[R-pkg-devel] corrupted NAMESPACE file
Spencer Graves
@pencer@gr@ve@ @end|ng |rom e||ect|vede|en@e@org
Sat Jan 21 03:47:34 CET 2023
On 1/20/23 7:32 PM, Duncan Murdoch wrote:
> 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.
I got the same negative results after deleting "LazyData: true" from
DESCRIPTION. (That's what I would expect, because there are 17 other
*.rda files in the data subdirectory that are are mentioned in NAMESPACE
and are not creating a problem. In 2009 the package included both
"data/refinery.rda" and "man/refinery.Rd". They were erroneously
removed at some point. I'm now trying to restore them.)
Thanks,
Spencer
>
> 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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