[Rd] object.size vs lobstr::obj_size
I have posted this question on R-help where it was suggested to me that I might get a better response on R-devel. So far I have gotten no response. The post I am talking about is here: https://stat.ethz.ch/pipermail/r-help/2020-February/465700.html My apologies for cross-posting, which I am aware is impolite and I should have posted on R-devel in the first place - but I wasn't sure. Here is my question again: I am currently working through Advanced R by H. Wickham and came across the `lobstr::obj_size` function which appears to calculate the size of an object by taking into account whether the same object has been referenced multiple times, e.g. x <- runif(1e6) y <- list(x, x, x) lobstr::obj_size(y) # 8,000,128 B # versus: object.size(y) # 24000224 bytes Reading through `?object.size` in the "Details" it reads: [...] but does not detect if elements of a list are shared [...]. My questions are: (1) is the result of `obj_size()` the "correct" one when it comes to actual size used in memory? (2) And if yes, why wouldn't `object.size()` be updated to reflect the more precise calculation of an object in question similar to `obj_size()`? There are probably valid reasons for this and any insight would be greatly appreciated. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] dimnames incoherence?
Hi,
I was bitten by a little incoherence in dimnames assignment or may be I
missed some point.
Here is the case. If I assign row names via dimnames(a)[[1]], when
nrow(a)=1 then an error is thrown. But if I do the same when nrow(a) > 1
it's OK. Is one of this case works unexpectedly? Both? Neither?
a=as.matrix(1)
dimnames(a)[[1]]="a" # error: 'dimnames' must be a list
aa=as.matrix(1:2)
dimnames(aa)[[1]]=c("a", "b") # OK
In the second case, dimnames(aa) is not a list (like in the first case)
but it works.
I would expect that the both work or neither.
Your thoughts are welcome.
Best,
Serguei.
PS the same apply for dimnames(a)[[2]]<-.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Mageia 7
Matrix products: default
BLAS/LAPACK: /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.6.so
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] multbxxc_1.0.1 rmumps_5.2.1-11
[3] arrApply_2.1 RcppArmadillo_0.9.800.4.0
[5] Rcpp_1.0.3 slam_0.1-47
[7] nnls_1.4
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1 codetools_0.2-16
__
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Re: [Rd] dimnames incoherence?
> Serguei Sokol
> on Wed, 19 Feb 2020 15:21:21 +0100 writes:
> Hi,
> I was bitten by a little incoherence in dimnames assignment or may be I
> missed some point.
> Here is the case. If I assign row names via dimnames(a)[[1]], when
> nrow(a)=1 then an error is thrown. But if I do the same when nrow(a) > 1
> it's OK. Is one of this case works unexpectedly? Both? Neither?
> a=as.matrix(1)
> dimnames(a)[[1]]="a" # error: 'dimnames' must be a list
> aa=as.matrix(1:2)
> dimnames(aa)[[1]]=c("a", "b") # OK
> In the second case, dimnames(aa) is not a list (like in the first case)
> but it works.
> I would expect that the both work or neither.
I agree (even though I'm strongly advising people to use '<-'
instead of '=');
which in this case helps you get the name of the function really
involved: It is `dimnames<-` (which is implemented in C
entirely, for matrices and other arrays).
> Your thoughts are welcome.
I think we'd be happy if you report this formally on R's
bugzilla - https://bugs.r-project.org/ - as a bug.
--> https://www.r-project.org/bugs.html
>From reading bugs.html you note that you should ask for an account there;
as I'm one of the people who get such request by e-mail, in this
case, I can do it directly (if you confirm you'd want in a
private e-mail).
> Best,
> Serguei.
> PS the same apply for dimnames(a)[[2]]<-.
(of course)
NB *and* importantly, the buglet is still in current versions of R
Best,
Martin
>> sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Mageia 7
> Matrix products: default
> BLAS/LAPACK: /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.6.so
> locale:
> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
> other attached packages:
> [1] multbxxc_1.0.1 rmumps_5.2.1-11
> [3] arrApply_2.1 RcppArmadillo_0.9.800.4.0
> [5] Rcpp_1.0.3 slam_0.1-47
> [7] nnls_1.4
> loaded via a namespace (and not attached):
> [1] compiler_3.6.1 tools_3.6.1 codetools_0.2-16
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] dimnames incoherence?
How far would you like to go with the automatic creation of dimnames in
nested replacement operations on arrays? It currently works nicely with [<-
> a <- array(numeric(), dim=c(2,0,1)); dimnames(a)[3] <- list("One")
> str(a)
num[1:2, 0 , 1]
- attr(*, "dimnames")=List of 3
..$ : NULL
..$ : NULL
..$ : chr "One"
It works most of the time (except for length=1) for [[<-
> a <- array(numeric(), dim=c(2,0,1)); dimnames(a)[[1]] <- c("X1","X2")
> a <- array(numeric(), dim=c(2,0,1)); dimnames(a)[[2]] <- character()
> a <- array(numeric(), dim=c(2,0,1)); dimnames(a)[[3]] <- "Z1"
Error in dimnames(a)[[3]] <- "Z1" : 'dimnames' must be a list
It does not work at all for names<-.
> a <- array(numeric(), dim=c(2,0,1)); names(dimnames(a)) <- c("X","Y","Z")
Error in names(dimnames(a)) <- c("X", "Y", "Z") :
attempt to set an attribute on NULL
> a <- array(numeric(), dim=c(2,0,1)); dimnames(a)<-vector("list",3);
names(dimnames(a)) <- c("X","Y","Z")
> str(a)
num[1:2, 0 , 1]
- attr(*, "dimnames")=List of 3
..$ X: NULL
..$ Y: NULL
..$ Z: NULL
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Feb 19, 2020 at 6:24 AM Serguei Sokol
wrote:
> Hi,
>
> I was bitten by a little incoherence in dimnames assignment or may be I
> missed some point.
> Here is the case. If I assign row names via dimnames(a)[[1]], when
> nrow(a)=1 then an error is thrown. But if I do the same when nrow(a) > 1
> it's OK. Is one of this case works unexpectedly? Both? Neither?
>
> a=as.matrix(1)
> dimnames(a)[[1]]="a" # error: 'dimnames' must be a list
>
> aa=as.matrix(1:2)
> dimnames(aa)[[1]]=c("a", "b") # OK
>
> In the second case, dimnames(aa) is not a list (like in the first case)
> but it works.
> I would expect that the both work or neither.
>
> Your thoughts are welcome.
> Best,
> Serguei.
>
> PS the same apply for dimnames(a)[[2]]<-.
>
> > sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Mageia 7
>
> Matrix products: default
> BLAS/LAPACK: /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.6.so
>
> locale:
> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.UTF-8LC_COLLATE=fr_FR.UTF-8
> [5] LC_MONETARY=fr_FR.UTF-8LC_MESSAGES=fr_FR.UTF-8
> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] multbxxc_1.0.1rmumps_5.2.1-11
> [3] arrApply_2.1 RcppArmadillo_0.9.800.4.0
> [5] Rcpp_1.0.3slam_0.1-47
> [7] nnls_1.4
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.1 tools_3.6.1 codetools_0.2-16
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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__
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Re: [Rd] dimnames incoherence?
> Martin Maechler
> on Wed, 19 Feb 2020 18:06:57 +0100 writes:
> Serguei Sokol
> on Wed, 19 Feb 2020 15:21:21 +0100 writes:
>> Hi,
>> I was bitten by a little incoherence in dimnames assignment or may be I
>> missed some point.
>> Here is the case. If I assign row names via dimnames(a)[[1]], when
>> nrow(a)=1 then an error is thrown. But if I do the same when nrow(a) > 1
>> it's OK. Is one of this case works unexpectedly? Both? Neither?
>> a=as.matrix(1)
>> dimnames(a)[[1]]="a" # error: 'dimnames' must be a list
>> aa=as.matrix(1:2)
>> dimnames(aa)[[1]]=c("a", "b") # OK
>> In the second case, dimnames(aa) is not a list (like in the first case)
>> but it works.
>> I would expect that the both work or neither.
> I agree (even though I'm strongly advising people to use '<-'
> instead of '=');
> which in this case helps you get the name of the function really
> involved: It is `dimnames<-` (which is implemented in C
> entirely, for matrices and other arrays).
As a matter of fact, I wrote too quickly, the culprit here is
the `[[<-` function (rather than `dimnames<-`),
which has a special "inconsistency" feature when used to "add to NULL";
almost surely inherited from S, but I now think we should
consider dropping on the occasion of aiming for R 4.0.0 :
It's documented in ?Extract that length 1 `[[.]]`-assignment works
specially for NULL (and dimnames(.) are NULL here).
Note you need to read and understand one of the tougher sections
in the official 'R Language Definition' Manual,
section -- 3.4.4 Subset assignment ---
i.e.,
https://cran.r-project.org/doc/manuals/r-release/R-lang.html#Subset-assignment
notably this part:
Nesting of complex assignments is evaluated recursively
names(x)[3] <- "Three"
is equivalent to
`*tmp*` <- x
x <- "names<-"(`*tmp*`, value="[<-"(names(`*tmp*`), 3, value="Three"))
rm(`*tmp*`)
and then, apply this to ourdimnames(a)[[1]] <- "a"
and so replace
- 'names<-' by 'dimnames<-'
- '[<-' by '[[<-'
--
Here is the rest of my analysis as valid R code
{this is not new, Peter Dalgaard had explained this 10 or 20
years ago to a mailing list audience IIRC} :
## MM: The problematic behavior (bug ?) is in `[[<-`, not in `dimnames<-` :
`[[<-`(NULL, 1, "a" ) # gives "a" (*not* a list)
`[[<-`(NULL, 1, c("a","b")) # gives list(c("a","b")) !!
##==> in C code: in subassign.c [ ~/R/D/r-devel/R/src/main/subassign.c ]
##==> function (~ 340 lines)
##do_subassign2_dflt(SEXP call, SEXP op, SEXP args, SEXP rho)
## has
"
line svn r. svn auth. c.o.d.e...
-- - --
1741 4166 ihaka if (isNull(x)) {
1742 45446 ripley if (isNull(y)) {
1743 76166 luke UNPROTECT(2); /* args, y */
1744 4166 ihaka return x;
1745 45446 ripley }
1746 35680murdoch if (length(y) == 1)
1747 68094 luke x = allocVector(TYPEOF(y), 0);
1748 24954 ripley else
1749 68094 luke x = allocVector(VECSXP, 0);
1750 1820 ihaka }
-- - --
"
## so clearly, in case the value is of length 1, no list is created .
## For dimnames<- Replacing NULL by list() should be done in both cases , and
then things work :
`[[<-`(list(), 1, "a" ) # gives list( "a" )
`[[<-`(list(), 1, c("a","b")) # gives list(c("a","b")) !!
## but the problem here is that `[[<-` at this time in the game
## does *not* know that it comes from dimnames<-
---
If we change the behavior NULL--[[--assignment from
`[[<-`(NULL, 1, "a" ) # gives "a" (*not* a list)
to
`[[<-`(NULL, 1, "a" ) # gives list("a")
then we have more consistency there *and* your bug is fixed too.
Of course, in other situations back-compatibility would be
broken as well.
At the moment, I think we (R Core Team) should consider doing
that here.
Martin
>> Your thoughts are welcome.
> I think we'd be happy if you report this formally on R's
> bugzilla - https://bugs.r-project.org/ - as a bug.
--> https://www.r-project.org/bugs.html
>> From reading bugs.html you note that you should ask for
>> an account there;
> as I'm one of the people who get such request by e-mail,
> in this case, I can do it directly (if you confirm you'd
> want in a private e-mail).
>> Best, Serguei.
>> PS the same apply for dimnames(a)[[2]]<-.
> (of course)
> NB *and* importantly, the buglet is still in current
> versions of R
> Best, Martin
>>> sessionInfo()
>> R version 3.6.1 (2019-07-05) Platform:
>> x86_64-pc-linux-gnu (64-bit) Running under: Mageia 7
>> Matrix products: default BLAS/LAPACK:
>> /home/opt/OpenBLAS/lib/libopenblas_sandybridge-r0.3.6.so
>>
