{"action":"closed","issue":{"url":"https://api.github.com/repos/yihui/knitr/issues/1048","labels_url":"https://api.github.com/repos/yihui/knitr/issues/1048/labels{/name}","comments_url":"https://api.github.com/repos/yihui/knitr/issues/1048/comments","events_url":"https://api.github.com/repos/yihui/knitr/issues/1048/events","html_url":"https://github.com/yihui/knitr/issues/1048","id":83964300,"number":1048,"title":"pandoc with custom --from overrides it with default \"markdown\"","user":{"login":"anoeee","id":11232032,"avatar_url":"https://avatars.githubusercontent.com/u/11232032?v=3","gravatar_id":"","url":"https://api.github.com/users/anoeee","html_url":"https://github.com/anoeee","followers_url":"https://api.github.com/users/anoeee/followers","following_url":"https://api.github.com/users/anoeee/following{/other_user}","gists_url":"https://api.github.com/users/anoeee/gists{/gist_id}","starred_url":"https://api.github.com/users/anoeee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anoeee/subscriptions","organizations_url":"https://api.github.com/users/anoeee/orgs","repos_url":"https://api.github.com/users/anoeee/repos","events_url":"https://api.github.com/users/anoeee/events{/privacy}","received_events_url":"https://api.github.com/users/anoeee/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-02T10:42:55Z","updated_at":"2015-06-15T09:27:43Z","closed_at":"2015-06-15T09:27:43Z","body":"Hi,\r\n     My embedded configurations specify the from attribute and I noticed that the command generated with pandoc() repeats the \"-f\" option. I saw that you hardcoded \"-f markdown\" in pandoc.R. In my case this means that the option  autolink_bare_uris is not set. I believe this is due to the fact that the second -f overrides the first.\r\n\r\nHere is my configuration:\r\n\r\n```\r\n<!--pandoc\r\nt: latex \r\nlatex-engine: xelatex \r\nf: autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures \r\ntemplate: \"default.tex\"\r\nhighlight-style: tango\r\no: \"report201506021033.pdf\"\r\n-->\r\n```\r\n\r\nAnd pandoc() outputs (I've cleared unnecessary paths to files):\r\n\r\n```\r\n> pandoc(\"report201506021033.md\"), format=\"latex\") # LaTeX/PDF\r\nexecuting pandoc --latex-engine=xelatex -f autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --template=\"default.tex\" --highlight-style=tango  -f markdown -t latex -o \"report201506021033.pdf\" \"report201506021033.utf8md\"\r\n[1] \"\\\"report201506021033.pdf\\\"\"\r\n```\r\n\r\nThanks and congrats for a great library!\r\n\r\nAndré Morais"}}