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From: Steven Delean <steven.delean@adelaide.edu.au>
To: Steven Delean <steven.delean@adelaide.edu.au>
Cc: Jack Kamm <jackkamm@gmail.com>,
	"emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: Bug: HTML not formatted correctly from R source code block [9.3.6 (9.3.6-23-g01ee25-elpaplus @ /home/opdfa/.emacs.d/elpa/org-plus-contrib-20200309/)]
Date: Thu, 12 Mar 2020 01:16:42 +0000	[thread overview]
Message-ID: <20200312114641.60e7b493@t460> (raw)
In-Reply-To: <20200311133658.25b98cc8@t460>

Hello again Jack,

I am trying to use ob-session-async as a workaround for this problem.

In my R :session, the correct output is printed to screen, followed by a UUID if
I use :results output html, which is printed as, e.g.,
[1] "ob_comint_async_R_end_4d2e818b7c2544da6f026d0413c7ac6c"

Alternatively, if I use :results value html then the tempfile path is printed
[1] "ob_comint_async_R_file_/tmp/babel-6BGHQK/R-QNasco"

The problem, however, is that what is exported to html and displayed in the
exported block is either the actual UUID or the tempfile path and not the
results from evaluating the R code. In the case of the tempfile, the tempfile
exists but is empty.

Any advice as to how to resolve this would be greatly appreciated, thanks.

Best regards,

On Wed, 11 Mar 2020 13:37:01 +1030
Steven Delean <steven.delean@adelaide.edu.au> wrote:

> Hi Jack,
> Thanks for your response.
> Yes, I am using :session evaluation here, set using #+PROPERTY:
> However, ":results value html" does not work for me. In fact, this produces no
> table output at all in the resulting exported html file.
> The output sent to the R :session buffer is printed correctly (when using
> either :results value html or :results output html). As you say, it is the
> exporter that is removing ">" from the output.
> If I remove :session evaluation, I also get no output at all from these code
> blocks in the exported html.
> The change has been introduced within the last 12 months, as my scripts
> exported with correct html formatting when I used them for last years'
> classes.
> Best regards,
> Steve
> On Tue, 10 Mar 2020 17:17:48 -0700
> Jack Kamm <jackkamm@gmail.com> wrote:
> > Hi Steve,
> >
> > Steven Delean <steven.delean@adelaide.edu.au> writes:
> >
> > > HTML table produced from a source code block (using R code) does not
> > > display because html code is not formatted correctly in the exported html
> > > output.
> >
> > I believe this is the same issue as reported here:
> > https://lists.gnu.org/archive/html/emacs-orgmode/2020-02/msg00267.html
> >
> > Though, that thread was for ":session" blocks, and it's unclear whether
> > you're using session or non-session evaluation here.
> >
> > Anyways, that thread suggests that ":results value html" works
> > correctly, does switching to that work for you?
> >
> > If I'm correct, the basic problem is that ob-R tries to remove
> > interactive shell prompts like ">" from the output. This can also cause
> > other problems. I think it can be fixed by changing ob-R to use
> > `ess-eval-region' to evaluate code, I'll try to submit a patch for this
> > after 9.4 is released.

  reply	other threads:[~2020-03-12  1:16 UTC|newest]

Thread overview: 5+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2020-03-09 14:42 Bug: HTML not formatted correctly from R source code block [9.3.6 (9.3.6-23-g01ee25-elpaplus @ /home/opdfa/.emacs.d/elpa/org-plus-contrib-20200309/)] Steven Delean
2020-03-11  0:17 ` Jack Kamm
2020-03-11  3:07   ` Steven Delean
2020-03-12  1:16     ` Steven Delean [this message]
2020-11-01 19:02       ` Jack Kamm

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