[Rd] [RE: why does parent.frame() cycle when called from inside capture.output()?]
Thanks, Mark - I'm taking up your invitation to forward your message
to the list just because it gives us some valuable data on (1) how
long the behavior has been around, and (2) how many other people
(don't) understand the behavior, and (3) how we might fix or work
around it.
I notice some other people also seem to be diffident about posting on
R-devel; perhaps I should conclude that bugs like this are below the
radar for busy statisticians.
FWIW, after playing around a bit with mvbutils::mvb.parent.frame, I
now have a working "desubN" (see the attachment on my original
message, and this one). I don't really have a good understanding of
*why* it now works, and why the original version didn't work...
Thanks again Mark. Also, nice hacking.
Frederick
- Forwarded message from mark.braving...@data61.csiro.au -
Date: Mon, 12 Dec 2016 06:20:17 +
From: mark.braving...@data61.csiro.au
To: frede...@ofb.net
Subject: RE: [Rd] why does parent.frame() cycle when called from inside
capture.output()?
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Hi Frederik
[ I'm replying off-list in case you, or the rest of R-devel, don't find this
reply useful... please fwd to the list if it does help you ]
I'm the author of the 'debug' package. When I wrote it--- many years ago now---
I encountered some fairly strange behaviour with frames in the call stack,
which is reminiscent of what you're seeing. The debug package still works fine,
so I presume nothing has changed much.
If you load debug and then do ?mvb.sys.parent (and look at the code), you might
get *some* idea of what's going on. TBH I can't remember the details now...
HTH
Mark
Mark Bravington
CSIRO Marine Lab
Hobart
Australia
From: R-devel [r-devel-boun...@r-project.org] on behalf of frede...@ofb.net
[frede...@ofb.net]
Sent: 12 December 2016 16:54
To: r-devel@r-project.org
Cc: r-h...@r-project.org
Subject: [Rd] why does parent.frame() cycle when called from inside
capture.output()?
Hello R devel/help,
I ran into this strange behavior:
# showstack is supposed to walk through the stack of parent
# environments when it is called:
showstack = function() {
env = environment()
for(i in 1:12) {
env = do.call(parent.frame, list(), env=env)
print(env)
}
}
# a simple chain of functions:
g3=function(t) showstack()
g2=function(w) g3(w)
g1=function(z) g2(z)
g=function(y) g1(y)
g()
# outputs:
#
#
#
#
#
#
#
#
#
# ...
cat(capture.output(g()),sep="\n")
# outputs:
#
#
#
#
#
#
#
#
#
#
#
#
The strange thing of course is that the second call doesn't stay with
R_GlobalEnv, but in fact goes into a loop of period 4. I'm not so
surprised that the parent frame of the global environment is itself,
as in the first call, but it seems weird to have a loop of period 4...
Using `ls()` shows that two of the "loop" environments belong to
capture.output() and eval().
But if capture.output is really evaluating its input in the parent
frame, as it appears to be doing from its source code, then I would
have expected the output to be the same as the output I get by
evaluating the same expression in this frame.
I was trying to debug a function which attempts to be a multi-frame
version of deparse(substitute(...)). I'm attaching this function in
case anyone is curious. Perhaps my attachment can shed more light on
the problem I'm having.
Apologies if this is not a bug - I wasn't sure which mailing list to
send this to, and I took a guess.
Thanks,
Frederick
- End forwarded message -
# We can't just use `mvb.parent.frame` as a replacement for
# `parent.frame`, because the former throws an error when there is no
# parent frame - while we had relied on the latter gracefully giving
# us the global environment. So here's a wrapper which gives
# mvb.parent.frame the behavior we want:
my_mvb_parent=function() {
tryCatch(
mvb.parent.frame(2),
error=function(e) { globalenv()})
}
desubN <- function(y,n=1) {
env=environment();
for(i in 1:n) {
y = do.call(substitute, list(substitute(y)), env=env)
env = do.call(my_mvb_parent, list(), env=env)
}
deparse(y)
}
g2=function(t) {
for(i in 1:5) {
print(desubN(t,i))
print(capture.output(desubN(t,i)))
}
}
g1=function(z) g2(z)
g=function(y) g1(y)
g(log)
# now capture.output seems to give the same results as the bare
# expression
## [1] "t"
## [1] "[1] \"t\""
## [1] "z"
## [1] "[1] \"z\""
## [1] "y"
## [1] "[1] \"y\""
## [1] "log"
## [1] "[1] \"log\""
## [1] "log"
## [1] "[1] \"log\""
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Re: [Rd] Strange behavior when using progress bar (Fwd: Re: [R] The code itself disappears after starting to execute the for loop)
Thanks John,
As the problem can be reproduced, I would like to submit this as a bug
report. But I think someone will have to add me to Bugzilla first.
Given the few responses, I am not expecting that this will get a high
priority though...
Jon
On 12/7/2016 2:59 PM, Fox, John wrote:
Dear Martin and Jon,
I can reproduce this problem in the Windows GUI, where I observed it using
Jon's program after 75 iterations. I didn't observe the problem in a Windows
terminal or under RStudio, letting the program run for more than 200 iterations
in each case.
My system and session info:
- snip -
Sys.info()
sysname release version nodename
"Windows" "10 x64""build 14393" "JOHN-CARBON-X1"
machinelogin user effective_user
"x86-64" "John Fox" "John Fox" "John Fox"
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
- snip -
I hope this helps,
John
-
John Fox, Professor
McMaster University
Hamilton, Ontario
Canada L8S 4M4
Web: socserv.mcmaster.ca/jfox
-Original Message-
From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Martin
Maechler
Sent: December 7, 2016 5:58 AM
To: Jon Skoien
Cc: r-devel@r-project.org
Subject: Re: [Rd] Strange behavior when using progress bar (Fwd: Re: [R] The
code itself disappears after starting to execute the for loop)
Jon Skoien
on Wed, 7 Dec 2016 11:04:04 +0100 writes:
> I would like to ask once more if this is reproducible also for others?
> If yes, should I submit it as a bug-report?
> Best,
> Jon
Please Windows users .. this is possibly only for you!
Note that I do *not* see problems on Linux (in ESS; did not try RStudio).
Please also indicate in which form you are running R.
Here it does depend if this is inside RStudio, ESS, the "Windows GUI", the
"Windows terminal", ...
Martin Maechler,
ETH Zurich
> On 11/28/2016 11:26 AM, Jon Skoien wrote:
>> I first answered to the email below in r-help, but as I did not see
>> any response, and it looks like a bug/unwanted behavior, I am also
>> posting here. I have observed this in RGui, whereas it seems not to
>> happen in RStudio.
>>
>> Similar to OP, I sometimes have a problem with functions using the
>> progress bar. Frequently, the console is cleared after x iterations
>> when the progress bar is called in a function which is wrapped in a
>> loop. In the example below, this happened for me every ~44th
>> iteration. Interestingly, it seems that reduction of the sleep times
>> in this function increases the number of iterations before clearing.
>> In my real application, where the progress bar is used in a much
>> slower function, the console is cleared every 2-3 iteration, which
>> means that I cannot scroll back to check the output.
testit <- function(x = sort(runif(20)), ...) {
pb <- txtProgressBar(...)
for(i in c(0, x, 1)) {Sys.sleep(0.2); setTxtProgressBar(pb, i)}
Sys.sleep(1)
close(pb)
}
it <- 0
while (TRUE) {testit(style = 3); it <- it + 1; print(paste("done", it))}
>> Is this only a problem for a few, or is it reproducible? Any hints to
>> what the problem could be, or if it can be fixed? I have seen this in
>> some versions of R, and could also reproduce in 3.3.2.
"some versions of R" ... all on Windows ?
>>
>> Best wishes,
>> Jon
>>
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 8.1 x64 (build 9600)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
[.]
> Jon Olav Skøien
> Joint Research Centre - European Commission
> Institute for Space, Security & Migration
> Disaster Risk Management Unit
> Via E. Fermi 2749, TP 122, I-21027 Ispra (VA), ITALY
> jon.sko...@jrc.ec.europa.eu
> Tel: +39 0332 789205
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--
Jon Olav Skøien
Joint Research Centre - European Commission
Institute for Space, Security & Migration
Disaster Risk Management Unit
Via E. Fermi 2749, TP 122,
Re: [Rd] accessing data by packagename::dataname from within package code fails.
I have narrowed down the problem.
The error
Error : 'AminoAcids' is not an exported object from 'namespace:bibliospec'
Error : unable to load R code in package 'bibliospec'
occurs only if I try to access the data using bibliospec::AminoAcids
within the initialize method of an R reference class.
It does work, as far as I tested everywhere else. In other methods of
a reference class as well as in free functions.
It also does not work in the initialization list to the initialize function.
So I also can't do something like
initialize = function(aminoAcids=bibliospec::AminoAcids){
I guess this is an R FEATURE.
But then where and how is the best practice to initialize class
members with default values?
Thank you.
On 12 December 2016 at 15:45, Witold E Wolski wrote:
> I am wrting a package called bibliospec.
> I have a dataset in data/AminoAcids.tsv and would like to be able to
> access it with
>
> bibliospec::AminoAcids
>
> from within my package code.
>
> R CMD build gives me the error:
> Error : 'AminoAcids' is not an exported object from 'namespace:bibliospec'
>
> I am able to access the data in package code with
> data(AminoAcids)
> AminoAcids
>
> but this will give me a NOTE with R CMD check
>
> Also, after loading the packagepackage I am able to access the data with
> bibliospec::AminoAcids
>
> But I can't access it from the package bibliospec code.
> So why can't I access bibliospec::AminoAcids from within package code?
>
> Help appreciated
>
> Witold
> --
> Witold Eryk Wolski
--
Witold Eryk Wolski
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Re: [Rd] [R-pkg-devel] accessing data by packagename::dataname from within package code fails.
You can define the data in the R directory. You can keep it all in a *.R
file
by wrapping the text of the *.csv file in quotes and using
read.table(text="quoted stuff"), as in:
theData <- read.csv(header=TRUE, text="
English,Digit
One,1
Two,2
Three,3")
N <- nrow(theData)
You need to make sure 'theData' is defined before using it so put
everything requiring
it in one file or use the Collate: directive in the DESCRIPTION file.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, Dec 12, 2016 at 12:34 PM, Witold E Wolski
wrote:
> I have narrowed down the problem.
> The error
> Error : 'AminoAcids' is not an exported object from 'namespace:bibliospec'
> Error : unable to load R code in package 'bibliospec'
>
> occurs only if I try to access the data using bibliospec::AminoAcids
>
> within the initialize method of an R reference class.
> It does work, as far as I tested everywhere else. In other methods of
> a reference class as well as in free functions.
> It also does not work in the initialization list to the initialize
> function.
> So I also can't do something like
> initialize = function(aminoAcids=bibliospec::AminoAcids){
>
>
> I guess this is an R FEATURE.
>
> But then where and how is the best practice to initialize class
> members with default values?
>
> Thank you.
>
>
>
>
>
> On 12 December 2016 at 15:45, Witold E Wolski wrote:
> > I am wrting a package called bibliospec.
> > I have a dataset in data/AminoAcids.tsv and would like to be able to
> > access it with
> >
> > bibliospec::AminoAcids
> >
> > from within my package code.
> >
> > R CMD build gives me the error:
> > Error : 'AminoAcids' is not an exported object from
> 'namespace:bibliospec'
> >
> > I am able to access the data in package code with
> > data(AminoAcids)
> > AminoAcids
> >
> > but this will give me a NOTE with R CMD check
> >
> > Also, after loading the packagepackage I am able to access the data with
> > bibliospec::AminoAcids
> >
> > But I can't access it from the package bibliospec code.
> > So why can't I access bibliospec::AminoAcids from within package code?
> >
> > Help appreciated
> >
> > Witold
> > --
> > Witold Eryk Wolski
>
>
>
> --
> Witold Eryk Wolski
>
> __
> r-package-de...@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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Re: [Rd] accessing data by packagename::dataname from within package code fails.
Witold,
Are you using the sys data approach to actually put your data into your
package's namespace? From ?data (Good practices section)
Use of ‘data’ within a function without an ‘envir’ argument has
the almost always undesirable side-effect of putting an object in
the user's workspace (and indeed, of replacing any object of that
name already there). It would almost always be better to put the
object in the current evaluation environment by ‘data(..., envir =
environment())’. However, two alternatives are usually
preferable, both described in the ‘Writing R Extensions’ manual.
• For sets of data, set up a package to use lazy-loading of
data.
• For objects which are system data, for example lookup tables
used in calculations within the function, use a file
‘R/sysdata.rda’ in the package sources or create the objects
by R code at package installation time.
A sometimes important distinction is that the second approach
places objects in the namespace but the first does not. So if it
is important that the function sees ‘mytable’ as an object from
the package, it is system data and the second approach should be
used. In the unusual case that a package uses a lazy-loaded
dataset as a default argument to a function, that needs to be
specified by ‘::’, e.g., ‘survival::survexp.us’.
It does seem a bit strange that the :: works elsewhere but not in
initialize, but I don't have time to track that down atm.
Best,
~G
On Mon, Dec 12, 2016 at 12:34 PM, Witold E Wolski
wrote:
> I have narrowed down the problem.
> The error
> Error : 'AminoAcids' is not an exported object from 'namespace:bibliospec'
> Error : unable to load R code in package 'bibliospec'
>
> occurs only if I try to access the data using bibliospec::AminoAcids
>
> within the initialize method of an R reference class.
> It does work, as far as I tested everywhere else. In other methods of
> a reference class as well as in free functions.
> It also does not work in the initialization list to the initialize
> function.
> So I also can't do something like
> initialize = function(aminoAcids=bibliospec::AminoAcids){
>
>
> I guess this is an R FEATURE.
>
> But then where and how is the best practice to initialize class
> members with default values?
>
> Thank you.
>
>
>
>
>
> On 12 December 2016 at 15:45, Witold E Wolski wrote:
> > I am wrting a package called bibliospec.
> > I have a dataset in data/AminoAcids.tsv and would like to be able to
> > access it with
> >
> > bibliospec::AminoAcids
> >
> > from within my package code.
> >
> > R CMD build gives me the error:
> > Error : 'AminoAcids' is not an exported object from
> 'namespace:bibliospec'
> >
> > I am able to access the data in package code with
> > data(AminoAcids)
> > AminoAcids
> >
> > but this will give me a NOTE with R CMD check
> >
> > Also, after loading the packagepackage I am able to access the data with
> > bibliospec::AminoAcids
> >
> > But I can't access it from the package bibliospec code.
> > So why can't I access bibliospec::AminoAcids from within package code?
> >
> > Help appreciated
> >
> > Witold
> > --
> > Witold Eryk Wolski
>
>
>
> --
> Witold Eryk Wolski
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
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Associate Scientist (Bioinformatics)
Genentech Research
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Re: [Rd] [RE: why does parent.frame() cycle when called from inside capture.output()?]
Hi Frederik
Goodo, glad you found mvbutils::mvb.parent.frame useful. I had forgotten that
it's in mvbutils rather than debug package. This all dates back about 15
years...
To be fair, I don't think R's behaviour with duplicated-but-aliased frames in
the call stack is a "bug"--- everything normal just works--- and it's not
something to be "fixed" IMO, since it's clearly built-in by design and who
knows what else would break if it got changed? But, working round it is indeed
sometimes necessary...
[ BTW I'm not particularly diffident about posting to R-devel--- eg here I
am!--- but I'm generally too busy to check out my own answers thoroughly, so
rather than risk opening up blind alleys, I tend to suggest things off-list. In
the cases where I'm sure that I do have a good answer, someone else has already
usually responded... ]
bye
mark
Mark Bravington
CSIRO Marine Lab
Hobart
Australia
From: frede...@ofb.net [frede...@ofb.net]
Sent: 12 December 2016 19:23
To: R-devel@r-project.org
Cc: Bravington, Mark (Data61, Hobart); r-h...@r-project.org
Subject: [RE: [Rd] why does parent.frame() cycle when called from inside
capture.output()?]
Thanks, Mark - I'm taking up your invitation to forward your message
to the list just because it gives us some valuable data on (1) how
long the behavior has been around, and (2) how many other people
(don't) understand the behavior, and (3) how we might fix or work
around it.
I notice some other people also seem to be diffident about posting on
R-devel; perhaps I should conclude that bugs like this are below the
radar for busy statisticians.
FWIW, after playing around a bit with mvbutils::mvb.parent.frame, I
now have a working "desubN" (see the attachment on my original
message, and this one). I don't really have a good understanding of
*why* it now works, and why the original version didn't work...
Thanks again Mark. Also, nice hacking.
Frederick
- Forwarded message from mark.braving...@data61.csiro.au -
Date: Mon, 12 Dec 2016 06:20:17 +
From: mark.braving...@data61.csiro.au
To: frede...@ofb.net
Subject: RE: [Rd] why does parent.frame() cycle when called from inside
capture.output()?
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autolearn=ham
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X-My-Tags: inbox r-devel
Hi Frederik
[ I'm replying off-list in case you, or the rest of R-devel, don't find this
reply useful... please fwd to the list if it does help you ]
I'm the author of the 'debug' package. When I wrote it--- many years ago now---
I encountered some fairly strange behaviour with frames in the call stack,
which is reminiscent of what you're seeing. The debug package still works fine,
so I presume nothing has changed much.
If you load debug and then do ?mvb.sys.parent (and look at the code), you might
get *some* idea of what's going on. TBH I can't remember the details now...
HTH
Mark
Mark Bravington
CSIRO Marine Lab
Hobart
Australia
From: R-devel [r-devel-boun...@r-project.org] on behalf of frede...@ofb.net
[frede...@ofb.net]
Sent: 12 December 2016 16:54
To: r-devel@r-project.org
Cc: r-h...@r-project.org
Subject: [Rd] why does parent.frame() cycle when called from inside
capture.output()?
Hello R devel/help,
I ran into this strange behavior:
# showstack is supposed to walk through the stack of parent
# environments when it is called:
showstack = function() {
env = environment()
for(i in 1:12) {
env = do.call(parent.frame, list(), env=env)
print(env)
}
}
# a simple chain of functions:
g3=function(t) showstack()
g2=function(w) g3(w)
g1=function(z) g2(z)
g=function(y) g1(y)
g()
# outputs:
#
#
#
#
#
#
#
#
#
# ...
cat(capture.output(g()),sep="\n")
# outputs:
#
#
#
#
#
#
#
#
#
#
#
#
The strange thing of course is that the second call doesn't stay with
R_GlobalEnv, but in fact goes into a loop of period 4. I'm not so
surprised that the parent frame of the global environment is itself,
as in the first call, but it seems weird to have a loop of period 4...
Using `ls()` shows that two of the "loop" environments belong to
capture.output() and eval().
But if capture.output is really evaluating its input in the parent
frame, as it appears to be doing from its source code, then I would
have expected the output to be the same as the output I get by
evaluating the same expression in this frame.
I was trying to debug a function which attempts to be a multi-frame
version of deparse(substitute(...)). I'm attaching this function in
case anyone is curious. Perhaps my attachment can shed more light on
the problem I'm having.
Apologies if this is not a bug -
