Re: [R-pkg-devel] corrupted NAMESPACE file
On 20/01/2023 9:47 p.m., 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.)
I just cloned the repository, and saw the same error as you saw. Then I
followed my advice, and removed `refinery` from the NAMESPACE file, and
the error went away.
Since you don't have `LazyData: true` in the current version, you need
to run `data(refinery)` to make that dataset available. That does work.
I also tried restoring `LazyData:true` as well as removing `refinery`
from NAMESPACE, and that works too, without the need to call
`data(refinery)`. The variable is just available.
I'm not sure which *.rda files you are talking about that "are mentioned
in NAMESPACE". Now that I've removed `refinery` in my copy, I don't see
any of them.
Duncan Murdoch
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
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: 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 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: 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
Re: [R-pkg-devel] corrupted NAMESPACE file
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
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: 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 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: 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
Re: [R-pkg-devel] corrupted NAMESPACE file
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
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: 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 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: 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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
Re: [R-pkg-devel] corrupted NAMESPACE file
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
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: 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 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: 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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] corrupted NAMESPACE file
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
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: 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 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: 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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] corrupted NAMESPACE file
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 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: 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 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: 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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Re: [R-pkg-devel] corrupted NAMESPACE file
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.
On Sat, 21 Jan 2023 at 05:09, Bill Dunlap 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: 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 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: 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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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
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Re: [R-pkg-devel] corrupted NAMESPACE file
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: 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 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: 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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Re: [R-pkg-devel] corrupted NAMESPACE file
On 20/01/2023 12:15 p.m., Spencer Graves 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 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: 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?
I think Uwe's suggestion was to check out the file, apply his two steps,
and commit it again. Your showNonASCIIfile() call was trying to work on
something else. Maybe your other commands were too?
Another possibility is to roll back all your changes to that file until
you have a copy you can work with. I think commit ab455089 is probably
the bad one; Github shows invisible changes to the first line. You
don't want those.
Duncan Murdoch
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Re: [R-pkg-devel] corrupted NAMESPACE file
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 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: 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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Re: [R-pkg-devel] corrupted NAMESPACE file
On 20.01.2023 15:53, Ivan Krylov wrote:
В Fri, 20 Jan 2023 08:41:25 -0600
Spencer Graves 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: 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, ..)
Best,
Uwe Ligges
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Re: [R-pkg-devel] corrupted NAMESPACE file
В Fri, 20 Jan 2023 08:41:25 -0600
Spencer Graves 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: 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.
--
Best regards,
Ivan
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