[R-pkg-devel] corrupted NAMESPACE file

[Duncan Murdoch]

On 20/01/2023 8:16 p.m., Spencer Graves wrote:
> 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 think if you declare something as data by putting it in the data 
directory and using LazyData:true, you shouldn't also declare it as an 
export in the NAMESPACE file.

Duncan Murdoch

> 
> 
> 	  ???
> 	  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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