAN (R 3.6.3)
 crayon        1.4.1   2021-02-08 [1] CRAN (R 3.6.3)
 cyclocomp   * 1.1.0   2016-09-10 [1] CRAN (R 3.6.0)
 desc          1.3.0   2021-03-05 [1] CRAN (R 3.6.3)
 devtools    * 2.4.0   2021-04-07 [1] CRAN (R 3.6.3)
 digest        0.6.27  2020-10-24 [1] CRAN (R 3.6.3)
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 3.6.3)
 evaluate      0.14    2019-05-28 [1] CRAN (R 3.6.0)
 fastmap       1.1.0   2021-01-25 [1] CRAN (R 3.6.3)
 fs            1.5.0   2020-07-31 [1] CRAN (R 3.6.3)
 glue          1.4.2   2020-08-27 [1] CRAN (R 3.6.3)
 htmltools     0.5.1.1 2021-01-22 [1] CRAN (R 3.6.3)
 knitr         1.32    2021-04-14 [1] CRAN (R 3.6.3)
 lazyeval      0.2.2   2019-03-15 [1] CRAN (R 3.6.0)
 lifecycle     1.0.0   2021-02-15 [1] CRAN (R 3.6.3)
 magrittr      2.0.1   2020-11-17 [1] CRAN (R 3.6.3)
 memoise       2.0.0   2021-01-26 [1] CRAN (R 3.6.3)
 pkgbuild      1.2.0   2020-12-15 [1] CRAN (R 3.6.3)
 pkgload       1.2.1   2021-04-06 [1] CRAN (R 3.6.3)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 3.6.2)
 processx      3.5.1   2021-04-04 [1] CRAN (R 3.6.3)
 ps            1.6.0   2021-02-28 [1] CRAN (R 3.6.3)
 purrr         0.3.4   2020-04-17 [1] CRAN (R 3.6.3)
 R6            2.5.0   2020-10-28 [1] CRAN (R 3.6.3)
 rdoc        * 0.1.0   2019-05-16 [1] CRAN (R 3.6.0)
 remotes       2.3.0   2021-04-01 [1] CRAN (R 3.6.3)
 rex           1.2.0   2020-04-21 [1] CRAN (R 3.6.3)
 rlang         0.4.10  2020-12-30 [1] CRAN (R 3.6.3)
 rmarkdown     2.7     2021-02-19 [1] CRAN (R 3.6.3)
 rprojroot     2.0.2   2020-11-15 [1] CRAN (R 3.6.3)
 rticles       0.19    2021-03-04 [1] CRAN (R 3.6.3)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0)
 stringi       1.5.3   2020-09-09 [1] CRAN (R 3.6.3)
 stringr       1.4.0   2019-02-10 [1] CRAN (R 3.6.0)
 testthat    * 3.0.2   2021-02-14 [1] CRAN (R 3.6.3)
 usethis     * 2.0.1   2021-02-10 [1] CRAN (R 3.6.3)
 withr         2.4.2   2021-04-18 [1] CRAN (R 3.6.3)
 xfun          0.22    2021-03-11 [1] CRAN (R 3.6.3)
 yaml          2.2.1   2020-02-01 [1] CRAN (R 3.6.2)

[1] /home/lrevilla/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

[cderv]

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:

rticles/tests/testit/test-formats.R

Line 51 in e894ed5

test_format("joss")

[llrs]

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!!

[cderv]

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.

[llrs]

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

[cderv]

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/

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