[R-pkg-devel] corrupted NAMESPACE file

[Spencer Graves]

Hello, All:


	  My attempts to fix this problem exposed what seems to be a completely 
unrelated problem:  All five GitHub Actions end now with:


Error: package or namespace load failed for ‘fda’ in namespaceExport(ns, 
exports):
  undefined exports: refinery


	  The package includes ~man/refinery.Rd, ~data/refinery.rda, and 
NAMESPACE includes "export( ... refinery, ...)".


	  ???
	  I have Bitdefender installed on this computer.  A "Quick Scan" 
produced nothing just now.


	  Thanks,
	  Spencer


On 1/20/23 5:08 PM, Duncan Murdoch wrote:
> 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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