Shiny: Could not find bibliography file:

rmarkdown
shiny
rstudio

#1

I have a shiny app that runs locally but it will not run when the bibtex file is input with GitHub.

Success: bibliography: /Users/PJO/Desktop/Basic/doc/CF.bib
Failure: bibliography: https://github.com/PJOssenbruggen/Basic/tree/master/doc/CF.bib

Question: How do I call my GitHub repo so it can find CF.bib?

R Markdown message:

Could not find bibliography file: https://github.com/PJOssenbruggen/Basic/tree/master/doc/CF.bib
Error running filter /usr/local/bin/pandoc-citeproc:
Filter returned error status 1
Warning: Error in : pandoc document conversion failed with error 83
...

Here is the front matter and some code:

---
title: "Headway"
output: html_document
bibliography: https://github.com/PJOssenbruggen/Basic/tree/master/doc/CF.bib  #(failure)
#bibliography: /Users/PJO/Desktop/Basic/doc/CF.bib (success)
runtime: shiny
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
devtools::install_github("PJOssenbruggen/Basic")
library(Basic)
#devtools::install_github('rstudio/rmarkdown')
#library(rmarkdown)
```
\>

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 os       macOS High Sierra 10.13.4   
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2018-04-23                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────
 package     * version     date       source                               
 ansistrings   1.0.0.9000  2018-04-12 Github (r-lib/ansistrings@4e4d309)   
 assertthat    0.2.0       2017-04-11 CRAN (R 3.4.0)                       
 backports     1.1.2       2017-12-13 CRAN (R 3.4.3)                       
 Basic       * 0.1.0       2018-04-22 Github (PJOssenbruggen/Basic@43e8fd6)
 bindr         0.1.1       2018-03-13 CRAN (R 3.4.4)                       
 bindrcpp      0.2.2       2018-03-29 CRAN (R 3.4.4)                       
 bitops        1.0-6       2013-08-17 CRAN (R 3.4.0)                       
 callr         2.0.3       2018-04-20 Github (r-lib/callr@3e433ba)         
 cli           1.0.0.9002  2018-04-12 Github (r-lib/cli@c408924)           
 clisymbols    1.2.0       2017-05-21 CRAN (R 3.4.0)                       
 commonmark    1.4         2017-09-01 CRAN (R 3.4.1)                       
 crayon        1.3.4       2018-04-12 Github (gaborcsardi/crayon@95b3eae)  
 debugme       1.1.0       2017-10-22 CRAN (R 3.4.2)                       
 desc          1.1.1       2017-08-03 CRAN (R 3.4.1)                       
 devtools    * 1.13.5.9000 2018-04-12 Github (hadley/devtools@13ee56b)     
 digest        0.6.15      2018-01-28 CRAN (R 3.4.3)                       
 dplyr       * 0.7.4       2017-09-28 CRAN (R 3.4.2)                       
 evaluate      0.10.1      2017-06-24 CRAN (R 3.4.1)                       
 fda         * 2.4.7       2017-08-14 CRAN (R 3.4.1)                       
 glue          1.2.0       2017-10-29 CRAN (R 3.4.2)                       
 hms           0.4.2       2018-03-10 CRAN (R 3.4.4)                       
 htmltools     0.3.6       2017-04-28 CRAN (R 3.4.0)                       
 httpuv        1.3.6.2     2018-03-02 CRAN (R 3.4.3)                       
 knitr       * 1.20        2018-02-20 CRAN (R 3.4.3)                       
 lattice       0.20-35     2017-03-25 CRAN (R 3.4.4)                       
 magrittr      1.5         2014-11-22 CRAN (R 3.4.0)                       
 MASS        * 7.3-49      2018-02-23 CRAN (R 3.4.4)                       
 Matrix      * 1.2-14      2018-04-09 CRAN (R 3.4.4)                       
 memoise       1.1.0       2017-04-21 CRAN (R 3.4.0)                       
 mime          0.5         2016-07-07 CRAN (R 3.4.0)                       
 pillar        1.2.1       2018-02-27 CRAN (R 3.4.3)                       
 pkgbuild      1.0.0       2018-04-12 Github (r-lib/pkgbuild@4ee12af)      
 pkgconfig     2.0.1       2017-03-21 CRAN (R 3.4.0)                       
 pkgload       1.0.0       2018-04-12 Github (r-lib/pkgload@a9184a0)       
 prettyunits   1.0.2       2015-07-13 CRAN (R 3.4.2)                       
 progress      1.1.2.9003  2018-04-12 Github (r-lib/progress@e525de4)      
 R6            2.2.2       2017-06-17 CRAN (R 3.4.0)                       
 Rcpp          0.12.16     2018-03-13 CRAN (R 3.4.4)                       
 RCurl         1.95-4.10   2018-01-04 CRAN (R 3.4.3)                       
 RJSONIO       1.3-0       2014-07-28 CRAN (R 3.4.0)                       
 rlang         0.2.0       2018-02-20 CRAN (R 3.4.3)                       
 rmarkdown   * 1.9.8       2018-04-16 Github (rstudio/rmarkdown@81dabbc)   
 roxygen2    * 6.0.1       2017-02-06 CRAN (R 3.4.0)                       
 rprojroot     1.3-2       2018-01-03 CRAN (R 3.4.3)                       
 rsconnect     0.8.8       2018-04-22 Github (rstudio/rsconnect@31aaf03)   
 rstudioapi  * 0.7         2017-09-07 CRAN (R 3.4.1)                       
 sde         * 2.0.15      2016-04-13 CRAN (R 3.4.0)                       
 selectr       0.4-1       2018-04-06 CRAN (R 3.4.4)                       
 sessioninfo   1.0.1.9000  2018-04-12 Github (r-lib/sessioninfo@c871d01)   
 shiny       * 1.0.5       2017-08-23 CRAN (R 3.4.2)                       
 stringi       1.1.7       2018-03-12 CRAN (R 3.4.4)                       
 stringr       1.3.0       2018-02-19 CRAN (R 3.4.3)                       
 testthat    * 2.0.0       2017-12-13 CRAN (R 3.4.3)                       
 tibble        1.4.2       2018-01-22 CRAN (R 3.4.3)                       
 usethis     * 1.3.0.9000  2018-04-12 Github (r-lib/usethis@acd9e70)       
 withr         2.1.2       2018-03-15 CRAN (R 3.4.4)                       
 xml2          1.2.0       2018-01-24 CRAN (R 3.4.2)                       
 xtable        1.8-2       2016-02-05 CRAN (R 3.4.0)                       
 yaml          2.1.18      2018-03-08 CRAN (R 3.4.4)                       
 zoo         * 1.8-1       2018-01-08 CRAN (R 3.4.3)

#2

I found a workaround.