From JHZhang at mdanderson.org  Thu Sep 18 20:58:34 2014
From: JHZhang at mdanderson.org (Zhang,Jun)
Date: Thu, 18 Sep 2014 18:58:34 +0000
Subject: [Rd] formatR 1.0 caused error
In-Reply-To: <CANROs4doyL_+rBfuOnNv415BYXux4qV5GpSFAs3E9LdsH_xpBw@mail.gmail.com>
References: <8EE4E2C595735A4EAEC2A3311537FE4D276D757A@DCPWPEXMBX03.mdanderson.edu>
	<CANROs4doyL_+rBfuOnNv415BYXux4qV5GpSFAs3E9LdsH_xpBw@mail.gmail.com>
Message-ID: <8EE4E2C595735A4EAEC2A3311537FE4D276D85F4@DCPWPEXMBX03.mdanderson.edu>

Yihui,
I installed knitr_1.6.18, and user reported no warning any more. In my other related posting I thought rmarkdown was the problem, actually there are two part of the problems. Using older version of rmarkdown caused no html file generated, which is more serious, and the warning was cleared by your development knitr.
Thanks!
Jun  

-----Original Message-----
From: xieyihui at gmail.com [mailto:xieyihui at gmail.com] On Behalf Of Yihui Xie
Sent: Thursday, September 18, 2014 1:39 PM
To: Zhang,Jun
Cc: r-devel at r-project.org
Subject: Re: [Rd] formatR 1.0 caused error

Sorry, but this is a wrong list to write to. I'll reply anyway this time...

The formatR package should be irrelevant in this case -- you were seeing warnings of deprecation. The error came from elsewhere. It is hard to say what the problem was without a reproducible example.
Anyway, to "fix" the warnings, you can install the development version of knitr (which I plan to release to CRAN relatively soon):

  install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.com'), type = 'source')

You posted your sessionInfo() but it seems you deleted an important
part: the versions of packages, which makes it even more difficult for others to tell what the problem could possibly be.

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Web: http://yihui.name


On Thu, Sep 18, 2014 at 1:07 PM, Zhang,Jun <JHZhang at mdanderson.org> wrote:
> Recently in our R 3.1.0 installation the package formatR was upgraded to version 1.0, doing my usual thing, I got the following error, and the destination html file was not generated.
> What can I do if I want to stay at the current formatR version?
>
> Jun
>
> Error: unrecognized fields specified in html_dependency: attachment In 
> addition: Warning messages:
> 1: 'function (...)
> {
>     .Deprecated("tidy_source", package = "formatR")
>     tidy_source(...)
> }' is deprecated.
> Use 'tidy_source' instead.
> See help("Deprecated") and help("formatR-deprecated").
> 2: In tidy_source(...) :
>   The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
> 3: 'function (...)
> {
>     .Deprecated("tidy_source", package = "formatR")
>     tidy_source(...)
> }' is deprecated.
> Use 'tidy_source' instead.
> See help("Deprecated") and help("formatR-deprecated").
> 4: In tidy_source(...) :
>   The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
> 5: 'function (...)
> {
>     .Deprecated("tidy_source", package = "formatR")
>     tidy_source(...)
> }' is deprecated.
> Use 'tidy_source' instead.
> See help("Deprecated") and help("formatR-deprecated").
> 6: In tidy_source(...) :
>   The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)


[Rd] formatR 1.0 caused error
Zhang,Jun