Undefined control sequence Error in vitae::awesomecv output: when used with tinytex package #80

jooyoungseo · 2019-09-05T14:37:50Z

I cannot render an Rmd file using vitae::awesomecv() output format along with tinytex package.

Please help me with the issue using the following reproducible scripts:

tinytex:::is_tinytex()
#> [1] TRUE
options(tinytex.verbose = TRUE)

file <- rmarkdown::draft(
  "test", 
  "awesomecv", 
  "vitae",
  create_dir = TRUE,
  edit = FALSE
)

rmarkdown::render(input = file, output_format = "vitae::awesomecv")
#> processing file: test.Rmd
#> Registered S3 method overwritten by 'R.oo':
#>   method        from       
#>   throw.default R.methodsS3
#> Warning in RefManageR::as.BibEntry(.): rownames of data.frame not
#> meaningful for creating keys
#> Writing 12 Bibtex entries ...
#> OK
#> Results written to file 'curie.bib'
#> output file: test.knit.md
#> "C:/ANACON~1/Scripts/pandoc" +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.tex --table-of-contents --toc-depth 2 --template "C:\PROGRA~1\R\R-36~1.1\library\vitae\RMARKD~1\TEMPLA~1\AWESOM~1\RESOUR~1\AWESOM~1.TEX" --number-sections --highlight-style tango --pdf-engine xelatex --biblatex --lua-filter "C:/Program Files/R/R-3.6.1/library/rmarkdown/rmd/lua/pagebreak.lua" --wrap preserve --variable tables=yes --standalone --include-in-header "C:\Users\JooYoung\AppData\Local\Temp\RtmpcddSv7\cv-header28986d732d44.tex"
#> tlmgr search --file --global "/authoryear.dbx"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains authoryear.dbx
#> tlmgr search --file --global "/authoryear-comp.dbx"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains authoryear-comp.dbx
#> tlmgr search --file --global "/biblatex-dm.cfg"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains biblatex-dm.cfg
#> tlmgr search --file --global "/tikzlibrarytopaths.code.tex"
#> Trying to automatically install missing LaTeX packages...
#> tlmgr install pgf
#> tlmgr search --file --global "/authoryear.dbx"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains authoryear.dbx
#> tlmgr search --file --global "/authoryear-comp.dbx"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains authoryear-comp.dbx
#> tlmgr search --file --global "/biblatex-dm.cfg"
#> Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)): Failed
#> to find a package that contains biblatex-dm.cfg
#> tlmgr search --file --global "/tikzlibrarytopaths.code.tex"
#> ! Undefined control sequence.
#> <argument> blx@catg@bib-C:\Users 
#>                                  \JooYoung \AppData \Local \Temp \RtmpGsrLqX...
#> l.153 ...prex48f825735eea\test\curie.bib-865299.4}
#> Error: Failed to compile test.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See test.log for more info.

^{Created on 2019-09-05 by the reprex package (v0.3.0.9000)}

Session info

sessioninfo::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.1 (2019-07-05)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_United States.1252  
#>  ctype    English_United States.1252  
#>  tz       America/New_York            
#>  date     2019-09-05                  
#> 
#> - Packages --------------------------------------------------------------
#>  package     * version    date       lib
#>  assertthat    0.2.1      2019-03-21 [1]
#>  bibtex        0.4.2      2017-06-30 [1]
#>  bookdown      0.13.2     2019-09-01 [1]
#>  cli           1.1.0      2019-03-19 [1]
#>  crayon        1.3.4      2017-09-16 [1]
#>  curl          4.0        2019-07-22 [1]
#>  digest        0.6.20     2019-07-04 [1]
#>  dplyr         0.8.3.9000 2019-08-15 [1]
#>  evaluate      0.14       2019-05-28 [1]
#>  glue          1.3.1.9000 2019-08-08 [1]
#>  highr         0.8        2019-03-20 [1]
#>  htmltools     0.3.6      2017-04-28 [1]
#>  httr          1.4.1      2019-08-05 [1]
#>  jsonlite      1.6        2018-12-07 [1]
#>  knitr         1.24.4     2019-09-04 [1]
#>  lubridate     1.7.4.9000 2019-08-08 [1]
#>  magrittr      1.5        2014-11-22 [1]
#>  pillar        1.4.2      2019-06-29 [1]
#>  pkgconfig     2.0.2      2018-08-16 [1]
#>  plyr          1.8.4      2016-06-08 [1]
#>  purrr         0.3.2.9000 2019-08-09 [1]
#>  R.cache       0.13.0     2018-01-04 [1]
#>  R.methodsS3   1.7.1      2016-02-16 [1]
#>  R.oo          1.22.0     2018-04-22 [1]
#>  R.utils       2.9.0      2019-06-13 [1]
#>  R6            2.4.0      2019-02-14 [1]
#>  Rcpp          1.0.2.1    2019-08-08 [1]
#>  RefManageR    1.2.12     2019-04-03 [1]
#>  rlang         0.4.0.9002 2019-08-23 [1]
#>  rmarkdown     1.15.1     2019-09-03 [1]
#>  rvest         0.3.4      2019-08-08 [1]
#>  scholar       0.1.7      2019-08-08 [1]
#>  selectr       0.4-1      2018-04-06 [1]
#>  sessioninfo   1.1.1      2018-11-05 [1]
#>  stringi       1.4.3      2019-03-12 [1]
#>  stringr       1.4.0.9000 2019-08-08 [1]
#>  tibble      * 2.1.3      2019-06-06 [1]
#>  tidyselect    0.2.5.9000 2019-08-12 [1]
#>  tinytex       0.15.2     2019-09-03 [1]
#>  vitae       * 0.2.0      2019-09-03 [1]
#>  withr         2.1.2      2018-03-15 [1]
#>  xfun          0.9        2019-08-21 [1]
#>  xml2          1.2.2.9000 2019-08-15 [1]
#>  yaml          2.2.0      2018-07-25 [1]
#>  source                               
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (rstudio/bookdown@56166fe)    
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (tidyverse/dplyr@85faf79)     
#>  CRAN (R 3.6.1)                       
#>  Github (tidyverse/glue@7ac044a)      
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (yihui/knitr@079dc84)         
#>  Github (tidyverse/lubridate@cd82679) 
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (tidyverse/purrr@c755bb9)     
#>  CRAN (R 3.6.0)                       
#>  CRAN (R 3.6.0)                       
#>  CRAN (R 3.6.0)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (RcppCore/Rcpp@1789f09)       
#>  CRAN (R 3.6.1)                       
#>  Github (r-lib/rlang@15e799c)         
#>  Github (rstudio/rmarkdown@ff285a0)   
#>  Github (hadley/rvest@c820e48)        
#>  Github (jkeirstead/scholar@9a9e92f)  
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.0)                       
#>  Github (hadley/stringr@0b90f91)      
#>  CRAN (R 3.6.1)                       
#>  Github (tidyverse/tidyselect@4de95ee)
#>  Github (yihui/tinytex@f8e025c)       
#>  Github (ropenscilabs/vitae@f21a70b)  
#>  CRAN (R 3.6.1)                       
#>  CRAN (R 3.6.1)                       
#>  Github (r-lib/xml2@5bf8de1)          
#>  CRAN (R 3.6.0)                       
#> 
#> [1] C:/Program Files/R/R-3.6.1/library

The text was updated successfully, but these errors were encountered:

jooyoungseo · 2019-09-14T15:20:09Z

@mitchelloharawild, do you have any idea about how to address this issue?
Does it have something to do with this issue?
I can't wait to utilize this awesome package.

robjhyndman · 2019-09-15T00:12:26Z

It looks like your bib file contains windows paths and it is interpreting them as LaTeX commands. Remove the paths, or change the back slashes to forward slashes.

jooyoungseo · 2019-09-15T15:15:44Z

Thank you very much for your kind advice @robjhyndman; however, I have just used the basic awesomecv template provided by vitae.
I have not changed any path at all.
FYI, if I do not use vitae::bibliography_entries() function in an Rmd file, it does not cause any issue; in other words, on Windows, an Rmd file containing vitae::bibliography_entries() throws that issues.
Would you mind testing that for me on Windows?

achamess · 2019-09-22T03:51:35Z

I'm having similar issues. If I open up a fresh template for moderncv and run it, I get the following:

usr/local/bin/pandoc +RTS -K512m -RTS Untitled.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output Untitled.tex --table-of-contents --toc-depth 2 --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/vitae/rmarkdown/templates/moderncv/resources/moderncv.tex --number-sections --highlight-style tango --pdf-engine pdflatex --biblatex --wrap preserve --variable theme=casual --variable tables=yes --standalone --include-in-header /var/folders/gx/mfdx8g856wvdtp0dw7k8h2s80000gn/T//RtmpWUkBz4/cv-header1bae50e1532e.tex 
output file: Untitled.knit.md

tlmgr search --file --global '/authoryear.dbx'
tlmgr search --file --global '/authoryear-comp.dbx'
tlmgr search --file --global '/biblatex-dm.cfg'
tlmgr search --file --global '/Untitled.bbl'
! Undefined control sequence.
\onlynumberslink ...tl {#1}\regex_replace_all:nnN 
                                                  {[^0-9+]}{}\l_onlynumbersl...
l.191 \end{document}

Error: Failed to compile Untitled.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Untitled.log for more info.
In addition: Warning messages:
1: package 'tibble' was built under R version 3.5.2 
2: In RefManageR::as.BibEntry(.) :
  rownames of data.frame not meaningful for creating keys
3: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear.dbx
4: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear-comp.dbx
5: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains biblatex-dm.cfg
6: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains Untitled.bbl
Execution halted

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3     purrr_0.3.2     readr_1.3.1     tidyr_1.0.0     tibble_2.1.3    ggplot2_3.2.1  
 [9] tidyverse_1.2.1 vitae_0.2.0    

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5  xfun_0.9          haven_2.1.1       lattice_0.20-38   colorspace_1.4-1  generics_0.0.2    vctrs_0.2.0      
 [8] htmltools_0.3.6   yaml_2.2.0        rlang_0.4.0       R.oo_1.22.0       pillar_1.4.2      withr_2.1.2       glue_1.3.1       
[15] R.utils_2.9.0     selectr_0.4-1     readxl_1.3.1      modelr_0.1.5      plyr_1.8.4        R.cache_0.13.0    lifecycle_0.1.0  
[22] cellranger_1.1.0  munsell_0.5.0     gtable_0.3.0      rvest_0.3.4       R.methodsS3_1.7.1 evaluate_0.14     knitr_1.24       
[29] scholar_0.1.7     curl_3.3          broom_0.5.2       Rcpp_1.0.2        backports_1.1.4   scales_1.0.0      jsonlite_1.6     
[36] hms_0.5.1         digest_0.6.20     stringi_1.4.3     bibtex_0.4.2      grid_3.5.0        cli_1.1.0         tools_3.5.0      
[43] magrittr_1.5      lazyeval_0.2.2    RefManageR_1.2.12 crayon_1.3.4      pkgconfig_2.0.2   zeallot_0.1.0     xml2_1.2.2       
[50] lubridate_1.7.4   assertthat_0.2.1  rmarkdown_1.15    httr_1.4.1        rstudioapi_0.10   R6_2.4.0          nlme_3.1-141     
[57] compiler_3.5.0

mitchelloharawild · 2019-09-22T04:02:49Z

Thank you very much for your kind advice @robjhyndman; however, I have just used the basic awesomecv template provided by vitae.
I have not changed any path at all.
FYI, if I do not use vitae::bibliography_entries() function in an Rmd file, it does not cause any issue; in other words, on Windows, an Rmd file containing vitae::bibliography_entries() throws that issues.
Would you mind testing that for me on Windows?

Is this now working with the latest development version? I've just pushed a change which resolves some related issues. (586a8dd)

achamess · 2019-09-22T04:24:37Z

Still not working. I think it's related to the tlmgr package. I'm using a Mac. I think the tlmgr needs me to be root to download the templates? Awesome CV works for me, but none of the others.

This is what I'm getting

output file: test.knit.md

tlmgr search --file --global '/authoryear.dbx'
tlmgr search --file --global '/authoryear-comp.dbx'
tlmgr search --file --global '/biblatex-dm.cfg'
! Undefined control sequence.
l.87 \DeclareSortingTemplate
                            {ty}{ 

Error: Failed to compile test.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See test.log for more info.
In addition: Warning messages:
1: In RefManageR::as.BibEntry(.) :
  rownames of data.frame not meaningful for creating keys
2: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear.dbx
3: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear-comp.dbx
4: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains biblatex-dm.cfg
Execution halted

achamess · 2019-09-22T04:26:30Z

With classic CV template (no changes made, just a fresh Rmd template from the package), I get this:

output file: Untitled.knit.md

tlmgr search --file --global '/authoryear.dbx'
tlmgr search --file --global '/authoryear-comp.dbx'
tlmgr search --file --global '/biblatex-dm.cfg'
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
tlmgr search --file --global '/tikzlibraryshapes.code.tex'
tlmgr search --file --global '/tikzlibrarybackgrounds.code.tex'
tlmgr search --file --global '/tikzlibrarymindmap.code.tex'
tlmgr search --file --global '/tikzlibrarytrees.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
You don't have permission to change the installation in any way,
specifically, the directory /usr/local/texlive/2017/tlpkg/ is not writable.
Please run this program as administrator, or contact your local admin.
tlmgr: An error has occurred. See above messages. Exiting.
tlmgr update --self
tlmgr: package repository http://mirror.utexas.edu/ctan/systems/texlive/tlnet (not verified: gnupg not available)
You don't have permission to change the installation in any way,
specifically, the directory /usr/local/texlive/2017/tlpkg/ is not writable.
Please run this program as administrator, or contact your local admin.
tlmgr: An error has occurred. See above messages. Exiting.
fmtutil [ERROR]: format directory not writable: /usr/local/texlive/2017/texmf-var/web2c
tlmgr install pgf
You don't have permission to change the installation in any way,
specifically, the directory /usr/local/texlive/2017/tlpkg/ is not writable.
Please run this program as administrator, or contact your local admin.
tlmgr: An error has occurred. See above messages. Exiting.
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
! Undefined control sequence.
l.276 \DeclareSortingTemplate
                             {ty}{ 

Error: Failed to compile Untitled.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Untitled.log for more info.
In addition: Warning messages:
1: package 'tibble' was built under R version 3.5.2 
2: In RefManageR::as.BibEntry(.) :
  rownames of data.frame not meaningful for creating keys
3: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear.dbx
4: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains authoryear-comp.dbx
5: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains biblatex-dm.cfg
Execution halted

mitchelloharawild · 2019-09-22T04:28:00Z

You don't have permission to change the installation in any way,
specifically, the directory /usr/local/texlive/2017/tlpkg/ is not writable.
Please run this program as administrator, or contact your local admin.

Looks like this is a permissions issue. Can you grant the process additional privileges?

achamess · 2019-09-22T04:31:57Z

I could, but not sure where or how. Can I add a sudo somewhere?

mitchelloharawild · 2019-09-22T04:51:45Z

The package trying to be installed is pgf, so try installing that manually from the terminal with
sudo tlmgr install pgf.

achamess · 2019-09-22T04:58:11Z

Thanks. I did this. It was already present. I went even further and modified the directory where tlmgr puts packages so that it was writable. It changed the error message slightly now:

output file: Untitled.knit.md

tlmgr search --file --global '/authoryear.dbx'
tlmgr search --file --global '/authoryear-comp.dbx'
tlmgr search --file --global '/biblatex-dm.cfg'
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirrors.rit.edu/CTAN/systems/texlive/tlnet (not verified: gpg unavailable)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/authoryear.dbx'
tlmgr search --file --global '/authoryear-comp.dbx'
tlmgr search --file --global '/biblatex-dm.cfg'
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'

Why is it searching for those files through tlmgr?

achamess · 2019-09-22T15:45:23Z

FYI: I used the Tinytex installation and that got around most of the issues. But now I have parallel installs of LaTex on my computer. Not ideal, but works for now.

mitchelloharawild · 2019-09-23T00:06:29Z

Great, glad that worked out for you.
Closing as we recommend using tinytex for those having trouble managing their own LaTeX installation.

mitchelloharawild closed this as completed Sep 23, 2019

jooyoungseo mentioned this issue Sep 23, 2019

tinytex does miss some LaTeX packages for vitae package output rendering. rstudio/tinytex#142

Closed

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Undefined control sequence Error in vitae::awesomecv output: when used with tinytex package #80

Undefined control sequence Error in vitae::awesomecv output: when used with tinytex package #80

jooyoungseo commented Sep 5, 2019

jooyoungseo commented Sep 14, 2019

robjhyndman commented Sep 15, 2019 •

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mitchelloharawild commented Sep 23, 2019

Undefined control sequence Error in vitae::awesomecv output: when used with tinytex package #80

Undefined control sequence Error in vitae::awesomecv output: when used with tinytex package #80

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jooyoungseo commented Sep 5, 2019

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robjhyndman commented Sep 15, 2019 • edited Loading

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robjhyndman commented Sep 15, 2019 •

edited

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