Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On Apr 10, 2011, at 19:54 , wrote: > On Sun, 10 Apr 2011, Hadley Wickham wrote: > Okay, I understand what you are trying to do. Yes, you have fooled codetools in this instance. >>> >>> ...but notice that the codetools warning is just that: It _is_ acknowledged >>> that these things occasionally happen by design. There are a couple of >>> cases in base R too: >>> >>> * checking R code for possible problems ... NOTE >>> glm.fit: no visible binding for global variable ‘n’ >> >> Are you sure that's not a bug? There's: >> >> aic.model <- aic(y, n, mu, weights, dev) + 2 * rank >> >> and n.ok is defined, but n isn't defined anywhere. > > It is (or should be) defined by the call to > >eval(family$initialize) > ...iff actually used by family$aic. And, it is a different n from n.ok (a vector, the per-element size parameter of the binomial) >> >>> quantile.ecdf: no visible binding for global variable ‘y’ >> >> I wonder why it warns on y, but not nobs. > > It does when run on stats:::quantile.ecdf directly: > >> codetools::checkUsage(stats:::quantile.ecdf) > : no visible binding for global variable ‘nobs’ > : no visible binding for global variable ‘y’ > > Maybe in the context where you saw this nobs is defined in an > enclosing environment. > It came from make check-devel, so I suspect that it picks up stats:::nobs() (which would be horribly wrong, but, well...) > luke > >> >> Hadley -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On Sun, 10 Apr 2011, Hadley Wickham wrote: Okay, I understand what you are trying to do. Yes, you have fooled codetools in this instance. ...but notice that the codetools warning is just that: It _is_ acknowledged that these things occasionally happen by design. There are a couple of cases in base R too: * checking R code for possible problems ... NOTE glm.fit: no visible binding for global variable ‘n’ Are you sure that's not a bug? There's: aic.model <- aic(y, n, mu, weights, dev) + 2 * rank and n.ok is defined, but n isn't defined anywhere. It is (or should be) defined by the call to eval(family$initialize) quantile.ecdf: no visible binding for global variable ‘y’ I wonder why it warns on y, but not nobs. It does when run on stats:::quantile.ecdf directly: codetools::checkUsage(stats:::quantile.ecdf) : no visible binding for global variable ‘nobs’ : no visible binding for global variable ‘y’ Maybe in the context where you saw this nobs is defined in an enclosing environment. luke Hadley -- Luke Tierney 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] Wish there were a "strict mode" for R interpreter. What about You?
>> Okay, I understand what you are trying to do. Yes, you have fooled >> codetools in this instance. > > ...but notice that the codetools warning is just that: It _is_ acknowledged > that these things occasionally happen by design. There are a couple of cases > in base R too: > > * checking R code for possible problems ... NOTE > glm.fit: no visible binding for global variable ‘n’ Are you sure that's not a bug? There's: aic.model <- aic(y, n, mu, weights, dev) + 2 * rank and n.ok is defined, but n isn't defined anywhere. > quantile.ecdf: no visible binding for global variable ‘y’ I wonder why it warns on y, but not nobs. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On Apr 10, 2011, at 15:10 , Duncan Murdoch wrote:
> On 11-04-09 9:22 PM, Spencer Graves wrote:
>> On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
>>> On 11-04-09 7:02 PM, Spencer Graves wrote:
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
>>>
>>> What is ETB? Your code is looking for a global variable by that name,
>>> and that's what codetools is telling you.
>>
>> Duncan: Thanks for the question.
>>
>>
>> ETB is a data object in my package. codetools can't find it because
>> data(ETB) is needed before ETB becomes available. codetools is not
>> smart enough to check to see if ETB is a data object in the package.
>
> Okay, I understand what you are trying to do. Yes, you have fooled codetools
> in this instance.
...but notice that the codetools warning is just that: It _is_ acknowledged
that these things occasionally happen by design. There are a couple of cases in
base R too:
* checking R code for possible problems ... NOTE
glm.fit: no visible binding for global variable ‘n’
quantile.ecdf: no visible binding for global variable ‘y’
I can't seem to spot the 'n' just now, though...
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
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Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 4/10/2011 6:10 AM, Duncan Murdoch wrote:
On 11-04-09 9:22 PM, Spencer Graves wrote:
On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson
wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block
anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around
here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used.
Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to
fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I
don't feel
it's appropriate. For example, I define a data object ETB in a
package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
What is ETB? Your code is looking for a global variable by that name,
and that's what codetools is telling you.
Duncan: Thanks for the question.
ETB is a data object in my package. codetools can't find it because
data(ETB) is needed before ETB becomes available. codetools is not
smart enough to check to see if ETB is a data object in the package.
Okay, I understand what you are trying to do. Yes, you have fooled
codetools in this instance.
I'm sorry: I did not intend to fool codetools. ;-)
I just wanted to provide sensible defaults in a way that seemed
obvious to me.
Thanks again for all your work on Rtools and the R project more
generally. Spencer
Duncan Murdoch
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
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Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 11-04-09 9:22 PM, Spencer Graves wrote:
On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson
wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
What is ETB? Your code is looking for a global variable by that name,
and that's what codetools is telling you.
Duncan: Thanks for the question.
ETB is a data object in my package. codetools can't find it because
data(ETB) is needed before ETB becomes available. codetools is not
smart enough to check to see if ETB is a data object in the package.
Okay, I understand what you are trying to do. Yes, you have fooled
codetools in this instance.
Duncan Murdoch
__
R-devel@r-project.org mailing list
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Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson
wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
What is ETB? Your code is looking for a global variable by that name,
and that's what codetools is telling you.
Duncan: Thanks for the question.
ETB is a data object in my package. codetools can't find it because
data(ETB) is needed before ETB becomes available. codetools is not
smart enough to check to see if ETB is a data object in the package.
Spencer
Duncan Murdoch
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson
wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
What is ETB? Your code is looking for a global variable by that name,
and that's what codetools is telling you.
Duncan: Thanks for the question.
ETB is a data object in my package. codetools can't find it because
data(ETB) is needed before ETB becomes available. codetools is not
smart enough to check to see if ETB is a data object in the package.
Spencer
Duncan Murdoch
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
What is ETB? Your code is looking for a global variable by that name,
and that's what codetools is telling you.
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
library(codetools)
checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Is this run by "R CMD check"? I've seen this message.
"R CMD check" will give this message sometimes when I don't feel
it's appropriate. For example, I define a data object ETB in a package,
then give that as the default in a function call like
f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD
check", I get "no visible binding for global variable 'ETB'", even
though the function is tested and works during R CMD check.
Spencer
Hadley
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson wrote:
> Years ago, I did lots of Perl programming. Perl will let you be lazy
> and write functions that refer to undefined variables (like R does),
> but there is also a strict mode so the interpreter will block anything
> when a variable is mentioned that has not been defined. I wish there
> were a strict mode for checking R functions.
>
> Here's why. We have a lot of students writing R functions around here
> and they run into trouble because they use the same name for things
> inside and outside of functions. When they call functions that have
> mistaken or undefined references to names that they use elsewhere,
> then variables that are in the environment are accidentally used. Know
> what I mean?
>
> dat <- whatever
>
> someNewFunction <- function(z, w){
> #do something with z and w and create a new "dat"
> # but forget to name it "dat"
> lm (y, x, data=dat)
> # lm just used wrong data
> }
>
> I wish R had a strict mode to return an error in that case. Users
> don't realize they are getting nonsense because R finds things to fill
> in for their mistakes.
>
> Is this possible? Does anybody agree it would be good?
> library(codetools)
> checkUsage(someNewFunction)
: no visible binding for global variable ‘y’
: no visible binding for global variable ‘x’
: no visible binding for global variable ‘dat’
Which also picks up another bug in your function ;)
Hadley
--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
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Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?
On 11-04-09 3:51 PM, Paul Johnson wrote:
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat<- whatever
someNewFunction<- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
It would be really bad, unless done carefully.
In your function the free (undefined) variables are dat and lm. You
want to be warned about dat, but you don't want to be warned about lm.
What rule should R use to determine that?
(One possible rule would work in a package with a namespace. In that
case, all variables must be found in declared dependencies, the search
could stop before it got to globalenv(). But it seems unlikely that
your students are writing packages with namespaces.)
Duncan Murdoch
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[Rd] Wish there were a "strict mode" for R interpreter. What about You?
Years ago, I did lots of Perl programming. Perl will let you be lazy
and write functions that refer to undefined variables (like R does),
but there is also a strict mode so the interpreter will block anything
when a variable is mentioned that has not been defined. I wish there
were a strict mode for checking R functions.
Here's why. We have a lot of students writing R functions around here
and they run into trouble because they use the same name for things
inside and outside of functions. When they call functions that have
mistaken or undefined references to names that they use elsewhere,
then variables that are in the environment are accidentally used. Know
what I mean?
dat <- whatever
someNewFunction <- function(z, w){
#do something with z and w and create a new "dat"
# but forget to name it "dat"
lm (y, x, data=dat)
# lm just used wrong data
}
I wish R had a strict mode to return an error in that case. Users
don't realize they are getting nonsense because R finds things to fill
in for their mistakes.
Is this possible? Does anybody agree it would be good?
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas
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