[R-pkg-devel] corrupted NAMESPACE file
Uwe Ligges
||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de
Sat Jan 21 08:47:35 CET 2023
On 21.01.2023 03:47, Spencer Graves wrote:
>
>
> 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.)
So you have declared LazyData: true?
How does the other package access the data object? By imprt directives?
Perhaps you exported the data in the past via the NAMSPACE file? But
then it has to be in sysdata.rda?
Sorry for the confusion with the BOM.
The encoding sting for UTF-16 with byte order mark is "UTF-16BE".
I'd believe much more should have gone wrong then. Perhaps it was some
editor that really messed it up?
Best,
Uwe Ligges
>
> 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
>>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-package-devel using r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
More information about the R-package-devel
mailing list