data.table column expression breaks in easyHtmlReport, works in plain knitr

Question

I am trying to do some data.table manipulations in an Rmd file. The file works just fine with knit. However, when I run it through easyHtmlReport, it doesn't work: my data.table by expressions fail with ‘Error: object 'userId' not found’, where userId is one of the columns in my data table that I am using in the j expression. The broken expression is:

expt.daystat = expt.users[,list(count=length(userId)),
                          keyby=list(day, status)]

As I said, it works fine in plain knit but breaks in easyHtmlReport.

I suspect that this is a bug in the `EasyHTMLReport` package. The `knit` function accepts an `envir` argument that needs to be passed along, and inspecting the code for `easyHtmlReport`, it doesnt seem to be doing that. `data.table` does non-standard evaluation and so bugs like this are most likely due to environments. I would suggest you file a bug report. — Ramnath, Feb 10 '14 at 23:53
Thanks @Ramnath. I've experimented with adding `envir` code to `EasyHTMLReport`, and it does fix the problem. I've reported the issue to the author. — Michael Ekstrand, Feb 15 '14 at 16:53
Hi @MichaelEkstrand - I'd appreciate it if you could provide answer to your question. I'm encountering the issue, and my simplistic solution based on your advice was to add `envir=new.env(parent = .GlobalEnv)` into the control argument which doesn't work so seeing your solution would be helpful! — Steph Locke, Jul 01 '14 at 13:26
@StephLocke I've re-pinged the author about getting the bug fix incorporated into the CRAN version. In the mean time, see answer for the workaround. — Michael Ekstrand, Jul 09 '14 at 13:45

score 3 · Accepted Answer · answered Jul 08 '14 at 13:48

@Ramnath is correct. Line 40 of EasyHTMLReport.R is:

knit(input=f,output=md.file)

Update this line with:

knit(input = f, output = md.file, envir = envir)

Update the signature of the function from:

easyHtmlReport <-
    function(rmd.file,from,to,subject,headers=list(),control=list(),
        markdown.options=c("hard_wrap","use_xhtml","smartypants"),
        stylesheet="", echo.disable=TRUE, is.debug=F){

to:

easyHtmlReport <-
    function(rmd.file,from,to,subject,headers=list(),control=list(),
        markdown.options=c("hard_wrap","use_xhtml","smartypants"),
        stylesheet="", echo.disable=TRUE, is.debug=FALSE, envir = parent.frame()){

If you don't want to rebuild the package you should be able to make this change using the edit function.

score 3 · Answer 2 · answered Jul 09 '14 at 14:01

3

I wanted to post my alternative solution that I ended up using. It utilises mailR which allows multiple recipients and enables the easy implementation of html without worrying about mime_part commands.

library(mailR)
library(markdown)
library(knitr)

from     <-  "me@me.com"
to       <-  "me@me.com"
subject  <-  "Test"
message  <-  markdownToHTML(knit("Test.Rmd"))
send.mail(from,to,subject,message,html=TRUE,smtp=list( host.name="smtp.test.com"))

answered Jul 09 '14 at 14:01

Steph Locke

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This post gives you some more info. on using mailR with markdown: http://stackoverflow.com/questions/24346856/mailr-how-to-send-rmarkdown-documents-as-body-in-email/24355800#24355800 – Rahul Premraj Jul 11 '14 at 14:37

data.table column expression breaks in easyHtmlReport, works in plain knitr

2 Answers2