Re: [Rd] CRAN: MacOS X binary: not available, see check log?
On Apr 15, 2010, at 2:26 AM, Henrik Bengtsson wrote: > For a couple of days, MacOS X binaries are not build on CRAN (for my > recently uploaded packages only?): > AFAICS your package was posted on Apr 13 so at the earliest it can be built in the Apr 14 run = yesterday. There was no Apr 14 run because the R build failed on Apr 13. I was chasing the subsequent issues yesterday and I think the latest R build is now working so today's package update should be on CRAN soon. Don't forget that packages have to swim across the Atlantic to get built and then back as binaries, so the migration can take a day or two ;). Cheers, Simon > The R.oo package is listed as "MacOS X binary: not available, see > check log?", but the 'check log' show no errors > URL: http://cran.r-project.org/web/packages/R.oo/ > > Is this a known issue? > > /Henrik > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] callNextMethod() and NAMESPACE
Hello there,
I define a accessor method for one of my classes, i.e.
setMethod(f = "[",
signature = "NG_data",
definition = function(x,i,j,drop){
if(all(is.na(match(j,x...@shortnames)) == FALSE)){
return(x[,match(j,x...@shortnames)]) }else{
callNextMethod()
}
}
)
where the class "NG_data" inherits from the "data.frame" class. Hence I
added the line
exportMethods("[")
to my NAMESPACE file. After package building, installing and loading, I
try to use this accessor method
myObject[,1]
but I get the error message:
Error in callNextMethod() : bad object found as method (class "function")
Interestingly, if I then execute the setMethod(f = "["... in the
command prompt
myObject[,1]
works. Does anybody has a clue what could go wrong?
Adrian Waddell
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[Rd] "°" not accepted under MacOSX
I am developping a package (pgirmess) that since long does not go
through CRAN MacOSX checks, just because I have this command in one of
the examples.
text(mydata[,3],mydata[,4],paste(round(dirs,0),"°"),cex=0.7)
It makes:
text(mydata[,3],mydata[,4],paste(round(dirs,0),"+
+
+
+ cleanEx()
+ nameEx("distNode")
Error: unexpected symbol in:
"cleanEx()
nameEx("distNode"
Execution halted
The description file (following some earlier recommandation) includes:
Encoding: latin1
Is there any way to make "°" accepted by MacOSX checks ?
Cheers,
Patrick
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Re: [Rd] "°" not accepted under MacOSX
The subject line is untrue.
We recommend in 'Writing R Extensions' that you encode such characters
as \u sequences, in this case "\u00b0". However, this is more
likely to be a locale problem on the check server, as pgirmess checks
out on my Mac. In fact, the top of the log is
# using R version 2.11.0 beta (2010-04-12 r51689)
# using session charset: ASCII
# checking for file 'pgirmess/DESCRIPTION' ... OK
# this is package 'pgirmess' version '1.4.4'
# package encoding: latin1
and you cannot reencode latin1 to ASCII
I don't know why you would choose to use something that makes your
package fail on many Japanese or Greek or Russian systems, and of
course in C locales. Plotmath is portable, and these days "\u00b0" is
also pretty portable.
On Thu, 15 Apr 2010, Patrick Giraudoux wrote:
I am developping a package (pgirmess) that since long does not go through
CRAN MacOSX checks, just because I have this command in one of the examples.
text(mydata[,3],mydata[,4],paste(round(dirs,0),"°"),cex=0.7)
It makes:
text(mydata[,3],mydata[,4],paste(round(dirs,0),"+
+
+
+ cleanEx()
+ nameEx("distNode")
Error: unexpected symbol in:
"cleanEx()
nameEx("distNode"
Execution halted
The description file (following some earlier recommandation) includes:
Encoding: latin1
Is there any way to make "°" accepted by MacOSX checks ?
Cheers,
Patrick
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University of Oxford, Tel: +44 1865 272861 (self)
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Re: [Rd] "°" not accepted under MacOSX
Prof Brian Ripley a écrit : The subject line is untrue. We recommend in 'Writing R Extensions' that you encode such characters as \u sequences, in this case "\u00b0". However, this is more likely to be a locale problem on the check server, as pgirmess checks out on my Mac. In fact, the top of the log is # using R version 2.11.0 beta (2010-04-12 r51689) # using session charset: ASCII # checking for file 'pgirmess/DESCRIPTION' ... OK # this is package 'pgirmess' version '1.4.4' # package encoding: latin1 and you cannot reencode latin1 to ASCII I don't know why you would choose to use something that makes your package fail on many Japanese or Greek or Russian systems, and of course in C locales. Plotmath is portable, and these days "\u00b0" is also pretty portable. Thanks a lot. Strictly speaking, I did not choose: I was just not familiar with \u encoding, and will document on it now I have a good hint to start with... Thanks again, Patrick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
On Mon, 12 Apr 2010, William Dunlap wrote:
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Henrik Bengtsson
Sent: Monday, April 12, 2010 8:24 AM
To: Duncan Murdoch
Cc: r-devel; Michael Dewey
Subject: Re: [Rd] R CMD check tells me 'no visible binding
for globalvariable ', what does it mean?
On Mon, Apr 12, 2010 at 5:08 PM, Duncan Murdoch
wrote:
On 12/04/2010 10:51 AM, Michael Dewey wrote:
When I run R CMD check on a package I have recently
started work on I get
the following:
* checking R code for possible problems ... NOTE
addlinear: no visible binding for global variable 'x'
I appreciate that this is only a NOTE and so I assume is
R's equivalent of
'This is perfectly legal but I wonder whether it is really what you
intended' but I would like to understand it.
In the relevant function addlinear the following function
is defined
locally:
orfun <- function(x, oddsratio) {1/(1+1/(oddsratio *
(x/(1-x}
and then used later in curve
curve(orfun(x, exp(estimate)), from = 0.001, to =
0.999, add = TRUE)
These are the only occurrences of 'x'.
Is it just telling me that I have never assigned a value
to x? Or is it
more sinister than that? As far as I can tell the function
does what I
intended.
The curve() function evaluates the first argument in a
strange way, and this
confuses the code checking. (The variable name "x" is
special to curve().)
I think you can avoid the warning by rewriting that call to
curve() as
curve(function(x) orfun(x, exp(estimate)), from = 0.001, to
= 0.999, add =
TRUE)
...or
x <- NULL; rm(x); # Dummy to trick R CMD check
curve(orfun(x, exp(estimate)), from = 0.001, to = 0.999, add = TRUE)
Or we could come up with a scheme to telling the usage checking functions
in codetools that some some or all arguments of certain functions
are evaluated in odd ways so it should not check them. E.g.,
irregularUsage(curve, expr)
irregularUsage(lm, subset, formula) # subset and formula arguments of lm
irregularUsage(expression, ...) # ... arguments to expression
Perhaps one could add such indications to the NAMESPACE file
or to a new file in a package. The former is kludgy but the
latter requires changes to the packaging system.
This is done at the moment in a very ad hoc way for functions in the
core packages. I will make a note to add something for curve. This
is an interesting case, as only the variable 'x' should be viewed as
special for code analysis purposes if I understand the intent in curve
properly.
Providing a mechanism for user functions to be annotated for code
analysis might be useful, and might help in making the handling of
core package functions with special evaluation rulesa little less ad
hloc. On the other hand I'm not sure I want to do anything that
encourages further use of nonstantard evaluation in new code.
luke
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
/Henrik
Duncan Murdoch
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University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
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Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
Speaking as a copious generator of CMD CHECK notes: I don't see that there's a
problem to be solved here-- i.e. I don't see why it's worth changing good code
or adding conventions just to circumvent CMD CHECK notes. (If the code is bad,
of course it should be changed!) As the original poster said, the CMD CHECK
note is only a note, not a warning-- it's checking for "*possible* problems".
With my packages, especially debug & mvbutils, CHECK issues 100s of lines of
"notes", which (after inspection) I don't worry about-- they arise from RCMD
CHECK not understanding my code (eg non-default scopings), not from coding
errors. I would be very unhappy at having to add enormous amounts of
"explanation" to the packages simply to alleviate a non-problem!
Similarly, some compilers give notes about possibly non-initialized variables
etc, but these are often a result of the compiler not understanding the code. I
do look at them, and decide whether there are problems that need fixing or
not-- it's no big deal to ignore them if not useful. Presumably the RCMD CHECK
notes are useful to some coders, in which case good; but nothing further really
seems needed.
Mark
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l...@stat.uiowa.edu wrote:
> On Mon, 12 Apr 2010, William Dunlap wrote:
>
>>
>>> -Original Message-
>>> From: r-devel-boun...@r-project.org
>>> [mailto:r-devel-boun...@r-project.org] On Behalf Of Henrik Bengtsson
>>> Sent: Monday, April 12, 2010 8:24 AM
>>> To: Duncan Murdoch
>>> Cc: r-devel; Michael Dewey
>>> Subject: Re: [Rd] R CMD check tells me 'no visible binding for
>>> globalvariable ', what does it mean?
>>>
>>> On Mon, Apr 12, 2010 at 5:08 PM, Duncan Murdoch
>>> wrote:
On 12/04/2010 10:51 AM, Michael Dewey wrote:
>
> When I run R CMD check on a package I have recently started work
> on I get the following:
>
> * checking R code for possible problems ... NOTE
> addlinear: no visible binding for global variable 'x'
>
> I appreciate that this is only a NOTE and so I assume is R's
> equivalent of 'This is perfectly legal but I wonder whether it is
> really what you intended' but I would like to understand it.
>
> In the relevant function addlinear the following function is
> defined locally:
>
> orfun <- function(x, oddsratio) {1/(1+1/(oddsratio *
> (x/(1-x}
>
> and then used later in curve
>
> curve(orfun(x, exp(estimate)), from = 0.001, to = 0.999,
> add = TRUE)
>
> These are the only occurrences of 'x'.
>
> Is it just telling me that I have never assigned a value to x? Or
> is it more sinister than that? As far as I can tell the function
> does what I intended.
The curve() function evaluates the first argument in a strange
way, and this confuses the code checking. (The variable name "x"
is special to curve().)
I think you can avoid the warning by rewriting that call to
curve() as
curve(function(x) orfun(x, exp(estimate)), from = 0.001, to =
0.999, add = TRUE)
>>>
>>> ...or
>>>
>>> x <- NULL; rm(x); # Dummy to trick R CMD check curve(orfun(x,
>>> exp(estimate)), from = 0.001, to = 0.999, add = TRUE)
>>
>> Or we could come up with a scheme to telling the usage checking
>> functions in codetools that some some or all arguments of certain
>> functions are evaluated in odd ways so it should not check them.
>> E.g., irregularUsage(curve, expr) irregularUsage(lm, subset,
>> formula) # subset and formula arguments of lm
>> irregularUsage(expression, ...) # ... arguments to expression
>> Perhaps one could add such indications to the NAMESPACE file or to a
>> new file in a package. The former is kludgy but the latter requires
>> changes to the packaging system.
>>
>
> This is done at the moment in a very ad hoc way for functions in the
> core packages. I will make a note to add something for curve. This
> is an interesting case, as only the variable 'x' should be viewed as
> special for code analysis purposes if I understand the intent in
> curve properly.
>
> Providing a mechanism for user functions to be annotated for code
> analysis might be useful, and might help in making the handling of
> core package functions with special evaluation rulesa little less ad
> hloc. On the other hand I'm not sure I want to do anything that
> encourages further use of nonstantard evaluation in new code.
>
> luke
>
>> Bill Dunlap
>> Spotfire, TIBCO Software
>> wdunlap tibco.com
>>
>>
>>>
>>> /Henrik
>>>
Duncan Murdoch
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>>>
>>> __
>>> R-devel@r-pr
