[R] Input encoding problem when using sweave with xetex
Duncan Murdoch
murdoch.duncan at gmail.com
Thu May 13 03:23:07 CEST 2010
On 12/05/2010 7:07 PM, Erich Studerus wrote:
> Thanks again. It finally worked after copying the Sweave.sh file to a path
> that contains no spaces. Is there a special command for windows specific
> path names with spaces?
>
Putting the path in double quotes might work, but I've no idea how to
tell lyx to do that.
Duncan Murdoch
> Erich
>
>
> On Wed, 12 May 2010 18:04:44 -0400
> Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>
>> On 12/05/2010 5:12 PM, Erich Studerus wrote:
>>
>>> You were right, that I would run into trouble with all these "". However,
>>> the second method doesn't work either. Somehow, the UTF8Sweave.sh file is
>>> not found during the compilation of my document. It says "can't open perl
>>> script .../bin/UTF8Sweave.sh: No such file or directory". I double checked
>>> that a file with this name is present in the same folder as the original
>>> Sweave.sh file and that the "Sweave" is changed to "UTF8Sweave" in the LyX
>>> preference file. Any idea, what could be wrong?
>>>
>>>
>> Sorry, I forgot that if you make up your own command to be run by R CMD
>> then you need to give the full path to it, and you can't suppress the .sh
>> suffix. So your command should be
>>
>> R CMD /path/to/UTF8Sweave.sh $$i
>>
>>
>> (where /path/to/ is the actual path to where you decide to keep this file,
>> which needn't be in rhome/bin).
>>
>> Duncan Murdoch
>>
>>
>>
>>> Erich
>>>
>>>
>>> On Wed, 12 May 2010 16:20:03 -0400
>>> Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>>
>>>
>>>> On 12/05/2010 3:55 PM, Erich Studerus wrote:
>>>>
>>>>
>>>>> Thanks again. Putting options(encoding="") into the R code chunk before
>>>>> calling the read.xls function indeed did the trick. Now, I have one last
>>>>> question: How can I edit the LyX preference file to call R with
>>>>> options(encoding='UTF-8'). I prefer to edit the LyX preference file rather
>>>>> than the Sweave.sh file, because I want to run R with UTF-8 only when I
>>>>> use
>>>>> XeTeX. By editing the LyX preference file, I assume it would be possible
>>>>> to
>>>>> define different R encoding setups for different converters.
>>>>>
>>>>>
>>>>>
>>>> One way would be to change
>>>>
>>>> R CMD Sweave $$i
>>>>
>>>> in
>>>>
>>>> \converter "literate" "latex" "R CMD Sweave $$i" ""
>>>>
>>>> to
>>>>
>>>> echo "library(\"utils\"); options(encoding=\"UTF-8\"); Sweave(\"$$i\")" |
>>>> R --no-restore --slave
>>>>
>>>> but you may run into trouble because there's an extra set of "" to go
>>>> around there, and I don't know how Lyx handles escaping all those quotes.
>>>> So probably an easier way to go would be to take the Sweave.sh file
>>>> that you've already edited, and copy it into UTF8Sweave.sh in the same
>>>> directory. Then you can change the Lyx preference line to
>>>>
>>>> \converter "literate" "latex" "R CMD UTF8Sweave $$i" ""
>>>>
>>>> and things should work. (Then you can restore the original Sweave.sh file
>>>> for cases where you don't
>>>> want UTF-8.)
>>>>
>>>> Duncan Murdoch
>>>>
>>>>
>>>>
>>>>> Erich
>>>>>
>>>>>
>>>>> On Wed, 12 May 2010 14:43:52 -0400
>>>>> Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>>>>
>>>>>
>>>>>> On 12/05/2010 2:29 PM, Erich Studerus wrote:
>>>>>>
>>>>>>
>>>>>>> Thank you! I edited the Sweave.sh file and it works now for reading
>>>>>>>
>>>>>>>
>>>>> data
>>>>>
>>>>>
>>>>>>> stored as R data files, but the read.xls function from the
>>>>>>>
>>>>>>>
>>>>> gdata-package
>>>>>
>>>>>
>>>>>>> does no longer work.
>>>>>>>
>>>>>>> options('encoding'='UTF-8')
>>>>>>> require(gdata)
>>>>>>> read.xls("http://www.schwerhoerigkeit.pop.ch/hoergeraete_test.xls",
>>>>>>> stringsAsFactors = F)[2,2]
>>>>>>>
>>>>>>> This gives NA as output and a warning that there was an invalid entry
>>>>>>>
>>>>>>>
>>>>> for
>>>>>
>>>>>
>>>>>>> the connection. Is there a way to use read.xls with UTF-8 encoding?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> I don't know, you'd have to ask its authors. But you can probably set
>>>>>> options(encoding="") before calling it. (I'm assuming the read.xls() is
>>>>>>
>>>>>>
>>>>> in
>>>>>
>>>>>
>>>>>> a code chunk in your Sweave file. I would guess that you don't need to
>>>>>>
>>>>>>
>>>>> set
>>>>>
>>>>>
>>>>>> the encoding back to UTF-8 afterwards, but you might: it all depends on
>>>>>> when Sweave() opens its
>>>>>> output file.)
>>>>>>
>>>>>> Duncan Murdoch
>>>>>>
>>>>>>
>>>>>>> On Wed, 12 May 2010 12:45:51 -0400
>>>>>>> Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> On 12/05/2010 11:36 AM, Erich Studerus wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> Putting \usepackage[cp1252]{inputenc} into my preamble is not an
>>>>>>>>>
>>>>>>>>>
>>>>>>> option,
>>>>>>>
>>>>>>>
>>>>>>>>> because XeTeX unlike LaTeX needs UTF-8 has input encoding. My goal
>>>>>>>>>
>>>>>>>>>
>>>>> is
>>>>>
>>>>>
>>>>>>> also
>>>>>>>
>>>>>>>
>>>>>>>>> to have a LyX document that can be compiled both on Mac and Windows.
>>>>>>>>>
>>>>>>>>> I usually compile my Lyx-Sweave documents by one click of a button
>>>>>>>>>
>>>>>>>>>
>>>>> from
>>>>>
>>>>>
>>>>>>>>> within Lyx. R code chunks are therefore executed by calling R from
>>>>>>>>>
>>>>>>>>>
>>>>> the
>>>>>
>>>>>
>>>>>>>>> command line. If anybody knows how to run R with
>>>>>>>>>
>>>>>>>>>
>>>>>>> options(encoding="UTF-8")
>>>>>>>
>>>>>>>
>>>>>>>>> from the command line under windows, that would be helpful.
>>>>>>>>>
>>>>>>>>> The command that calls R during compilation is contained in this
>>>>>>>>>
>>>>>>>>>
>>>>> file:
>>>>>
>>>>>
>>>>>>>>> http://cran.r-project.org/contrib/extra/lyx/preferences
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> You can do it with a little work. If you look at the
>>>>>>>>
>>>>>>>>
>>>>>>> rhome/bin/Sweave.sh
>>>>>>>
>>>>>>>
>>>>>>>> file, you'll see that
>>>>>>>>
>>>>>>>> R CMD Sweave file.Rnw
>>>>>>>>
>>>>>>>> just executes something like
>>>>>>>>
>>>>>>>> echo "library(\"utils\"); Sweave(\"file.Rnw\")" | R --no-restore
>>>>>>>>
>>>>>>>>
>>>>> --slave
>>>>>
>>>>>
>>>>>>>> What you want is to execute
>>>>>>>>
>>>>>>>> echo "library(\"utils\"); options(encoding="UTF-8");
>>>>>>>>
>>>>>>>>
>>>>>>> Sweave(\"file.Rnw\")"
>>>>>>>
>>>>>>>
>>>>>>>> | R --no-restore --slave
>>>>>>>>
>>>>>>>> You could edit the rhome/bin/Sweave.sh file appropriately if you
>>>>>>>>
>>>>>>>>
>>>>> always
>>>>>
>>>>>
>>>>>>>> want Sweave to use UTF-8, or you could edit your Lyx preference file
>>>>>>>>
>>>>>>>>
>>>>> to
>>>>>
>>>>>
>>>>>>> put
>>>>>>>
>>>>>>>
>>>>>>>> in a line like this instead of what it had.
>>>>>>>>
>>>>>>>> Duncan Murdoch
>>>>>>>>
>>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-help at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>> PLEASE do read the posting guide
>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>>
>>>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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