Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
At 01:09 16/04/2010, mark.braving...@csiro.au 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.
As the original poster can I endorse that, I was trying to improve my
understanding. I was not worried by it.
Just to follow up on the suggestions made for eliminating the note I
posted that Duncan's suggestion worked.
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)
It does remove the note but then throws an error when called
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
Henrik's suggestion of setting x to a value and then removing it
works but in the light of the discussions I think I will just leave
the note in place.
Thanks to everyone for their help and suggestions
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
murd...@stats.uwo.ca 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
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, mark.braving...@csiro.au 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
murd...@stats.uwo.ca 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
__
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?
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, mark.braving...@csiro.au 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
murd...@stats.uwo.ca 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
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, mark.braving...@csiro.au 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
murd...@stats.uwo.ca 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
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
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 tlum...@u.washington.edu 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
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
murd...@stats.uwo.ca 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
__
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
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu__
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?
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
murd...@stats.uwo.ca 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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Re: [Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?
-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
murd...@stats.uwo.ca 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.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
/Henrik
Duncan Murdoch
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