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Error in BibOptions(): could not find function "BibOptions" #60

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jooyoungseo opened this issue Jan 22, 2020 · 1 comment
Closed

Error in BibOptions(): could not find function "BibOptions" #60

jooyoungseo opened this issue Jan 22, 2020 · 1 comment
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@jooyoungseo
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citr::tidy_bib_file() function does not work properly without explicitly loading RefManageR package.

Please see the reproducible code below:

# Download test Rmd and bib files:
utils::download.file("https://jooyoungseo.com/test.Rmd", destfile = "test.Rmd")
utils::download.file("https://jooyoungseo.com/test.bib", destfile = "test.bib")

## Create tidy bib file:
citr::tidy_bib_file(
  rmd_file = "test.Rmd"
  , messy_bibliography = "test.bib"
  , file = "tidy_references.bib"
)
#> Removing 119 unneeded bibliography entries.
#> Error in BibOptions(): could not find function "BibOptions"

# Loading RefManageR
library(RefManageR)

# Create tidy bib file:
citr::tidy_bib_file(
  rmd_file = "test.Rmd"
  , messy_bibliography = "test.bib"
  , file = "tidy_references.bib"
)
#> Removing 119 unneeded bibliography entries.
#> Writing 4 Bibtex entries ... OK
#> Results written to file 'tidy_references.bib'

Created on 2020-01-21 by the reprex package (v0.3.0.9001)

Session info 
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.2 (2019-12-12)
#>  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     2020-01-21                  
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version    date       lib source                              
#>  assertthat    0.2.1      2019-03-21 [2] CRAN (R 3.6.2)                      
#>  backports     1.1.5      2019-10-02 [2] CRAN (R 3.6.1)                      
#>  bibtex        0.4.2.2    2020-01-02 [2] CRAN (R 3.6.2)                      
#>  citr          0.3.2      2020-01-09 [1] Github (crsh/citr@e09de2e)          
#>  cli           2.0.1      2020-01-08 [1] CRAN (R 3.6.2)                      
#>  crayon        1.3.4      2017-09-16 [2] CRAN (R 3.6.2)                      
#>  digest        0.6.23     2019-11-23 [2] CRAN (R 3.6.2)                      
#>  evaluate      0.14       2019-05-28 [2] CRAN (R 3.6.2)                      
#>  fansi         0.4.1      2020-01-08 [1] CRAN (R 3.6.2)                      
#>  fastmap       1.0.1      2019-10-08 [2] CRAN (R 3.6.2)                      
#>  fs            1.3.1      2019-05-06 [2] CRAN (R 3.6.2)                      
#>  glue          1.3.1      2019-03-12 [2] CRAN (R 3.6.2)                      
#>  highr         0.8        2019-03-20 [2] CRAN (R 3.6.2)                      
#>  htmltools     0.4.0.9002 2020-01-17 [1] Github (rstudio/htmltools@e07546c)  
#>  httpuv        1.5.2      2019-09-11 [2] CRAN (R 3.6.2)                      
#>  httr          1.4.1      2019-08-05 [2] CRAN (R 3.6.2)                      
#>  jsonlite      1.6        2018-12-07 [2] CRAN (R 3.6.2)                      
#>  knitr         1.27.2     2020-01-21 [1] Github (yihui/knitr@ab191b0)        
#>  later         1.0.0      2019-10-04 [2] CRAN (R 3.6.2)                      
#>  lubridate     1.7.4      2018-04-11 [2] CRAN (R 3.6.2)                      
#>  magrittr      1.5        2014-11-22 [2] CRAN (R 3.6.2)                      
#>  mime          0.8        2019-12-19 [2] CRAN (R 3.6.2)                      
#>  miniUI        0.1.1.1    2018-05-18 [2] CRAN (R 3.6.0)                      
#>  pillar        1.4.3      2019-12-20 [2] CRAN (R 3.6.2)                      
#>  pkgconfig     2.0.3      2019-09-22 [2] CRAN (R 3.6.2)                      
#>  plyr          1.8.5      2019-12-10 [2] CRAN (R 3.6.2)                      
#>  promises      1.1.0      2019-10-04 [2] CRAN (R 3.6.2)                      
#>  purrr         0.3.3      2019-10-18 [2] CRAN (R 3.6.2)                      
#>  R6            2.4.1      2019-11-12 [2] CRAN (R 3.6.2)                      
#>  Rcpp          1.0.3      2019-11-08 [2] CRAN (R 3.6.2)                      
#>  RefManageR  * 1.2.13     2020-01-03 [2] Github (ropensci/RefManageR@be9d663)
#>  reprex        0.3.0.9001 2020-01-14 [1] Github (tidyverse/reprex@9639e88)   
#>  rlang         0.4.2      2019-11-23 [2] CRAN (R 3.6.2)                      
#>  rmarkdown     2.1.1      2020-01-21 [1] Github (rstudio/rmarkdown@18ba267)  
#>  sessioninfo   1.1.1      2018-11-05 [2] CRAN (R 3.6.2)                      
#>  shiny         1.4.0.9001 2020-01-16 [1] Github (rstudio/shiny@cdbdb45)      
#>  stringi       1.4.5      2020-01-11 [1] CRAN (R 3.6.2)                      
#>  stringr       1.4.0.9000 2020-01-21 [1] Github (hadley/stringr@cc6e322)     
#>  styler        1.2.0      2019-10-17 [2] CRAN (R 3.6.2)                      
#>  tibble        2.1.3      2019-06-06 [2] CRAN (R 3.6.2)                      
#>  withr         2.1.2      2018-03-15 [2] CRAN (R 3.6.2)                      
#>  xfun          0.12.2     2020-01-17 [1] Github (yihui/xfun@9ecdc33)         
#>  xml2          1.2.2      2019-08-09 [2] CRAN (R 3.6.2)                      
#>  xtable        1.8-4      2019-04-21 [2] CRAN (R 3.6.2)                      
#>  yaml          2.2.0      2018-07-25 [2] CRAN (R 3.6.0)                      
#> 
#> [1] C:/Users/JooYoung/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.2/library
@crsh crsh added the bug label Jan 23, 2020
@crsh crsh closed this as completed in 0a56c35 Feb 11, 2020
@crsh
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crsh commented Feb 11, 2020

I just pushed a commit, that should fix this. When it's convenient for you, let me know if it works.

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@crsh @jooyoungseo