{"action":"opened","issue":{"url":"https://api.github.com/repos/rstudio/rticles/issues/54","labels_url":"https://api.github.com/repos/rstudio/rticles/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/rstudio/rticles/issues/54/comments","events_url":"https://api.github.com/repos/rstudio/rticles/issues/54/events","html_url":"https://github.com/rstudio/rticles/issues/54","id":122167930,"number":54,"title":"Citations not working?","user":{"login":"zkamvar","id":3639446,"avatar_url":"https://avatars.githubusercontent.com/u/3639446?v=3","gravatar_id":"","url":"https://api.github.com/users/zkamvar","html_url":"https://github.com/zkamvar","followers_url":"https://api.github.com/users/zkamvar/followers","following_url":"https://api.github.com/users/zkamvar/following{/other_user}","gists_url":"https://api.github.com/users/zkamvar/gists{/gist_id}","starred_url":"https://api.github.com/users/zkamvar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zkamvar/subscriptions","organizations_url":"https://api.github.com/users/zkamvar/orgs","repos_url":"https://api.github.com/users/zkamvar/repos","events_url":"https://api.github.com/users/zkamvar/events{/privacy}","received_events_url":"https://api.github.com/users/zkamvar/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-12-15T01:00:43Z","updated_at":"2015-12-15T01:00:43Z","closed_at":null,"body":"I've noticed that the examples are not adding the citations correctly. I can't tell whether or not this is stemming from rticles, rmarkdown, or pandoc. Pandoc used to render these and add the bibliography as plain text, but now it's simply leaving the latex citations alone. Does anyone have any insight on this?\r\n\r\nNote, I'm using MacTeX 2015.\r\n\r\n\r\nHere's my sessioninfo:\r\n\r\n```r\r\ndevtools::session_info()\r\n\r\nSession info --------------------------------------------------------------\r\n\r\n setting  value                       \r\n version  R version 3.2.3 (2015-12-10)\r\n system   x86_64, darwin13.4.0        \r\n ui       X11                         \r\n language (EN)                        \r\n collate  en_US.UTF-8                 \r\n tz       America/Los_Angeles         \r\n date     2015-12-14                  \r\n\r\nPackages ------------------------------------------------------------------\r\n\r\n package    * version date       source                            \r\n colorspace   1.2-6   2015-03-11 CRAN (R 3.2.0)                    \r\n devtools     1.9.1   2015-09-11 CRAN (R 3.2.0)                    \r\n digest       0.6.8   2014-12-31 CRAN (R 3.2.0)                    \r\n evaluate     0.8     2015-09-18 CRAN (R 3.2.0)                    \r\n formatR      1.2.1   2015-09-18 CRAN (R 3.2.0)                    \r\n ggplot2    * 2.0.0   2015-12-15 Github (hadley/ggplot2@a6494bf)   \r\n gtable       0.1.2   2012-12-05 CRAN (R 3.2.0)                    \r\n htmltools    0.2.6   2014-09-08 CRAN (R 3.2.0)                    \r\n knitr        1.11    2015-08-14 CRAN (R 3.2.2)                    \r\n labeling     0.3     2014-08-23 CRAN (R 3.2.0)                    \r\n magrittr     1.5     2014-11-22 CRAN (R 3.2.0)                    \r\n memoise      0.2.1   2014-04-22 CRAN (R 3.2.0)                    \r\n munsell      0.4.2   2013-07-11 CRAN (R 3.2.0)                    \r\n plyr         1.8.3   2015-06-12 CRAN (R 3.2.0)                    \r\n Rcpp         0.12.2  2015-11-15 CRAN (R 3.2.2)                    \r\n rmarkdown    0.8.3   2015-12-15 Github (rstudio/rmarkdown@558e380)\r\n rticles      1.0     2015-12-15 Github (rstudio/rticles@a4f3dbe)  \r\n scales       0.3.0   2015-08-25 CRAN (R 3.2.0)                    \r\n stringi      1.0-1   2015-10-22 CRAN (R 3.2.0)                    \r\n stringr      1.0.0   2015-04-30 CRAN (R 3.2.0)                    \r\n yaml         2.1.13  2014-06-12 CRAN (R 3.2.0)                    \r\n```\r\n\r\nHere's the output for the FrontiersTemplate:\r\n\r\n```\r\n\r\n\r\nprocessing file: deleteme.Rmd\r\n  |.........                                                        |  14%\r\n  ordinary text without R code\r\n\r\n  |...................                                              |  29%\r\nlabel: graph (with options) \r\nList of 3\r\n $ echo    : logi TRUE\r\n $ message : logi FALSE\r\n $ fig.show: chr \"hide\"\r\n\r\nLoading required package: ggplot2\r\ncropping deleteme_files/figure-latex/graph-1.pdf\r\nPDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.\r\n==> 1 page written on `deleteme_files/figure-latex/graph-1.pdf'.\r\n  |............................                                     |  43%\r\n  ordinary text without R code\r\n\r\n  |.....................................                            |  57%\r\nlabel: sessioninfo\r\n  |..............................................                   |  71%\r\n  ordinary text without R code\r\n\r\n  |........................................................         |  86%\r\nlabel: Figure-1 (with options) \r\nList of 10\r\n $ ref.label : chr \"graph\"\r\n $ results   : chr \"hide\"\r\n $ echo      : logi FALSE\r\n $ message   : logi FALSE\r\n $ fig.height: num 4\r\n $ fig.width : num 4\r\n $ fig.align : chr \"center\"\r\n $ fig.cap   : chr \"Figure caption\"\r\n $ out.width : chr \"85mm\"\r\n $ out.height: chr \"85mm\"\r\n\r\ncropping deleteme_files/figure-latex/Figure-1-1.pdf\r\nPDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.\r\n==> 1 page written on `deleteme_files/figure-latex/Figure-1-1.pdf'.\r\n  |.................................................................| 100%\r\n  ordinary text without R code\r\n\r\n\r\n/usr/local/bin/pandoc +RTS -K512m -RTS deleteme.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output deleteme.tex --template /Users/zhian/R/rticles/rmarkdown/templates/frontiers_article/resources/template.tex --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --natbib --bibliography test.BIB \r\noutput file: deleteme.knit.md\r\n\r\nLatexmk: This is Latexmk, John Collins, 5 February 2015, version: 4.43a.\r\n\r\nOutput created: deleteme.pdf\r\n```\r\n"}}