Reports Rmarkdown in Opal

[alby...@gmail.com]

Hi Yannick and all,

I am updating the data harmonisation of a study and I am testing in Opal (v.3.0.4) the reports in Rmarkdown. I have added a simple Report template in Rmd and it successfully generates an html file. However, I have two questions at this moment:

1) If the Rmd file calls other R files that include other functions (e.g. > source("otherFunct.R")), where do I place this file? I have tried unsuccessfully calling it on github (e.g., > devtools::source_url("https://raw.githubusercontent.com/.../otherFunct.R"); Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to raw.githubusercontent.com:443 )

2) The report generated with html, how could it be published on the main Mica website? At the moment, the way I can think of is copying the html in "Files" within the study. Is there another way?

Thanks so much in advance.

Best,

Albert

-----------------------------------------------------

Albert Sanchez Niubo, PhD

Researcher / Statistician

Parc Sanitari Sant Joan de Déu

Sant Boi de Llobregat (Barcelona)

albert.sanchez (at) pssjd.org

------------------------------------------------------

[Yannick Marcon]

Hi Albert,

1. Currently only the .Rmd files that are in the same folder as the main report template file are copied to the R server session workspace. I understand it is a bit restrictive and could be extended to all files and subfolders, so that one could also have R code, images etc. in the report execution environment. Could you fill-in a feature request? https://github.com/obiba/opal/issues

2. I need to test and will come back to you later.

Best

Yannick

--
You received this message because you are subscribed to the Google Groups "obiba-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to obiba-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/5226a9c3-60c4-4c74-a51b-6e497d59b823n%40googlegroups.com.

[alby...@gmail.com]

Thank you Yannick, I've just sent an issue as you told me.

Best,

Albert