Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
I think what people are also thinking about is that the policy for
publishing a package on CRAN is that it have to pass R CMD check with
no errors, warnings *or* notes. So, in that sense notes are no
different from warnings.
At least that's why I go about and add some rare ad hoc code patching
in my code.
/Henrik
On Fri, Apr 16, 2010 at 2:09 AM, wrote:
> 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
>
> --
> Mark Bravington
> CSIRO Mathematical & Information Sciences
> Marine Laboratory
> Castray Esplanade
> Hobart 7001
> TAS
>
> ph (+61) 3 6232 5118
> fax (+61) 3 6232 5012
> mob (+61) 438 315 623
>
> 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
Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
Dear all,
I think that "notes" were introduced precisely to differentiate between
situations that may be innocuous and those that are more serious, the latter
producing "warnings" and "errors." The Rcmdr package, for example, generates
a whack of notes for code that works correctly and that I don't know how to
rewrite to get rid of the notes -- not to say that it would necessarily be
impossible to do so. Eliminating all packages that produce R CMD check notes
from CRAN is not a good idea, in my opinion.
Best,
John
John Fox
Senator William McMaster
Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
web: socserv.mcmaster.ca/jfox
> -Original Message-
> From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org]
On
> Behalf Of Henrik Bengtsson
> Sent: April-16-10 4:39 AM
> To: Mark.Bravington
> Cc: murdoch; luke; r-devel; info
> Subject: Re: [Rd] R CMD check tells me 'no visible binding for
globalvariable
> ', what does it mean?
>
> I think what people are also thinking about is that the policy for
> publishing a package on CRAN is that it have to pass R CMD check with
> no errors, warnings *or* notes. So, in that sense notes are no
> different from warnings.
>
> At least that's why I go about and add some rare ad hoc code patching
> in my code.
>
> /Henrik
>
> On Fri, Apr 16, 2010 at 2:09 AM, wrote:
> > 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
> >
> > --
> > Mark Bravington
> > CSIRO Mathematical & Information Sciences
> > Marine Laboratory
> > Castray Esplanade
> > Hobart 7001
> > TAS
> >
> > ph (+61) 3 6232 5118
> > fax (+61) 3 6232 5012
> > mob (+61) 438 315 623
> >
> > 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
Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
On Apr 16, 2010, at 4:38 AM, Henrik Bengtsson wrote:
> I think what people are also thinking about is that the policy for
> publishing a package on CRAN is that it have to pass R CMD check with
> no errors, warnings *or* notes.
Can you cite your reference, please? I see only (R-ext 1.5 Submitting a package
to CRAN):
"Please ensure that you can run through the complete procedure with only
warnings that you understand and have reasons not to eliminate. In principle,
packages must pass R CMD check without warnings to be admitted to the main CRAN
package area. If there are warnings you cannot eliminate (for example because
you believe them to be spurious) send an explanatory note with your submission."
It talks explicitly about warnings, notes are not mentioned at all... That
said, you should examine all notes and make sure they are not indications of
problems.
Cheers,
Simon
> So, in that sense notes are no
> different from warnings.
>
> At least that's why I go about and add some rare ad hoc code patching
> in my code.
>
> /Henrik
>
> On Fri, Apr 16, 2010 at 2:09 AM, wrote:
>> 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
>>
>> --
>> Mark Bravington
>> CSIRO Mathematical & Information Sciences
>> Marine Laboratory
>> Castray Esplanade
>> Hobart 7001
>> TAS
>>
>> ph (+61) 3 6232 5118
>> fax (+61) 3 6232 5012
>> mob (+61) 438 315 623
>>
>> 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) irregularUsag
Re: [Rd] R CMD check tells me 'no visible binding for globalvariable'
Henrik wrote:
I think what people are also thinking about is that the policy for
publishing a package on CRAN is that it have to pass R CMD check with
no errors, warnings *or* notes. So, in that sense notes are no
different from warnings.
-
Getting rid of these notes would be very hard in the survival package.
The population survival routines (survexp, pyears) that have to deal
with dates try to be very accommodating wrt the date format the user
chose, so have constructions like
if (user date looks like a chron object) {
calculation using chron functions
}
else if (is from the date package) {
use mdy.date }
else if (Date object)
etc
Most of the functions inside the {} cause a warning note because of
course the necessary packages for each case are not present when
survival is built. Since we deal with medical studies that span
multiple years or even decades, I and others in my group benefit
directly from this date handling: it was not added solely from a
humanitarian impulse.
It's a minor nuisance, since I have to read through the messages after
each build to see if something I actually do need to worry about turns
up. It has happened, in which case I'm thankful for the message.
(Although it would be nice if there were a way to generate more context.
Once one was for an undefined variable 'n', which was not easy to find
using a text editor.)
Terry Therneau
__
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'
On Fri, 16 Apr 2010, Therneau, Terry M., Ph.D. wrote:
'Henrik' wrote:
I think what people are also thinking about is that the policy for
publishing a package on CRAN is that it have to pass R CMD check with
no errors, warnings *or* notes. So, in that sense notes are no
different from warnings.
I think that policy is a figment of his imagination. 'NOTE' was
introduced to allow tentative warnings: we for example note .Rd errors
that we can correct and warn (so far) on those we cannot.
-
Getting rid of these notes would be very hard in the survival package.
The population survival routines (survexp, pyears) that have to deal
with dates try to be very accommodating wrt the date format the user
chose, so have constructions like
if (user date looks like a chron object) {
calculation using chron functions
}
else if (is from the date package) {
use mdy.date }
else if (Date object)
etc
Most of the functions inside the {} cause a warning note because of
course the necessary packages for each case are not present when
survival is built. Since we deal with medical studies that span
multiple years or even decades, I and others in my group benefit
directly from this date handling: it was not added solely from a
humanitarian impulse.
It's a minor nuisance, since I have to read through the messages after
each build to see if something I actually do need to worry about turns
up. It has happened, in which case I'm thankful for the message.
(Although it would be nice if there were a way to generate more context.
Once one was for an undefined variable 'n', which was not easy to find
using a text editor.)
We do load all the Depends and Suggests packages when doing the
codetools checks, so I think that
Suggests: date, chron, timeDate
would solve this. It leaves
predict.coxph: no visible global function definition for ‘labels.lm’
predict.coxph: no visible global function definition for ‘Build.terms’
predict.survreg: no visible global function definition for ‘labels.lm’
predict.survreg: no visible global function definition for ‘Build.terms’
survpenal.fit: no visible global function definition for ‘new.frame’
survpenal.fit: possible error in get("coxlist1", frame = rho): unused
argument(s) (frame = rho)
survpenal.fit: possible error in get("coxlist2", frame = rho): unused
argument(s) (frame = rho)
survreg.fit: no visible global function definition for ‘new.frame’
which are I think all from S-Plus specific code.
Brian Ripley
Terry Therneau
__
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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 Fri, 16 Apr 2010, Simon Urbanek wrote: On Apr 16, 2010, at 4:38 AM, Henrik Bengtsson wrote: I think what people are also thinking about is that the policy for publishing a package on CRAN is that it have to pass R CMD check with no errors, warnings *or* notes. Can you cite your reference, please? I see only (R-ext 1.5 Submitting a package to CRAN): "Please ensure that you can run through the complete procedure with only warnings that you understand and have reasons not to eliminate. In principle, packages must pass R CMD check without warnings to be admitted to the main CRAN package area. If there are warnings you cannot eliminate (for example because you believe them to be spurious) send an explanatory note with your submission." It talks explicitly about warnings, notes are not mentioned at all... That said, you should examine all notes and make sure they are not indications of problems. In my experience, if a package is new or previously checked without notes, the CRAN maintainers will likely ask you to look at them to make sure they aren't problems, but there isn't any difficulty in getting a package on CRAN if it has notes. A whole lot of packages on CRAN have notes even when checked on r-release. CMD check notes are the R equivalent of old-time lint warnings in C, and as the First Commandment says: Thou shalt run lint frequently and study its pronouncements with care, for verily its perception and judgement oft exceed thine. and the prophet (Henry Spencer) expands on this: ``Study'' doth not mean mindless zeal to eradicate every byte of lint output-if for no other reason, because thou just canst not shut it up about some things-but that thou should know the cause of its unhappiness and understand what worrisome sign it tries to speak of. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] winbuilder down
Please note that the "winbuilder" service will be down during the weekend (at least until sunday) due work on the power supply of the building. Best wishes, Uwe Ligges __ 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 Fri, Apr 16, 2010 at 5:51 PM, Thomas Lumley wrote: > On Fri, 16 Apr 2010, Simon Urbanek wrote: > >> >> On Apr 16, 2010, at 4:38 AM, Henrik Bengtsson wrote: >> >>> I think what people are also thinking about is that the policy for >>> publishing a package on CRAN is that it have to pass R CMD check with >>> no errors, warnings *or* notes. WRONG: As already said by other, it is indeed possible to get packages with 'notes' onto CRAN. I have at some point in history became to believe this, but I went back in my submission log and I only found one case and it is was more Kurt H. kindly suggesting that I should fix an incorrectly formatted license (reported as a NOTE). Thanks for making me aware of this. Sorry for adding noise! /Henrik >> >> Can you cite your reference, please? I see only (R-ext 1.5 Submitting a >> package to CRAN): >> >> "Please ensure that you can run through the complete procedure with only >> warnings that you understand and have reasons not to eliminate. In >> principle, packages must pass R CMD check without warnings to be admitted to >> the main CRAN package area. If there are warnings you cannot eliminate (for >> example because you believe them to be spurious) send an explanatory note >> with your submission." >> >> It talks explicitly about warnings, notes are not mentioned at all... That >> said, you should examine all notes and make sure they are not indications of >> problems. >> > > In my experience, if a package is new or previously checked without notes, > the CRAN maintainers will likely ask you to look at them to make sure they > aren't problems, but there isn't any difficulty in getting a package on CRAN > if it has notes. A whole lot of packages on CRAN have notes even when > checked on r-release. > > CMD check notes are the R equivalent of old-time lint warnings in C, and as > the First Commandment says: > Thou shalt run lint frequently and study its pronouncements with > care, for verily its perception and judgement oft exceed thine. > and the prophet (Henry Spencer) expands on this: > ``Study'' doth not mean mindless zeal to eradicate every byte of lint > output-if for no other reason, because thou just canst not shut it up about > some things-but that thou should know the cause of its unhappiness and > understand what worrisome sign it tries to speak of. > > > -thomas > > Thomas Lumley Assoc. Professor, Biostatistics > tlum...@u.washington.edu University of Washington, Seattle > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
