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formatR 1.0 caused error

4 messages · Zhang,Jun, Yihui Xie

Original
Zhang,Jun
# 
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'
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
Zhang,Jun
# 
Problem solved. User library location had an older rmarkdown, removed that, so that the current rmarkdown 0.3.3 at the system library location is being used.

-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Zhang,Jun
Sent: Thursday, September 18, 2014 1:08 PM
To: r-devel at r-project.org
Subject: [Rd] formatR 1.0 caused error

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'
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)



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Yihui Xie
# 
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:
Zhang,Jun
# 
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: