From xie at yihui.name  Thu Sep 18 20:38:58 2014
From: xie at yihui.name (Yihui Xie)
Date: Thu, 18 Sep 2014 13:38:58 -0500
Subject: [Rd] formatR 1.0 caused error
In-Reply-To: <8EE4E2C595735A4EAEC2A3311537FE4D276D757A@DCPWPEXMBX03.mdanderson.edu>
References: <8EE4E2C595735A4EAEC2A3311537FE4D276D757A@DCPWPEXMBX03.mdanderson.edu>
Message-ID: <CANROs4doyL_+rBfuOnNv415BYXux4qV5GpSFAs3E9LdsH_xpBw@mail.gmail.com>

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
Yihui Xie