[R-pkg-devel] corrupted NAMESPACE file

[Duncan Murdoch]

On 20/01/2023 6:02 p.m., Greg Hunt wrote:
> xFEFF isn't a BOM in a UTF-8 file, its not anything.   The UTF-8 BOM is a
> different sequence of bits.  If tools treat it as a BOM, that is arguably a
> problem.

You're right.  FEFF is the UTF-16 big endian BOM.  UTF-16 is a 16 bit 
encoding, not at all the same as UTF-8.  I don't know how to read UTF-16 
in R. Uwe's advice was for UTF-8.

Duncan Murdoch

> 
> On Sat, 21 Jan 2023 at 05:09, Bill Dunlap <williamwdunlap using gmail.com> wrote:
> 
>> Setting the locale to "C" (or perhaps some other non-UTF-8 locale) will
>> show the BOM bytes.  E.g., on Windows I get:
>>
>>> Sys.getlocale()
>> [1] "LC_COLLATE=English_United States.utf8;LC_CTYPE=English_United
>> States.utf8;LC_MONETARY=English_United
>> States.utf8;LC_NUMERIC=C;LC_TIME=English_United States.utf8"
>>> tools::showNonASCIIfile('
>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE')
>>> rawToChar(readBin('
>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE',
>> what="raw", n=20))
>> [1] "export(AmpPhasDec"
>>> Sys.setlocale(locale="C")
>> [1] "C"
>>> tools::showNonASCIIfile('
>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE')
>> 1: <ef><bb><bf>export(AmpPhasDecomp,
>>> rawToChar(readBin('
>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE',
>> what="raw", n=20))
>> [1] "\357\273\277export(AmpPhasDec"
>>
>> -Bill
>>
>>
>> On Fri, Jan 20, 2023 at 9:16 AM Spencer Graves <
>> spencer.graves using effectivedefense.org> wrote:
>>
>>> Hi, Ivan and Uwe:
>>>
>>>
>>>            Thanks for your suggestions, but I've so far been unable to get
>>> them
>>> to work.  see below.
>>>
>>>
>>> On 1/20/23 9:22 AM, Uwe Ligges wrote:
>>>>
>>>>
>>>> On 20.01.2023 15:53, Ivan Krylov wrote:
>>>>> В Fri, 20 Jan 2023 08:41:25 -0600
>>>>> Spencer Graves <spencer.graves using effectivedefense.org> пишет:
>>>>>
>>>>>> ** byte-compile and prepare package for lazy loading
>>>>>> Error in parse(nsFile, keep.source = FALSE, srcfile = NULL) :
>>>>>>      1:1: unexpected input
>>>>>
>>>>> tools::showNonASCIIfile('
>>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE')
>>>>> # 1: <ef><bb><bf>export(AmpPhaseDecomp,
>>>>>
>>>>> Your NAMESPACE file starts with a U+FEFF ZERO WIDTH NO-BREAK SPACE.
>>>>> You'll need to remove it, e.g. by re-creating the first line.
>>>>
>>>>
>>>> Note that this is also called "byte order mark" (BOM). Tell your editor
>>>> not to create files with BOM.
>>>>
>>>> You can also fix in R:
>>>>
>>>> x <- readLines(..., encoding="UTF-8-BOM")
>>>> writeLines(x, ......)
>>>
>>>
>>>            In RStudio 2022.12.0+353 (the current version),
>>>
>>>
>>> tools::showNonASCIIfile('
>>> https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE')
>>>
>>>
>>> returned "char(0)".  'readLines' and 'writeLines' as Uwe suggested
>>> failed to fix it for me.
>>>
>>>
>>>            The first problem I noticed with this was that RStudio could
>> not
>>> read
>>> the NAMESPACE file.  When I tried, it said, "File is binary rather than
>>> text so cannot be opened by the source editor."  I changed something
>>> using a different editor and did "git commit" and "git push", and got
>>> the error on GitHub that I reported above.  I copied the file elsewhere,
>>> deleted it locally and from GitHub, then recreated it in LibreOffice by
>>> manually typing the first and last lines then copying the rest from a
>>> copy I had saved elsewhere.  The RStudio would open the file, but I
>>> still get the same error message as above from both "R CMD build fda"
>>> locally and from GitHub Action at:
>>>
>>>
>>> https://github.com/JamesRamsay5/fda
>>>
>>>
>>>            Other suggestions?
>>>            Thanks,
>>>            Spencer Graves
>>>
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
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