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)