Re: [R] unable to collate and parse R files for package -- unexpected end of input

[Timothy W. Cook]

Thanks Duncan.  Exactly what I needed.  A push in the right direction to
finding it.
I've already found the file and I am sure to find the problem child soon.

Cheers,
Tim



On Sun, May 18, 2014 at 5:24 PM, Duncan Murdoch <murdoch.dun...@gmail.com>wrote:

> On 18/05/2014, 12:54 PM, Timothy W. Cook wrote:
>
>> This is the error I get attempting to build and install a package I wrote.
>>
>> I am using R Studio (but I did try with R CMDs as well).
>>
>> The file that is blamed in the error is the last file alphabetically.  If
>> I
>> remove that file.  I get the same error on the remaining last file
>> alphabetically.  So my guess is that it isn't actually one of these files.
>>   However, I have no clue how to troubleshoot this problem.  I am quite
>> new
>> to R.
>>
>
> This indicates that you open a block using "{" (or perhaps "[" or "("),
> but never close it.  Unfortunately the parser doesn't tell you where the
> opening brace was.
>
> A quick way to locate which file is to parse your source files one at a
> time; e.g.
>
> for (f in list.files("somedir/R", full.names=TRUE)) parse(f)
>
> This will get an error on the first file with unmatched braces.  It won't
> tell you where to look in that file, but it's usually not too hard to find
> that by looking.  There are ways to find the spot automatically, but
> they're not trivial:  see the discussion of partial parse results in
> ?parse, and fill in a bunch of blanks.  Here without much explanation is an
> example.
>
> f <- "some file with unbalanced braces"
> text <- readLines(f)
> src <- srcfile(text)
> parse(text=text, srcfile=src)  # Generates error
>
> d <- getParseData(src)
> d[d$token == "'{'" && d$parent == 0,]
>
> This will print something like
>
>     line1 col1 line2 col2  id parent token terminal text
> 217    37    3    37    3 217      0   '{'     TRUE    {
>
> telling you that the brace on line 37 was never matched.  If you don't
> find anything, try other kinds of parens or brackets, though they are less
> likely.
>
> Duncan Murdoch
>
>
>> I built a generator to create this R pkg.  But it is based on a very
>> similar one that works okay that I built by hand.
>>
>> They are available in their entirety on GitHub at:
>> https://github.com/mlhim/R_test_prj
>>
>> The one that works is:  ccdTest244AllDatatypes299a8123d9f7
>>
>> The one that doesn't work is: ccdTest244AllDatatypesa5c7aca0036f
>>
>> The 00install.out file isn't particularly enlightening:
>> ------------------------------------------------------------
>> -----------------
>> * installing *source* package 
>> ‘ccdTest244AllDatatypesa5c7aca0036f’
>> ...
>>
>> ** R
>> Error in parse(outFile) :
>>
>> /home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
>> 036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
>> unexpected end of input
>> 41:     return('
>> http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd
>> ')
>> 42: }
>>     ^
>> ERROR: unable to collate and parse R files for package
>> ‘ccdTest244AllDatatypesa5c7aca0036f’
>> * removing
>> ‘/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
>> 036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036f’
>>
>>
>>
>> * installing *source* package 
>> ‘ccdTest244AllDatatypesa5c7aca0036f’
>> ...
>>
>> ** R
>> Error in parse(outFile) :
>>
>> /home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
>> 036f.Rcheck/00_pkg_src/ccdTest244AllDatatypesa5c7aca0036f/R/meta :43:0:
>> unexpected end of input
>> 41:     return('
>> http://www.ccdgen.com/ccdlib/ccd-31598ac4-eac4-4f45-928e-a5c7aca0036f.xsd
>> ')
>> 42: }
>>     ^
>> ERROR: unable to collate and parse R files for package
>> ‘ccdTest244AllDatatypesa5c7aca0036f’
>> * removing
>> ‘/home/tim/MLHIM/git/R_test_prj/ccdTest244AllDatatypesa5c7aca0
>> 036f.Rcheck/ccdTest244AllDatatypesa5c7aca0036f’
>>
>> -------------------------------------------------------------
>>
>> Any help  is greatly appreciated.
>>
>> This is part of a large open source effort in healthcare interoperability
>> and data analysis.
>>
>> Thanks In Advance,
>> Tim
>>
>>
>> ============================================
>> Timothy Cook
>> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>> MLHIM http://www.mlhim.org
>>
>>         [[alternative HTML version deleted]]
>>
>>
>>
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>


-- 

============================================
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org

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