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 <williamwdun...@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.gra...@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.gra...@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






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