[Rd] Bug: broken exception handling in S4 methods
Hi all:
we have noticed for quite a while that certain errors cannot be handled
by R try, tryCatch etc blocks, but it was fairly difficult to understand
what were the conditions for this incorrect behaviour. Finally I stabbed
across a very understandable case, which is outlined in the (runnable)
example below.
The main message is: wrapping an S4 method call in a try block will not
help if an error occurs in evaluating an argument to such a call; this
works just fine for function calls (as opposed to S4 methods)
The particular example is a result of trying to write a unit test for a
constructor of a class object which should fail under certain
conditions. This failure obviously need to be caught for the unit test
to proceed. However, it is a general problem with handling some
exceptions in R.
# Consider a simple class MyClassA, which is derived from numeric and
for which
# we define a constructor (in form of a method). On its own this class
works nicely
# and so does exception handling of it:
setClass(MyClassA,
contains = numeric,
validity = function(object)
{
stopifnot(object[1] == object[2])
TRUE
}
)
setGeneric(MyClassA, function(x) standardGeneric(MyClassA))
setMethod(MyClassA,
signature(x = numeric),
function(x)
{
new(MyClassA, x)
}
)
## OK
er = try({ MyClassA(c(1,2)) })
## OK (error in constructor)
er = try({ MyClassA(c(1,2)) })
## OK (error evaluating argument to a function)
er = try({ sin(MyClassA(c(1,2))) })
# Now consider we define MyClassB that has MyClassA in a slot
# and we define a constructor that takes such objects:
setClassUnion(MyClassAOrNULL, c(MyClassA, NULL))
setClass(MyClassB,
representation(
ca = MyClassAOrNULL
),
prototype(ca = NULL)
)
setGeneric(MyClassB, function(x) standardGeneric(MyClassB))
setMethod(MyClassB,
signature(x = MyClassA),
function(x)
{
new(MyClassB, ca = x)
}
)
## OK
b = MyClassB(MyClassA(c(1,1)))
## FAILS (error evaluating argument to a method)
er = try({ MyClassB(MyClassA(c(1,2))) })
# As you see the last error cannot be handled
# Moreover. If we define a function and a method as function(x) x then
# the function can be handled by try, yet the method cannot:
f = function(x) x
setGeneric(g, function(x) standardGeneric(g))
setMethod(g, MyClassA, function(x) x)
## OK (error evaluating argument to a function)
er = try({ f(MyClassA(c(1,2))) })
## FAILS (error evaluating argument to a method)
er = try({ g(MyClassA(c(1,2))) })
sessionInfo()
R version 2.11.0 Patched (2010-05-05 r51914)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB
LC_COLLATE=en_GB
[5] LC_MONETARY=CLC_MESSAGES=en_GBLC_PAPER=en_GB
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB
LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics utils datasets grDevices methods
base
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@ahl.com
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Re: [Rd] POSIXlt matching bug
POSIXlt is a list and it is not a list of dates or times, it is a list
of
x - as.POSIXlt(Sys.Date())
names(x)
[1] sec min hour mday mon year wday yday
isdst
So if you want to match these things, you should use POSIXct or any
other numeric-based format (as POSIXct is just a double value for the
number of seconds since 1970-01-01) e.g.
z - as.POSIXct(Sys.Date())
x - as.POSIXct(Sys.Date())
z==x
[1] TRUE
match(z,x)
[1] 1
z %in% x
[1] TRUE
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of McGehee, Robert
Sent: 29 June 2010 15:46
To: r-b...@r-project.org; r-devel@r-project.org
Subject: [Rd] POSIXlt matching bug
I came across the below mis-feature/bug using match with
POSIXlt objects
(from strptime) in R 2.11.1 (though this appears to be an old issue).
x - as.POSIXlt(Sys.Date())
table - as.POSIXlt(Sys.Date()+0:5)
length(x)
[1] 1
x %in% table # I expect TRUE
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
match(x, table) # I expect 1
[1] NA NA NA NA NA NA NA NA NA
This behavior seemed more plausible when the length of a
POSIXlt object
was 9 (back in the day), however since the length was redefined, the
length of x no longer matches the length of the match function output,
as specified by the ?match documentation: A vector of the same length
as 'x'.
I would normally suggest that we add a POSIXlt method for match that
converts x into POSIXct or character first. However, match does not
appear to be generic. Below is a possible rewrite of match
that appears
to work as desired.
match - function(x, table, nomatch = NA_integer_,
incomparables = NULL)
.Internal(match(if(is.factor(x)||inherits(x, POSIXlt))
as.character(x) else x,
if(is.factor(table)||inherits(table, POSIXlt))
as.character(table) else table,
nomatch, incomparables))
That said, I understand some people may be very sensitive to the speed
of the match function, and may prefer a simple change to the ?match
documentation noting this (odd) behavior for POSIXlt.
Thanks, Robert
R.version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.1
year 2010
month 05
day31
svn rev52157
language R
version.string R version 2.11.1 (2010-05-31)
Robert McGehee, CFA
Geode Capital Management, LLC
One Post Office Square, 28th Floor | Boston, MA | 02109
Tel: 617/392-8396Fax:617/476-6389
mailto:robert.mcge...@geodecapital.com
This e-mail, and any attachments hereto, are intended for use by the
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and/or its affiliates. If you are not the intended recipient of this
e-mail, or if you have otherwise received this e-mail in error, please
immediately notify me by telephone (you may call collect), or
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Re: [Rd] Bug in R -e command
Hi Dirk, all:
your answer prompted me to look in another place, and yes I need to
withdraw the bug report: it was a problem on our side.
Thanks,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
-Original Message-
From: Dirk Eddelbuettel [mailto:e...@debian.org]
Sent: 07 May 2010 15:43
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] Bug in R -e command
On 7 May 2010 at 15:23, Sklyar, Oleg (London) wrote:
| Hi all:
|
| since about a month we encountered a problem with R -e
command: spaces
| in the command of R -e command are no more tolerated. This same
| issue affects 2.11 patched (05-05-2010), 2.10.1, and
current devel (at
| least the one of two weeks ago).
|
| (I skip the mid of the printouts, replaced with ...)
|
| * R -e message('aaa aaa')
| ARGUMENT 'aaa')' __ignored__
Isn't that a shell quoting issue? I tend to keep the
apostrophe on the
outside and the double-quote on the inside:
e...@ron:~ R --slave -e 'message(aaa aaa)'
aaa aaa
e...@ron:~ r -e 'message(aaa aaa)'
aaa aaa
e...@ron:~ Rscript -e 'message(aaa aaa)'
aaa aaa
but also note
e...@ron:~ R --slave -e message(\aaa aaa\)
aaa aaa
e...@ron:~ R --slave -e message('aaa aaa')
aaa aaa
e...@ron:~
so I can't even replicate your issue. What what it's worth,
the cutpaste
above came from M-x shell inside Emacs.
e...@ron:~ dpkg -l r-base-core littler bash emacs23 | tail -4
ii bash 4.1-3 The GNU Bourne Again SHell
ii emacs2323.1+1-5 The GNU Emacs editor (with
GTK+ user interfa
ii littler0.1.3-1GNU R scripting and
command-line front-end
ii r-base-core2.11.0-1 GNU R core of statistical
computation and gr
e...@ron:~
|
|
| R version 2.11.0 Patched (2010-05-05 r51914)
| Copyright (C) 2010 The R Foundation for Statistical Computing
| ...
|
| message('aaa
| +
| +
|
| * /releases/R/2.10/bin/R -e message('aaa aaa')
| ARGUMENT 'aaa')' __ignored__
|
|
| R version 2.10.1 Patched (2010-03-27 r51474)
| Copyright (C) 2010 The R Foundation for Statistical Computing
| ...
|
| message('aaa
| +
| +
|
| WORKING OLD VERSION:
|
| * /share/R/20090611/bin/R -e message('aaa aaa')
|
| R version 2.9.0 (2009-04-17)
| Copyright (C) 2009 The R Foundation for Statistical Computing
| ...
|
| message('aaa aaa')
| aaa aaa
|
|
|
|
| Dr Oleg Sklyar
| Research Technologist
| AHL / Man Investments Ltd
| +44 (0)20 7144 3803
| oskl...@maninvestments.comno more
|
|
**
| Please consider the environment before printing this email
or its attachments.
| The contents of this email are for the named addressees
...{{dropped:19}}
|
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[Rd] Bug in R -e command
Hi all:
since about a month we encountered a problem with R -e command: spaces
in the command of R -e command are no more tolerated. This same
issue affects 2.11 patched (05-05-2010), 2.10.1, and current devel (at
least the one of two weeks ago).
(I skip the mid of the printouts, replaced with ...)
* R -e message('aaa aaa')
ARGUMENT 'aaa')' __ignored__
R version 2.11.0 Patched (2010-05-05 r51914)
Copyright (C) 2010 The R Foundation for Statistical Computing
...
message('aaa
+
+
* /releases/R/2.10/bin/R -e message('aaa aaa')
ARGUMENT 'aaa')' __ignored__
R version 2.10.1 Patched (2010-03-27 r51474)
Copyright (C) 2010 The R Foundation for Statistical Computing
...
message('aaa
+
+
WORKING OLD VERSION:
* /share/R/20090611/bin/R -e message('aaa aaa')
R version 2.9.0 (2009-04-17)
Copyright (C) 2009 The R Foundation for Statistical Computing
...
message('aaa aaa')
aaa aaa
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.comno more
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Re: [Rd] Why no race condition when returning UNPROTECT-ed memory fromC?
Because there is no second thread to do that, R is single threaded. The
gc could only be run from within another R API command or macro, but
there is none in between.
Best
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Dominick Samperi
Sent: 14 April 2010 06:51
To: r-devel@r-project.org
Subject: [Rd] Why no race condition when returning
UNPROTECT-ed memory fromC?
Consider the C (or C++) code called from the .Call interface:
SEXP foo() {
SEXP *p = PROTECT(allocVector(REALSXP, 10));
...
UNPROTECT(1);
return p;
}
Why is there no danger that the allocated memory will be garbage
collected after the UNPROTECT, but before the return of p?
I have used code like this for some time and have never had a
problem, but I'm not sure if/why it is guaranteed to work.
Thanks,
Dominick
[[alternative HTML version deleted]]
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[Rd] Job: AHL Research Developer, R/python - top hedge fund, Oxford/London UK
Dear list subscribers, this is posted in appreciation of the level of skill that subscribers to this mailing list enjoy and in no way to abuse it. We are looking to hire a Research Developer with extensive R and/or python development skills. If interested (below), please contact me directly on oskl...@ahl.com: Man Group / AHL Research Developer [3040] Man is a world-leading alternative investment management business. With a broad range of funds for institutional and private investors globally, it is known for its performance, innovative product design and investor service. Man's funds under management at the end of year 2009 were roughly at $42 billion. The original business was founded in 1783. Today, Man Group plc is listed on the London Stock Exchange and is a member of the FTSE 100 Index with a market capitalisation of around £4 billion. Within Man AHL is a world-leading quantitative investment manager with an extensive history of performance and innovation. A pioneer in the application of systematic trading, we have been serving institutional and private clients since 1987. Further information can be found at www.ahl.com. As part of its investment in quantitative finance research, Man Group and its quantitative investment manager AHL have established a Research Laboratory at Oxford. The Laboratory is sharing the same offices with the Oxford-Man Institute of Quantitative Finance encouraging interaction between academic and commercial researchers. It pursues commercially driven research programmes primarily focussed on the needs of AHL but collaborates with the Institute through seminars, workshops and informal discussions. In our research we facilitate the use of the tools that are widely spread throughout the academic quantitative and statistical computing landscape, like Python and R. There is an immediate and on-going need to develop advanced and technologically modern computational tools and quantitative techniques to support the AHL research programmes. In addition, there are a number of potentially applicable Information Systems and Information Engineering academic research programmes, which require commercial evaluation and assessment. Working in close cooperation with the AHL Research teams, both in Oxford and London, and the AHL Technology group in London, the successful candidate will design, develop and implement necessary software libraries and frameworks in R, Python and other languages to support the Oxford research team in technology topics and develop recommendations on the use of software configuration management in the AHL research projects. Responsibilities: - Design and develop software libraries and frameworks in R and Python to support the Laboratory's research activities and write corresponding documentation and example code - Work with the AHL Technology and AHL Research teams to develop interfaces between various platforms, in particular Java, C/C++, R and Python to facilitate effective data and information exchange - Provide assistance, support and seminars to the researchers on the optimal use of R and Python libraries and Linux - Propose and implement algorithms to assist in data analysis tasks - Develop recommendations for the use of R and Python in research projects, code reuse and configuration management across the Laboratory and with the AHL Research technology to ensure maximum productivity - Collaborate with the Institute's computer science research team as required and keep up to date with the computer science research being undertaken at the Institute and in related University departments - Work with the AHL Technology Group to ensure that the technology experience and facilities at the Laboratory are fit for purpose - Act as the point of contact between the Oxford research staff and the London based AHL Technology group Requirements: - PhD or experienced MSc/Part III in quantitative research in maths, science, engineering or computer science - Fluent R or Python and at least one of C, C++, or Java; confidence with Linux, Unix or similar - Mathematical skills to 1st year post-graduate and excellent analytical skills - Experience in statistical analysis and modelling, optimisation algorithms, data visualisation, preferably with relation to large data sets - Passion for computer science and statistics and its application to financial markets - Good communication and team working skills coupled with capability for innovative thinking Advantageous - Knowledge of object oriented design, distributed computing, relational databases - Experience working with Beowulf-style Linux clusters, MPI, slurm, condor etc - Experience of software development in a dealer/trading desk environment Man Group, and all related entities, is an equal opportunity employer through the application of a policy of non-discrimination on the grounds of sex, marital or civil partner status, gender
[Rd] likely bug in 'serialize' or please explain the memory usage
Hi all,
assume the following problem: a function call takes a function object
and a data variable and calls this function with this data on a remote
host. It uses serialization to pass both the function and the data via a
socket connection to a remote host. The problem is that depending on the
way we call the same construct, the function may be serialized to
include the data, which was not requested as the example below
demonstrates (runnable). This is a problem for parallel computing. The
problem described below is actually a problem for Rmpi and any other
parallel implementation we tested leading to endless executions in some
cases, where the total data passed is huge.
Assume the below 'mycall' is the function that takes data and a function
object, serializes them and calls the remote host. To make it runable I
just print the size of the serialized objects. In a parallel apply
implemention it would serialize individual list elements and a function
and pass those over. Assuming 1 element is 1Mb and having 100 elements
and a function as simple as function(z) z we would expect to pass around
100Mb of data, 1 Mb to each individual process. However what happens is
that in some situations all 100Mb of data are passed to all the slaves
as the function is serialized to include all of the data! This always
happens when we make such a call from an S4 method when the function we
is defined inline, see last example.
Anybody can explain this, and possibly suggest a solution? Well, one is
-- do not define functions to call in the same environment as the caller
:(
I do not have immediate access to the newest version of R, so would be
grateful if sombody could test it in that and let me know if the problem
is still there. The example is runnable.
Thanks,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
---
mycall = function(x, fun) {
FUN = serialize(fun, NULL)
DAT = serialize(x, NULL)
cat(sprintf(length FUN=%d; length DAT=%d\n, length(FUN),
length(DAT)))
invisible(NULL) ## return results of a call on a remote host with
FUN and DAN
}
## the function variant I will be passing into mycall
innerfun = function(z) z
x = runif(1e6)
## test run from the command line
mycall(x, innerfun)
# output: length FUN=106; length DAT=822
## test run from within a function
outerfun1 = function(x) mycall(x, innerfun)
outerfun1(x)
# output: length FUN=106; length DAT=822
## test run from within a function, where function is defined within
outerfun2 = function(x) {
nestedfun = function(z) z
mycall(x, nestedfun)
}
outerfun2(x)
# output: length FUN=253; length DAT=822
setGeneric(outerfun3, function(x) standardGeneric(outerfun3))
## define a method
## test run from within a method
setMethod(outerfun3, numeric,
function(x) mycall(x, innerfun))
outerfun3(x)
# output@ length FUN=106; length DAT=822
## test run from within a method, where function is defined within
setMethod(outerfun3, numeric,
function(x) {
nestedfun = function(z) z
mycall(x, nestedfun)
})
## THIS WILL BE WRONG!
outerfun3(x)
# output: length FUN=8001680; length DAT=822
--
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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Re: [Rd] likely bug in 'serialize' or please explain the memory usage
Duncan,
thanks for suggestions, I will try attaching a new environment.
However this still does not explain the behaviour and does not confirm
that it is correct. What puzzles me most is that if I define a function
within another function then only the function gets serialized, yet when
this is withing an S4 method definition, then also the args. Both have
their own environments, so I do not see why it should be different. As
an interim measure I just removed all the inline function definitions
from these 'parallel' calls defining the functions as hidden outside of
the caller, a bit ugly but works. I'd be thankful if you could look at
the examples when you get some more time.
My main problem is less in ensuring that my code works, but in ensuring
that when users use these parallel functionalities with their code, they
do not get stuck in transferring data for ages simply because with every
function one gets all the data passed.
Best,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
-Original Message-
From: Duncan Murdoch [mailto:murd...@stats.uwo.ca]
Sent: 03 November 2009 11:59
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] likely bug in 'serialize' or please explain
the memory usage
I haven't had a chance to look really closely at this, but I
would guess
the problem is that in R functions are closures. The environment
attached to the function will be serialized along with it, so if you
have a big dataset in the same environment, you'll get that too.
I vaguely recall that the global environment and other system
environments are handled specially, so that's not true for functions
created at the top level, but I'd have to do some experiments
to confirm.
So the solution to your problem is to pay attention to the
environment
of the functions you create. If they need to refer to local
variables
in the creating frame, then
you'll get all of them, so be careful about what you create
there. If
they don't need to refer to the local frame you can just attach a new
smaller environment after building the function.
Duncan Murdoch
Sklyar, Oleg (London) wrote:
Hi all,
assume the following problem: a function call takes a
function object
and a data variable and calls this function with this data
on a remote
host. It uses serialization to pass both the function and
the data via a
socket connection to a remote host. The problem is that
depending on the
way we call the same construct, the function may be serialized to
include the data, which was not requested as the example below
demonstrates (runnable). This is a problem for parallel
computing. The
problem described below is actually a problem for Rmpi and any other
parallel implementation we tested leading to endless
executions in some
cases, where the total data passed is huge.
Assume the below 'mycall' is the function that takes data
and a function
object, serializes them and calls the remote host. To make
it runable I
just print the size of the serialized objects. In a parallel apply
implemention it would serialize individual list elements
and a function
and pass those over. Assuming 1 element is 1Mb and having
100 elements
and a function as simple as function(z) z we would expect
to pass around
100Mb of data, 1 Mb to each individual process. However
what happens is
that in some situations all 100Mb of data are passed to all
the slaves
as the function is serialized to include all of the data!
This always
happens when we make such a call from an S4 method when the
function we
is defined inline, see last example.
Anybody can explain this, and possibly suggest a solution?
Well, one is
-- do not define functions to call in the same environment
as the caller
:(
I do not have immediate access to the newest version of R,
so would be
grateful if sombody could test it in that and let me know
if the problem
is still there. The example is runnable.
Thanks,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
--
--
---
mycall = function(x, fun) {
FUN = serialize(fun, NULL)
DAT = serialize(x, NULL)
cat(sprintf(length FUN=%d; length DAT=%d\n, length(FUN),
length(DAT)))
invisible(NULL) ## return results of a call on a remote
host with
FUN and DAN
}
## the function variant I will be passing into mycall
innerfun = function(z) z
x = runif(1e6)
## test run from the command line
mycall(x, innerfun)
# output: length FUN=106; length DAT=822
## test run from within a function
outerfun1 = function(x) mycall(x, innerfun)
outerfun1(x)
# output: length FUN=106; length DAT=822
## test run from
Re: [Rd] Changing the compiler gfortran to ifort
on Unix alikes possibly:
env F77=/path/to/ifort ./configure --prefix=/where/to/install
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Fabio
Mathias Corrêa
Sent: 07 August 2009 14:44
To: r-devel@r-project.org
Subject: [Rd] Changing the compiler gfortran to ifort
I tried the manual R Installation and Administration to
change the gcc compiler to icc and ifort for gfotran. However
I could not find the correct path for the R to identify the
icc and ifort.
In which file I define the change of compiler?
Thanks very much!!!
Fábio Mathias Corrêa
Estatística e Experimentação Agropecuária/UFLA
Brazil
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Re: [Rd] CTRL-C during .Call causes R to quit to command line
If you use JNI or rJava, you should start the VM with -Xrs argument,
otherwise the descibed things happen as Java catches the Ctrl-C
interrupt
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Saptarshi Guha
Sent: 30 March 2009 04:24
To: r-devel@r-project.org
Subject: [Rd] CTRL-C during .Call causes R to quit to command line
Hello,
During a .Call e.g
while(TRUE){
value -rhsqnextKVR(rdr) ## has .Call in this function
if(is.null(value)) break;
}
if I press CTRL-C, R exits straight to the command line.
Q: How can I prevent this? I should point out that my library uses
JNI, so I'm not sure if that is causing it.
I'm using R-2.8 on Linux (RHEL 5)
Thank you in advance
Regards
Saptarshi
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[Rd] imporving performance of slicing on matrices and S4 their derivatives
Dear list.
It is a known issue that accessing slots of S4 objects and in particular
accessing .Data slots is slow in R. However, what surprises me are two
things demonstrated in the code below (runnable with 'inline', my times
are in the comments):
- copying data out of a large 3x1e7 .Data slot into a matrix can be
easily made 3-4 times faster than accessing a .Data slot which I believe
grabs a reference (and as copying can be avoided the acceleration should
be even more dramatic). It is surprising that this memory inefficient
operation is faster than such a simple thing like getting a reference!
- getting a column, or columns, from an atomic R matrix or actually an
S4 object derived from it, can be up to 10 times faster than using
standard slicing with the [-operator (yes, less generic, but with such
performance gain we do definitely use it).
My point is: should not [-operators for atomic objects and @.Data be
redesigned? The code here is just an example for double storage-mode and
without any checks though. Adding checks and colnames etc does not lead
to performance degradation.
I was originally thinking that the dispatch looking up a particular [
implementation for an object is the issue, but in fact it is not the
case as redefining [ or $ as S4 methods (!) to use the mcol below for an
S4 object shows the same performance gains as the diret use of use of
mcol/mcols!
Any comments welcome!
## --- code
## available from CRAN, needs compilers installed
library(inline)
## get 1 column of a matrix to use instead of [-operator
## (same performance gains if index is a character or on multiple
columns or
## when getting multiple columns as matrix and assigning the names from
input)
body = /* test for column extraction: no checks here for code
simplicity */
int nrow = Rf_nrows(m);
int i = INTEGER(index)[0] - 1;
SEXP res;
PROTECT(res = allocVector(REALSXP, nrow));
memcpy(REAL(res), (REAL(m)[i*nrow]), nrow*sizeof(double));
UNPROTECT(1);
return res;
mcol = cfunction(signature(m=matrix, index=integer), body=body,
includes=#include string.h)
## get A COPY of the @.Data slot from an object derived from
numeric/matrix
body = /* test performance of getting A COPY of @.Data, keeping
dimnames */
int nrow = Rf_nrows(m);
int ncol = Rf_ncols(m);
SEXP res, dim;
PROTECT(res = allocVector(REALSXP, nrow*ncol));
PROTECT(dim = allocVector(INTSXP, 2));
INTEGER(dim)[0] = nrow;
INTEGER(dim)[1] = ncol;
SET_DIM(res, dim);
if (GET_DIMNAMES(m)!= R_NilValue)
SET_DIMNAMES(res, Rf_duplicate(GET_DIMNAMES(m)));
if (ncol0 nrow0)
memcpy(REAL(res), REAL(m), nrow*ncol*sizeof(double));
UNPROTECT(2);
return res;
mcols = cfunction(signature(m=matrix), body=body,
includes=#include string.h)
## --- tests ---
m = matrix(runif(3e7), nc=3)
setClass(MyClass, representation(matrix, comment=character))
dat = new(MyClass, m, comment=test object)
mean(sapply(1:20, function(i) system.time(d...@.data)[1] ))
## output: [1] 0.2526
mean(sapply(1:20, function(i) system.time(mcols(dat))[1] ))
## output: [1] 0.08215
mean(sapply(1:50, function(i) system.time(m[,2])[1] ))
## output: [1] 0.1222
mean(sapply(1:50, function(i) system.time(mcol(m,2L))[1] ))
## output: [1] 0.02596
mean(sapply(1:50, function(i) system.time(dat[,2])[1] ))
## output: [1] 0.1269
mean(sapply(1:50, function(i) system.time(mcol(dat,2L))[1] ))
## output: [1] 0.02584
---
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-02 r47821)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
other attached packages:
[1] inline_0.3.3
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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[Rd] consistent segfaults in ROracle with one of the databases
Dear list.
Has anybody had any issues with ROracle, namely consistently leading to
a segmentation fault? One of our oracle databases seems to have certain
issues at the moment (do not know what exactly though) and if that one
is queried ROracle definitely fails with a segmentation fault. Any
ideas? Here is the trace and below is also a type of query that crashes
it:
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(RS_Ora_exec, ps = as(ps, integer), data = data,
data.classes = df.classes, buf.size = as.integer(ora.buf.size),
PACKAGE = .OraPkgName)
2: oraExecStatement(ps, ora.buf.size = as(ora.buf.size, integer))
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) {call - conditionCall(e)
if (!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call - sys.call(-4L)dcall -
deparse(call)[1L]prefix - paste(Error in, dcall, : )
LONG - 75Lmsg - conditionMessage(e)sm - strsplit(msg,
\n)[[1L]]if (14L + nchar(dcall, type = w) + nchar(sm[1L],
type = w) LONG) prefix - paste(prefix, \n
, sep = )}else prefix - Error : msg - paste(prefix,
conditionMessage(e), \n, sep = )
.Internal(seterrmessage(msg[1L]))if (!silent
identical(getOption(show.error.messages), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error))})
7: try({ps - oraPrepareStatement(con, statement, bind = NULL)
rs - oraExecStatement(ps, ora.buf.size = as(ora.buf.size,
integer))})
8: oraExecDirect(con, statement, ...)
9: oraQuickSQL(conn, statement, ...)
10: dbGetQuery(dotsConnection(), qry)
--
This is the type of query (template) that crashes it, I know this is not
too helpful as you cannot run it, but maybe someone spots a certain
pattern in it:
SELECT TIMESTAMP, VALUE, VM FROM
(WITH ev AS
(SELECT audit_key_new key, audit_date dt, audit_batch_nbr,
audit_date
FROM dots_audit.audit_event
WHERE table_name='VALUE_PROPERTY_MAP'),
jfsm AS
(SELECT audit_key, fund_id, fund_mult
FROM dots_audit.value_property_map WHERE property_id='%s'
UNION SELECT audit_key, value_id, value_mult
FROM dots.value_property_map WHERE property_id='%s')
SELECT DISTINCT
ev.dt - to_date('01011970','ddmm') TIMESTAMP,
jfsm.value_id VALUE,
jfsm.value_mult VM,
RANK() OVER (PARTITION BY audit_batch_nbr, value_id ORDER BY dt
DESC) r
FROM jfsm, ev WHERE audit_key=ev.key)
WHERE r=1 ORDER BY TIMESTAMP DESC
--
library(ROracle)
Loading required package: DBI
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-02 r47821)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=C;LC_MONETARY=C;LC_
MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M
EASUREMENT=en_GB;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
other attached packages:
[1] ROracle_0.5-9 DBI_0.2-4
--
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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[Rd] typo in sprintf format string segfaults R
typo as simple as %S instead of %s segfaults R devel:
*** R 2.9.0 (svn -r 47821) [/share/research/R-devel/20090203/lib64/R]
***
sprintf(%S%d, aaa, 1)
*** caught segfault ***
address 0x8000, cause 'memory not mapped'
Traceback:
1: sprintf(%S%d, aaa, 1)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
-
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-02 r47821)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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[Rd] Rd \usage clause for an S4 replace method
Given S4 methods [ and [-, how do I write the Rd-file usage clause for
the latter one?
What I have now is:
\S4method{[}{TimeSeries,TimeDate,missing}(x, i, j, ..., drop)
\S4method{[-}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ..., value)
which results in the following output:
## S4 method for signature 'TimeSeries, TimeDate, missing':
x[i, j, ..., drop]
\S4method{[-}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ..., value)
How should I document the latter? Thanks.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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Re: [Rd] S4 generic masking S3 generic when using namespace
Try using setGeneric(predict) without further arguments, this should
work as it will take the existing 'predict' definition and convert it
into S4 generic. This works nicely for me for all plot, print etc
methods
* R
*** R 2.9.0 (svn -r 47821) [/share/research/R-devel/20090203/lib64/R]
***
setGeneric(predict)
[1] predict
predict
standardGeneric for predict defined from package stats
function (object, ...)
standardGeneric(predict)
environment: 0xe24b080
Methods may be defined for arguments: object
Use showMethods(predict) for currently available ones.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Gad Abraham
Sent: 10 March 2009 10:02
To: R-devel@r-project.org
Subject: [Rd] S4 generic masking S3 generic when using namespace
Hi,
I have two example packages, test1 and test2, where the only code in
them is:
setGeneric(predict, function(object, ...)
standardGeneric(predict))
(get them from http://www.cs.mu.oz.au/~gabraham/test1.tar and
http://www.cs.mu.oz.au/~gabraham/test2.tar)
The difference between them is that first does not have a
namespace, and
loads fine. The second has a namespace but generates a warning:
library(test2)
Attaching package: 'test2'
The following object(s) are masked from package:stats :
predict
Is this an intended behaviour? If I ignore this masking warning, do I
risk unintended consequences later down the track?
Thanks,
Gad
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] test2_0.1
--
Gad Abraham
MEng Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabra...@csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham
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[Rd] interactive graphics for R: was Google Summer of Code 2009
Dear Simon, thanks for comments. I better give a bit of a background first. We are analysing time series of financial data, often multivariate and with say 200K samples. It is quite a frequent situation that one needs to display multivariate time series of say 200K rows and 10 columns over the whole time range and be able to zoom in to look for effects of interest. The obvious choice of plots is a multiplot window with a shared x-axis, in this case time, zooming should be done simultaneously in all time series displayed. I do understand this is a very specific example, but I am sure similar problems arise in other discilines: think of a genomic browser, sequencing or any other non-financial time series data etc. Essentially, no matter what the graphying or rendering technology used beneath (GTK, QT or anything else), my requirements, and yes they are in a way subjective, but on the other hand quite generic, would be a possibliity to produce multiplot windows (similar to say setting mfrow in par) with two simple features: zooming and panning simultaneously on all plots or independently. The support for Axis/pretty method callbacks is required because those are the methods that provide correct axis labeling independently on the class of the data. This is essentially the only thing that is not supported by the gtkdatabox widget as the rulers can only display numbers. On the other issues of interactivity, I agree it is quite a broad term, but the functionality I describe above is pretty much basic. As for Java objections: this is not because Java is slow on its own, but the interface is not native, requires a huge JVM for a fairly simple task and the interface is relatively slow and cumbersome. As soon as I see a package demonstrating good performance via rJava, I will be happy to say I was wrong. But essentially the same problem with 'playwith' package mentioned earlier -- it uses RGtk, gWidgets and therefore it is slow -- it is not that GTK is slow, but the complex binding from R via RGtk to GTK. If used natively, it is very fast. As for iPlots, the development has shifted a while ago from the 'old' iPlots to the new ones which are in development stage (as I said they are announced for the useR! conference). My point was not about telling you to use a specific software, it was rather about making you aware of the fact that what you describe already exists (ggobi definitely is IG in GTK) and/or is worked on (iPlots 3.0) with possibly better approach. Where can I find it to have a look? No matter that it is in development, if it fits the needs, I will only be happy to contribute what I can. 3) I have a prototype using gtkdatabox for very fast interactive plots in R using GTK, but it is limited by the capabilities of the gtkdatabox widget, not that of R or GTK as such. I don't know about your prototype, so I cannot really comment on that, but gtkdatabox is not IG, either. I cannot send you an example of an R package using gtkdatabox from the office, but I will create a small demo pack at home and will send it to you separately as to indicate what I am looking into. Possibly it is not IG, but this is essentially what I described above, although quite primitive (but it was a one-day project for me, not 3-months). I do think there is a need for an interactive graphics package for R. I do completely agree with that, but interactive means it satisfies basic requirements on IG such as the availability of selection, highlighting, queries, interactive change of parameters etc. This is not about 2d/3d clouds at all - that we have for decades already. Also this is not about hacks to glue on interactivity to existing graphics systems with a chewing gum. We need a versatile (possible extensible) set of interactive statistical plots -- at least that's what our experience shows. Agree completely. Cheers, Simon -Original Message- From: Simon Urbanek [mailto:simon.urba...@r-project.org] Sent: 19 February 2009 14:34 To: Sklyar, Oleg (London) Cc: Friedrich Leisch; r-devel@r-project.org; manuel.eugs...@stat.uni-muenchen.de Subject: Re: [Rd] Google Summer of Code 2009 On Feb 19, 2009, at 6:38 , Sklyar, Oleg (London) wrote: Two ideas: 1) A library for interactive plots in R R lacks functionality that would allow displaying of interactive plots with two distinct functionalities: zooming and panning. This functionality is extremely important for the analysis of large, high frequency, data sets spanning over large ranges (in time as well). The functionality should acknowledge Axis methods in callbacks on rescale (so that it could be extended to user-specific classes for axis generation) and should have a native C interface to R (i.e. no Java, but such cross platform widgets like GTK or QT or anything similar that does not require heavy
Re: [Rd] Google Summer of Code 2009
Two ideas: 1) A library for interactive plots in R R lacks functionality that would allow displaying of interactive plots with two distinct functionalities: zooming and panning. This functionality is extremely important for the analysis of large, high frequency, data sets spanning over large ranges (in time as well). The functionality should acknowledge Axis methods in callbacks on rescale (so that it could be extended to user-specific classes for axis generation) and should have a native C interface to R (i.e. no Java, but such cross platform widgets like GTK or QT or anything similar that does not require heavy-weight add-ons). GTK has been used successfully from within R in many applications (RGtk, rgobby, EBImage etc) on both *nix and Windows, and thus could be a preferential option, it is also extremely easy to integrate into R. The existing tools (e.g. iplots) are slow, unstable and lack support for time/date plots (or actually any non-standard axes) and they are all Java. We are looking into stanard xy-plots as well as image and 3D plots. Obviously one can think of further interactivity, but this would be too much for the Summer of Code project. A good prototype would already be a step forward. 2) Cross platform GUI debugger, preferably further Eclipse integration (beyond StatET capabilities) Tibco has recently released the S+ workbench for eclipse which has a reasonable support for non-command line debugging. In the R community, the StatET eclipse plugin mimics a lot of code development functionality of S+ workbench, but has poor support for in-line execution of R sessions in eclipse and does not have debugging capabilities. Supporting this project further, or developing a GUI debugger independent of eclipse, are both acceptable options. The debugger should allow breakpoints, variable views etc. For both of the above, our interest is mostly on the Linux side, but one should look into cross-platform solutions. Regards, Oleg Dr Oleg Sklyar Research Technologist AHL / Man Investments Ltd +44 (0)20 7144 3107 oskl...@maninvestments.com -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Friedrich Leisch Sent: 18 February 2009 22:54 To: r-devel@r-project.org Cc: manuel.eugs...@stat.uni-muenchen.de Subject: [Rd] Google Summer of Code 2009 Hi, in approximately one months time mentoring institutions can propose projects for the Google Summer of Code 2009, see http://code.google.com/soc/ Last year the R Foundation succesfully participated with 4 projects, see http://www.r-project.org/SoC08/ for details. We want to participate again this year. Our project proposals will be managed by Manuel Eugster (email address in CC). Manuel is one of my PhD students and mentored the Roxygen project last year. This mail is mainly intended to make you aware of the program, Manuel will send a followup email with more technical details in the next days. In this phase we are looking for potential mentors who can offer interesting projects to students. I don't think that we will get much more than 4-6 projects, so don't be disappointed if you propose something and don't get selected. There are two selection steps involved: (a) The R Foundation has to compile an official ideas list of projects, for which students can apply. Last year we had 8 of those. After that, we (b) get a certain number of slots from Google (4 last year) and all prospective project mentors can vote on which projects actually get funding. Currently we are looking for good ideas for phase (a). I give no guarantees that all ideas will get on our official ideas list, what we pick depends on the number of submissions and topics, respectively. We want to make sure to have a broad range of themes, it is unlikely, that we will, e.g., pick 10 database projects. Also keep in mind that students have only three months time. This is not a research exercise for the students, you should have a rough idea what needs to be done. Last year we had a majority of infrastructure projects, and only few with focus on statistical algorithms. We got a lot of applications for the latter, so don't hesitate to formulate projects in that direction. Important infrastructure may get precedence over specialized algorithms, though, because the whole community can benfit from those. But that will be a decision in phase (b), and we are not there yet. Please don't send any ideas to me right now, wait for the above mentioned email by Manuel on the technical details for idea submission. Best, Fritz -- -- - Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München
Re: [Rd] Google Summer of Code 2009
Simon, I would not like to take it offline as I disagree with your points and think it is fair to let other users know why. To make it clear first, I am most interested in 2D, not 3D plots, and rgobbi is not a good enough solution, unfortunately. 1) I spent loads of time looking for good, if any at all, interactive graphics packages for R. There are hardly many, and apart from rgl there are no good ones as I see it. I do accept that this can be subjective, but I think many people will share my opinion. 2) With respect to iplots: http://cran.r-project.org/web/packages/iplots/index.html states: Version:1.1-3 Depends:R (≥ 1.5.0), methods, rJava (≥ 0.5-0) http://www.rosuda.org/iplots/ states: News: * 2007/08/07 Released iplots_1.1-1 on CRAN... There might be version 3 available somewhere, but it is not obvious where and the above one is Java based. I have tried the above version about 4 months ago -- it was slow, unstable and did not have any support for time axis at all. If I find it, I will give it a try and will be able to post corresponding comments. 2) rggobi is not a solution for 2D graphics at all and this is what is missing in R. I would not mention rgobbi myself having had no look at it first. However, if somebody works on interactive 2D plots, there is no reason why this person should think of 3D as well to have all in one framework. 3) I have a prototype using gtkdatabox for very fast interactive plots in R using GTK, but it is limited by the capabilities of the gtkdatabox widget, not that of R or GTK as such. I do think there is a need for an interactive graphics package for R. Dr Oleg Sklyar Research Technologist AHL / Man Investments Ltd +44 (0)20 7144 3107 oskl...@maninvestments.com -Original Message- From: Simon Urbanek [mailto:simon.urba...@r-project.org] Sent: 19 February 2009 14:34 To: Sklyar, Oleg (London) Cc: Friedrich Leisch; r-devel@r-project.org; manuel.eugs...@stat.uni-muenchen.de Subject: Re: [Rd] Google Summer of Code 2009 On Feb 19, 2009, at 6:38 , Sklyar, Oleg (London) wrote: Two ideas: 1) A library for interactive plots in R R lacks functionality that would allow displaying of interactive plots with two distinct functionalities: zooming and panning. This functionality is extremely important for the analysis of large, high frequency, data sets spanning over large ranges (in time as well). The functionality should acknowledge Axis methods in callbacks on rescale (so that it could be extended to user-specific classes for axis generation) and should have a native C interface to R (i.e. no Java, but such cross platform widgets like GTK or QT or anything similar that does not require heavy-weight add-ons). GTK has been used successfully from within R in many applications (RGtk, rgobby, EBImage etc) on both *nix and Windows, and thus could be a preferential option, it is also extremely easy to integrate into R. The existing tools (e.g. iplots) are slow, unstable and lack support for time/date plots (or actually any non-standard axes) and they are all Java. We are looking into stanard xy-plots as well as image and 3D plots. Obviously one can think of further interactivity, but this would be too much for the Summer of Code project. A good prototype would already be a step forward. If primitive 3d scatterplot interactivity is all you want, go with rggobi. It's GTK and has all this already and much more. However, ggobi also shows why GTK is not a good choice for general interactive graphics toolkit - it [GTK] is slow and lacks reasonable graphics support. OpenGL is IMHO a better way to go since IG don't really leverage any of the widgets (you get them for free via R widgets packages anyway) and OpenGL gives you excellent speed, alpha-support and anti-aliasing etc. As you can imagine I don't agree with most of your statements above and I'm happy to discuss them in a separate thread. Just as an aside iPlots 3.0 (announced for useR!/DSC) are no longer Java based and have a native C interface. Cheers, S 2) Cross platform GUI debugger, preferably further Eclipse integration (beyond StatET capabilities) Tibco has recently released the S+ workbench for eclipse which has a reasonable support for non-command line debugging. In the R community, the StatET eclipse plugin mimics a lot of code development functionality of S+ workbench, but has poor support for in-line execution of R sessions in eclipse and does not have debugging capabilities. Supporting this project further, or developing a GUI debugger independent of eclipse, are both acceptable options. The debugger should allow breakpoints, variable views etc. For both of the above, our interest is mostly on the Linux side, but one should look into cross-platform solutions
Re: [Rd] Google Summer of Code 2009
Thanks for pointing out. playwith looks quite interesting
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Liviu Andronic [mailto:landronim...@gmail.com]
Sent: 19 February 2009 15:11
To: Sklyar, Oleg (London)
Cc: Simon Urbanek; Friedrich Leisch;
manuel.eugs...@stat.uni-muenchen.de; r-devel@r-project.org
Subject: Re: [Rd] Google Summer of Code 2009
On Thu, Feb 19, 2009 at 3:47 PM, Sklyar, Oleg (London)
oskl...@maninvestments.com wrote:
I do think there is a need for an interactive graphics
package for R.
There are also the GTK-based playwith, and latticist; unsure though
whether they fit your requirements.
Liviu
--
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Re: [Rd] Google Summer of Code 2009
Dear Yihui,
I am sure there are many possibilities available, but I am not looking for a
hack and rather for a versatile high-quality solution. It solution should be
fast, reliable and developed to a high standard. Moreover, on my X11 RHEL5
x86_64 I get the following:
getGraphicsEvent(onKeybd = keybd)
Error in getGraphicsEvent(onKeybd = keybd) :
graphics device does not support graphics events
Furthermore, one could think of a library displaying multiple plots, for
multivariate data, allowing simultaneous zoom into all of the plots.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Yihui Xie [mailto:xieyi...@gmail.com]
Sent: 19 February 2009 16:20
To: Sklyar, Oleg (London)
Cc: Liviu Andronic; Friedrich Leisch; Simon Urbanek;
manuel.eugs...@stat.uni-muenchen.de; r-devel@r-project.org
Subject: Re: [Rd] Google Summer of Code 2009
Well, for the first idea, isn't it easy enough to fulfill zooming or
panning using getGraphicsEvent() in the grDevices package? For example
(using keys +/-/Left/Right/Up/Down/* to zoom and pan):
##
# a demo for zooming and panning in R graphics
# by Yihui Xie xieyi...@gmail.com Feb 20, 2009
##
# a large number of points
plot(x - rnorm(5000), y - rnorm(5000), xlab = x, ylab = y)
xylim - c(range(x), range(y))
zoom - function(d, speed = 0.05) {
rx - speed * (xylim[2] - xylim[1])
ry - speed * (xylim[4] - xylim[3])
# global assignment '-' here!
xylim - xylim + d * c(rx, -rx, ry, -ry)
plot(x, y, xlim = xylim[1:2], ylim = xylim[3:4])
NULL
}
# Key `+`: zoom in; `-`: zoom out
# Left, Right, Up, Down: self-explaining
# `*`: reset
# Press other keys to quit
keybd - function(key) {
switch(key, `+` = zoom(1), `-` = zoom(-1), Left = zoom(c(-1,
1, 0, 0)), Right = zoom(c(1, -1, 0, 0)), Up = zoom(c(0,
0, 1, -1)), Down = zoom(c(0, 0, -1, 1)), `*` = plot(x,
y), Quit the program)
}
getGraphicsEvent(onKeybd = keybd)
##
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Thu, Feb 19, 2009 at 7:38 PM, Sklyar, Oleg (London)
oskl...@maninvestments.com wrote:
Two ideas:
1) A library for interactive plots in R
R lacks functionality that would allow displaying of
interactive plots with two distinct functionalities: zooming
and panning. This functionality is extremely important for
the analysis of large, high frequency, data sets spanning
over large ranges (in time as well). The functionality should
acknowledge Axis methods in callbacks on rescale (so that it
could be extended to user-specific classes for axis
generation) and should have a native C interface to R (i.e.
no Java, but such cross platform widgets like GTK or QT or
anything similar that does not require heavy-weight add-ons).
GTK has been used successfully from within R in many
applications (RGtk, rgobby, EBImage etc) on both *nix and
Windows, and thus could be a preferential option, it is also
extremely easy to integrate into R. The existing tools (e.g.
iplots) are slow, unstable and lack support for time/date
plots (or actually any non-standard axes) and they are all
Java. We are looking into stanard xy-plots as well as image
and 3D plots. Obviously one can think of further
interactivity, but this would be too much for the Summer of
Code project. A good prototype would already be a step forward.
2) Cross platform GUI debugger, preferably further Eclipse
integration (beyond StatET capabilities)
Tibco has recently released the S+ workbench for eclipse
which has a reasonable support for non-command line
debugging. In the R community, the StatET eclipse plugin
mimics a lot of code development functionality of S+
workbench, but has poor support for in-line execution of R
sessions in eclipse and does not have debugging capabilities.
Supporting this project further, or developing a GUI debugger
independent of eclipse, are both acceptable options. The
debugger should allow breakpoints, variable views etc.
For both of the above, our interest is mostly on the Linux
side, but one should look into cross-platform solutions.
Regards,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of
Friedrich Leisch
Sent: 18 February 2009 22:54
To: r-devel@r-project.org
Cc
Re: [Rd] setClassUnion with numeric; extending class union
Hi John, sorry for not posting more info. Strangely I get warnings about setClassUnion with numeric in a very special case: if I define it in a clean R session then there are no warnings, however if I load a number of my packages where there are other classes derived from numeric and exported then I get the following warnings: setClassUnion(numericOrNULL, c(numeric,NULL)) [1] numericOrNULL Warning messages: 1: In .checkSubclasses(class1, classDef, class2, classDef2, where1, : Subclass TimeDateBase of class numeric is not local and cannot be updated for new inheritance information; consider setClassUnion() 2: In .checkSubclasses(class1, classDef, class2, classDef2, where1, : Subclass TimeDate of class numeric is not local and cannot be updated for new inheritance information; consider setClassUnion() 3: In .checkSubclasses(class1, classDef, class2, classDef2, where1, : Subclass Time of class numeric is not local and cannot be updated for new inheritance information; consider setClassUnion() The class is operational even with those warnings though. Now, the above classes are defined as follows: ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - setClass(TimeDateBase, representation(numeric, mode=character), prototype(mode=posix) ) ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - setClass(TimeDate, representation(TimeDateBase, tzone=character), prototype(tzone=Europe/London) ) ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - setClass(Time, representation(TimeDateBase) ) Theses classes work perfectly fine on their own and are used throughout our code for all possible time and date operations extending the existing functionality of R and available third party packages by an order of magnitude. I do not see a relation between the above class definitions and the newly defined class union though apart from the fact that they are in a package namespace and therefore locked. Sorry I cannot provide more source code as the code is not yet public. It would definitely be nice to somehow have a .Data slot in NULL or even a data.frame, although I do understand that this is quite a substantial piece of work to make it all robust and backward compatible. sessionInfo() ## of a clean session R version 2.9.0 Under development (unstable) (2009-02-02 r47821) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics utils datasets grDevices methods base Any thoughts are greatly appreciated. Kind regards, Oleg Dr Oleg Sklyar Research Technologist AHL / Man Investments Ltd +44 (0)20 7144 3107 oskl...@maninvestments.com -Original Message- From: John Chambers [mailto:j...@r-project.org] Sent: 11 February 2009 20:40 To: Sklyar, Oleg (London) Cc: r-devel@r-project.org Subject: Re: [Rd] setClassUnion with numeric; extending class union So, I was intrigued and played around a bit more. Still can't get any warnings, but the following may be the issue. One thing NOT currently possible is to have a class that has NULL as its data part, because type NULL is abnormal and can't have attributes. So if you want a class that contains a union including NULL, you're in trouble generating a value from the class that is NULL. It's not really a consequence of the setUnion() per se. setClass(bar, contains = numericOrNULL) [1] bar zz = new(bar, NULL) Error in validObject(.Object) : invalid class bar object: invalid object for slot .Data in class bar: got class list, should be or extend class numericOrNULL (How one got from the error to the message is a question, but in any case this can't currently work.) As in my example and in your example with a slot called data, no problem in having a slot value that is NULL. Looking ahead, I'm working on some extensions that would allow classes to contain abnormal data types (externalptr, environment, ...) by using a reserved slot name, since one can not make the actual data type one of those types. John Chambers wrote: What warnings? Which part of the following is not what you're looking for? (The usual information is needed, like version of R, reproducible example, etc.) setClassUnion(numericOrNULL, c(numeric,NULL)) [1] numericOrNULL setClass(foo, representation(x=numericOrNULL)) [1] foo ff = new(foo, x= 1:10) fg = new(foo, x = NULL) ff An object of class foo Slot x: [1] 1 2 3 4 5 6 7 8 9 10 fg An object of class foo Slot x: NULL fk = new(foo) fk An object of class foo Slot x: NULL John Sklyar, Oleg (London) wrote: Dear list: I am looking for a good way to create an S4 class that would extend numeric, but would allow NULL instead of data as well. As far as I can see there is no way at the moment to do that, but please correct me if I am wrong. The best solution
[Rd] setClassUnion with numeric; extending class union
Dear list:
I am looking for a good way to create an S4 class that would extend
numeric, but would allow NULL instead of data as well. As far as I can
see there is no way at the moment to do that, but please correct me if I
am wrong. The best solution I came up with so far was the following (it
also indicates a problem of using setClassUnion with numeric as one of
the classes):
I define a class union of numeric and NULL:
Unfortunately the following works only with warnings:
setClassUnion(numericOrNULL, c(numeric,NULL))
So I do a workaround as:
setClass(aNumeric, contains=numeric)
setClassUnion(numericOrNULL, c(aNumeric,NULL))
Then I cannot really extend the above virtual class and can only use it
in a user-defined slot as follows:
setClass(myClass, representation(data=numericOrNULL))
new(myClass, data=runif(20))
new(myClass, data=NULL)
and this works.
Obviously it would be nicer to have something like the following:
setClass(myClass, contains=numericOrNULL)
new(myClass, runif(20)) ## .Data is not a slot of myClass
setClass(myClass, representation(numericOrNULL))
new(myClass, runif(20)) ## ibid
Technically I understand that the reason behind it failing to work is
that the virtual class numericOrNULL has not got the .Data slot from
numeric, but it would be nice to have such a functionality.
Any ideas about better ways for solving such a problem than the one
described above?
Thanks.
Best,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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[Rd] after some time R stopped returning from Rmpi calls
Hi,
this is not exactly a developer question, but maybe you have noticed
similar behaviour before. For quite some time R and Rmpi were working
perfectly for me until one day they just stopped doing so without any
changes in the configs. R still spawns jobs as requested, and if they
are small they run through and return, but as soon as their duration is
over 5s or so the spawned processes go to sleep and never return to the
head node. Below is the top of one of the slave nodes with the spawned
jobs, as you see their status is sleeping. It looks like a communication
problem between the master and the slave nodes, but this behaviour *is*
user specific: exactly the same script will work for some users and will
just lead to hanging for others.
Rmpi is installed with a default R CMD INSTALL without additional
arguments. LD_LIBRARY_PATH is set and the whole setup *was* working with
the same config.
Has anybody experienced similar problems with Rmpi and LAM before?
Thank you,
Oleg
RHEL 5 x86_64, 16core Opteron
LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University
It is quite a dated version of R I running now, but recent Rmpi.
sessionInfo()
R version 2.9.0 Under development (unstable) (2008-09-30 r46585)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
other attached packages:
[1] Rmpi_0.5-5
PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND
7699 osklyar 16 0 19128 1448 1000 S0 0.0 0:00.02 lamd
7807 osklyar 16 0 8652 992 824 S0 0.0 0:00.01 Rslaves.sh
7808 osklyar 16 0 8656 992 824 S0 0.0 0:00.01 Rslaves.sh
7809 osklyar 16 0 8652 992 824 S0 0.0 0:00.00 Rslaves.sh
7810 osklyar 17 0 8656 992 824 S0 0.0 0:00.01 Rslaves.sh
7811 osklyar 18 0 8656 992 824 S0 0.0 0:00.02 Rslaves.sh
7812 osklyar 18 0 8656 992 824 S0 0.0 0:00.02 Rslaves.sh
7813 osklyar 18 0 8656 992 824 S0 0.0 0:00.02 Rslaves.sh
7814 osklyar 18 0 8656 992 824 S0 0.0 0:00.02 Rslaves.sh
7815 osklyar 15 0 165m 60m 4568 S0 0.2 0:03.66 R
7816 osklyar 16 0 161m 56m 4568 S0 0.2 0:03.51 R
7817 osklyar 15 0 161m 56m 4584 S0 0.2 0:03.82 R
7818 osklyar 16 0 161m 56m 4568 S0 0.2 0:03.31 R
7819 osklyar 16 0 165m 61m 4568 S0 0.2 0:03.59 R
7820 osklyar 15 0 162m 58m 4568 S0 0.2 0:03.43 R
7821 osklyar 16 0 162m 58m 4568 S0 0.2 0:03.26 R
7824 osklyar 16 0 161m 56m 4568 S0 0.2 0:03.49 R
7973 osklyar 15 0 87208 1880 1140 S0 0.0 0:00.00 sshd
7974 osklyar 15 0 72332 1716 1276 S0 0.0 0:00.01 bash
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
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Re: [Rd] Return values from .Call and garbage collection
- R is not multithreaded (or so it was) and thus race condition cannot
occur
- I would think there is no call to GC at the time of assignment of the
return value to a variable. GC is only called within other R calls as R
as mentioned above is not multithreaded
Most likely issue is your code itself, out of range indexing, failure to
initialise all elements of the allocated structure correctly, 1 and not
0-based indexing, use of other R variables for initialisation that
should have been protected but were not etc.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Jon Senior
Sent: 27 January 2009 12:09
To: r-devel@r-project.org
Subject: [Rd] Return values from .Call and garbage collection
Hi all,
I'm posting this here as it discusses an issue with an
external C library. If it would be better in R-Help, then I'll repost.
I'm using an external library which I've written, which
provides a large set of data (500MB in a highly condensed
format) and the tools to return values from the data. The
functionality has been tested call by call and using valgrind
and works fine, with no memory leaks. After retrieval, I
process the data in R. A specific function is causing a
problem that appears to be related to the garbage collector
(judging by symptoms).
In the C code, a Matrix is created using
PROTECT(retVal = allocMatrix(INTSXP, x, y));
Values are written into this matrix using
INTEGER(retVal)[translatedOffset]=z;
where translatedOffset is a conversion from a row/column
pair to an offset as shown in R-exts.pdf.
The last two lines of the function call are:
UNPROTECT(1);
return retVal;
The shared library was compiled with R CMD SHLIB and is
called using .Call.
Which returns our completed SEXP object to R where processing
continues.
In R, we continue to process the data, replacing -1s with NAs
(I couldn't find a way to do that in that would make it back
into R), sorting it, and trimming it. All of these operations
are carried out on the original data.
If I carry out the processing step by step from the
interpreter, everything is fine and the data comes out how I
would expect. But when I run the R code to carry out those
steps, every now and again (Around 1/5th of the time), the
returned data is garbage. I'm expecting to receive a bias per
iteration that should be -5 = bias = 5, but for the
garbaged data, I'm getting results of the order of 100s of
thousands out (eg. -220627.7). If I call the routine which
carries out the processing for one iteration from the
intepreter, sometimes I get the correct data, sometimes (with
the same frequency) I get garbage.
There are two possibilities that I can envisage.
1) Race condition: R is starting to execute the R code after
the .Call before the .Call has returned, thus the data is corrupted.
2) Garbage collector: the GC is collecting my data between
the UNPROTECT(1); call and the assignment to an R variable.
The created matrices can be large (where x 1000, y
10), but the garbage doesn't appear to be related to the
size of the matrix.
Any ideas what steps I could take to proceed with this? Or
other possibilities than those I've suggested? For reasons of
confidentiality I'm unable to release test code, and the
large dataset might make testing difficult.
Thanks in advance
--
Jon Senior j...@restlesslemon.co.uk
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Re: [Rd] [Q] R CMD check signals error on code that works from UI
Because there is a % sign, which is stripped out by LaTeX used to build
the help system as a comment. Just look at how your example code is
output -- the string is unterminated because the matching quote is
masked by % latex comment
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Paul Roebuck
Sent: 15 January 2009 17:50
To: R Development Mailing List
Subject: [Rd] [Q] R CMD check signals error on code that works from UI
Add the following to example section of a dot-Rd manpage:
## :WHY: The following kills R CMD check but runs fine on console.
foos - c(aaa, bbb, ccc)
cat(sapply(foos,
function(foo) {
sprintf(name: %-18s upper: %s\n,
foo,
toupper(foo))
}), sep=)
R CMD check package stops with error:
...
* checking examples ... ERROR
Running examples in 'package-Ex.R' failed.
The error most likely occurred in:
...
## :WHY: The following kills R CMD check but runs fine on console.
foos - c(aaa, bbb, ccc)
cat(sapply(foos,
+function(foo) {
+sprintf(name:
+foo,
+toupper(foo))
+}), sep=)
+
+
+
+ cleanEx(); nameEx(sc80-registerNormalizationMethod)
Error: unexpected string constant in:
cleanEx(); nameEx(
Execution halted
Yet on console, it provides the expected:
name: aaaupper: AAA
name: bbbupper: BBB
name: cccupper: CCC
How do I work around this for manpage?
--
SIGSIG -- signature too long (core dumped)
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Re: [Rd] particulars of importing/loading libraries
Sorry Simon, you are right. I tried to recreate a problem that I had
with other packages where the packages were added to Depends but made a
mistake. However the problem remains if I do the following.
Added: pack1 to Depends of pack2. Now I create pack3 with the following
contents: it does not import pack1 directly, nor depends on it. It
rather imports pack2 and depends on pack2. I then expect the
functionality of pack1 to be available still if I only load pack3. But I
now get errors with pack3 calling the function from pack1. Does this
mean I need to import and depend on pack1 and methods explicitly in
pack3. I.e. do I have to import and depend on ALL the packages that may
be in use, even if they are imported by other that I depend on and
import:
pack3: DESCRIPTION -
Package: pack3
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), pack2
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack3
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
pack3: NAMESPACE --
import(pack2)
exportPattern(^[^\\.])
pack3: posix.R --
testPosix2 = function() {
z = as.POSIXct(testPosixVal)
print(z)
print(class(z))
z
}
Note, that the above function is the same as in pack2, just a different
name.
*** R 2.9.0 (svn -r 46585) [/share/research/R-devel/20081002/lib64/R]
***
library(pack3)
Loading required package: pack2
Loading required package: pack1
as.POSIXct(pack1::testPosixVal)
[1] 2009-01-13 15:29:50 UTC
testPosxi() ## called from pack2
[1] 2009-01-13 15:29:50 UTC
[1] POSIXt POSIXct
[1] 2009-01-13 15:29:50 UTC
testPosix2() ## called from pack3
Error in as.POSIXct.default(testPosixVal) :
do not know how to convert 'testPosixVal' to class POSIXlt
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Simon Urbanek [mailto:simon.urba...@r-project.org]
Sent: 14 January 2009 01:51
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
Oleg,
On Jan 13, 2009, at 11:00 , Sklyar, Oleg (London) wrote:
Dear List:
Sorry for posting maybe a trivial question, but I have a basic
understanding problem. If I have say pack1 and pack2, two R
packages,
and pack2 depends on and imports pack1 fully (as in the
code below),
is
there a way to make all the functionality of pack1 available for the
global and other environments (not only for the functions
called from
withing pack2) by loading pack2 only? I thought if pack2
depends on
and
imports pack1 and essentially reexports everything, one
should get the
full functionality simply by loading pack2. This does not
seem to be
the
case or I am missing something trivial in my NAMESPACE/DESCRIPTION
files?
If this is documented in Writing R Extensions, I would be thankful
for a
page number and maybe a quick fix in my example below as so
far I have
not been able to find a clear explanation.
The problem can be illustrated by the following simple
example (this
is
a simple code for 2 packages, pack1 and pack2; plus an example).
if you bothered to use R CMD check you would find your bug right away:
* checking package dependencies ... ERROR
Namespace dependencies not required:
pack1
You simply forgot to add pack1 to the Depends: line - that's
all. Once
you fix that, you'll see what happens:
library(pack2)
Loading required package: pack1
as.POSIXct(pack1::testPosixVal)
[1] 2009-01-14 01:38:08 UTC
Cheers,
S
Thank you for your replies.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
--- pack1: DESCRIPTION --
Package: pack1
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack1
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack1: NAMESPACE --
import(methods)
exportPattern(^[^\\.])
exportClasses(posixTime)
exportMethods(as.POSIXct)
--- pack1: posix.R --
setClass(posixTime, numeric)
setGeneric(as.POSIXct)
setMethod(as.POSIXct, signature(x=posixTime),
function(x, tz) {
z = x...@.data
attr(z,class) = c(POSIXt, POSIXct)
attr(z,tzone) = UTC
z
}
)
testPosixVal = new(posixTime, as.numeric(Sys.time()))
--- pack2: DESCRIPTION
Package: pack2
Version: 0.0.1
Date: 12 Jan 2009
Title: pack2 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack2
LazyLoad: yes
License: Proprietary
URL
Re: [Rd] particulars of importing/loading libraries
Thank you Simon.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Simon Urbanek [mailto:simon.urba...@r-project.org]
Sent: 14 January 2009 16:11
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
On Jan 14, 2009, at 10:52 , Sklyar, Oleg (London) wrote:
Well, this is very reasonable and this is how it should be I would
say. If it was consistent, there would be no problem as they would
be easy to nail down. However, the problem is now that if I load
pack3 only (which imports pack2 only) then as.POSIXct
exported from
pack1 is NOT available for functions in pack3,
Because pack3 didn't request it.
but is available for calls from the global env (see example
below).
It is obviously available for calls from functions in pack2
as there
it is imported directly. Although, why also testPosix() of
pack2 is
then available for calls from the global env as it was only loaded
as import for pack3?
Global environment is not encapsulated - you have access to anything
that has been attached - sort of implicitly importing anything that
has even been [exported and] attached (there is really no concept of
importing for the global environment, but the effect is
analogous).
This is a conceptual difference of the interactive use vs package
code. Unlike package code you don't know in advance what you will be
doing when you're working interactively, so I think it makes
sense to
assume that everything is implicitly imported.
Cheers,
S
In my understanding if pack3 does not depend on pack1 directly,
functionality of pack1 should not be available anywhere apart from
functions called from pack2 as well as functions in pack2 should
only be
available for calls by functions in pack3 but not in the
global env...
The semantics seems to be broken here, is it not?
library(pack3)
Loading required package: pack2
Loading required package: pack1
testPosix() ## from pack2
[1] 2009-01-13 15:29:50 UTC
[1] POSIXt POSIXct
[1] 2009-01-13 15:29:50 UTC
testPosix2()
Error in as.POSIXct.default(testPosixVal) :
do not know how to convert 'testPosixVal' to class POSIXlt
as.POSIXct(pack1::testPosixVal)
[1] 2009-01-13 15:29:50 UTC
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Simon Urbanek [mailto:simon.urba...@r-project.org]
Sent: 14 January 2009 15:38
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
On Jan 14, 2009, at 4:24 , Sklyar, Oleg (London) wrote:
Sorry Simon, you are right. I tried to recreate a problem
that I had
with other packages where the packages were added to Depends but
made a mistake. However the problem remains if I do the following.
Added: pack1 to Depends of pack2. Now I create pack3 with the
following contents: it does not import pack1 directly, nor depends
on it. It rather imports pack2 and depends on pack2. I then expect
the functionality of pack1 to be available still if I only
load pack3.
That is semantically not a reasonable requirement. pack3
cannot (and
should not) assume anything about the internals of pack2. If
it needs
a function from pack1, it has to import it from pack1. If pack2 re-
exported as.POSIXct then that would make it part of pack2's
interface
and then you're free to just depend on pack2.
Cheers,
S
But I
now get errors with pack3 calling the function from
pack1. Does this
mean I need to import and depend on pack1 and methods
explicitly in
pack3. I.e. do I have to import and depend on ALL the
packages that
may
be in use, even if they are imported by other that I depend on and
import:
pack3: DESCRIPTION -
Package: pack3
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), pack2
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack3
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
pack3: NAMESPACE --
import(pack2)
exportPattern(^[^\\.])
pack3: posix.R --
testPosix2 = function() {
z = as.POSIXct(testPosixVal)
print(z)
print(class(z))
z
}
Note, that the above function is the same as in pack2, just a
different
name.
*** R 2.9.0 (svn -r 46585)
[/share/research/R-devel/20081002/lib64/R]
***
library(pack3)
Loading required package: pack2
Loading required package: pack1
as.POSIXct(pack1::testPosixVal)
[1] 2009-01-13 15:29:50 UTC
testPosxi() ## called from pack2
[1] 2009-01-13 15:29:50 UTC
[1] POSIXt POSIXct
[1] 2009-01-13
[Rd] particulars of importing/loading libraries
Dear List:
Sorry for posting maybe a trivial question, but I have a basic
understanding problem. If I have say pack1 and pack2, two R packages,
and pack2 depends on and imports pack1 fully (as in the code below), is
there a way to make all the functionality of pack1 available for the
global and other environments (not only for the functions called from
withing pack2) by loading pack2 only? I thought if pack2 depends on and
imports pack1 and essentially reexports everything, one should get the
full functionality simply by loading pack2. This does not seem to be the
case or I am missing something trivial in my NAMESPACE/DESCRIPTION
files?
If this is documented in Writing R Extensions, I would be thankful for a
page number and maybe a quick fix in my example below as so far I have
not been able to find a clear explanation.
The problem can be illustrated by the following simple example (this is
a simple code for 2 packages, pack1 and pack2; plus an example).
Thank you for your replies.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
--- pack1: DESCRIPTION --
Package: pack1
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack1
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack1: NAMESPACE --
import(methods)
exportPattern(^[^\\.])
exportClasses(posixTime)
exportMethods(as.POSIXct)
--- pack1: posix.R --
setClass(posixTime, numeric)
setGeneric(as.POSIXct)
setMethod(as.POSIXct, signature(x=posixTime),
function(x, tz) {
z = x...@.data
attr(z,class) = c(POSIXt, POSIXct)
attr(z,tzone) = UTC
z
}
)
testPosixVal = new(posixTime, as.numeric(Sys.time()))
--- pack2: DESCRIPTION
Package: pack2
Version: 0.0.1
Date: 12 Jan 2009
Title: pack2 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack2
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack2: NAMESPACE --
import(pack1)
exportPattern(^[^\\.])
--- pack2: posix.R --
testPosix = function() {
z = as.POSIXct(testPosixVal)
print(z)
print(class(z))
z
}
-- test code to run from global env, showing problems ---
require(pack2)
## use as.POSIXct imported into pack2 from pack1 to do the conversion in
the fun
testPosix()
#~ [1] 2009-01-13 15:29:50 UTC
#~ [1] POSIXt POSIXct
#~ [1] 2009-01-13 15:29:50 UTC
## now try using it directly from the global env (pack1 was not
explicitly loaded)
as.POSIXct(pack1::testPosixVal)
#~ Error in as.POSIXct.default(pack1::testPosixVal) :
#~ do not know how to convert 'pack1::testPosixVal' to class POSIXlt
## now require pack1 explicitly and try again
require(pack1)
as.POSIXct(pack1::testPosixVal)
#~ [1] 2009-01-13 15:29:50 UTC
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Re: [Rd] particulars of importing/loading libraries
I was thinking of this, but this is going to be a pain if a package
imports 5 packs, is being imported by another one, which itself is
imported by yet another one and the only one one would like to load
explicitly is the last down the line. If I do not find a better solution
this is what I probably will have to do, reexport everything.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: 13 January 2009 16:31
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
Hi Oleg --
Sklyar, Oleg (London) oskl...@maninvestments.com writes:
Dear List:
Sorry for posting maybe a trivial question, but I have a basic
understanding problem. If I have say pack1 and pack2, two R
packages,
and pack2 depends on and imports pack1 fully (as in the
code below), is
there a way to make all the functionality of pack1 available for the
global and other environments (not only for the functions
called from
withing pack2) by loading pack2 only? I thought if pack2
depends on and
imports pack1 and essentially reexports everything, one
should get the
full functionality simply by loading pack2. This does not
seem to be the
case or I am missing something trivial in my NAMESPACE/DESCRIPTION
files?
I think that exportPattern does a simple ls() on the environment of
the package name space. The imported symbols are not defined in that
environment, but (I think) in a variable .__NAMESPACE__. and so are
not discovered. Arguably, exportPattern (and friends) should be
smarter. Pragmatically, you need to re-export imported symbols
explicitly. I haven't worked this through entirely, and could be
wrong...
Martin
If this is documented in Writing R Extensions, I would be
thankful for a
page number and maybe a quick fix in my example below as so
far I have
not been able to find a clear explanation.
The problem can be illustrated by the following simple
example (this is
a simple code for 2 packages, pack1 and pack2; plus an example).
Thank you for your replies.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
--- pack1: DESCRIPTION --
Package: pack1
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack1
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack1: NAMESPACE --
import(methods)
exportPattern(^[^\\.])
exportClasses(posixTime)
exportMethods(as.POSIXct)
--- pack1: posix.R --
setClass(posixTime, numeric)
setGeneric(as.POSIXct)
setMethod(as.POSIXct, signature(x=posixTime),
function(x, tz) {
z = x...@.data
attr(z,class) = c(POSIXt, POSIXct)
attr(z,tzone) = UTC
z
}
)
testPosixVal = new(posixTime, as.numeric(Sys.time()))
--- pack2: DESCRIPTION
Package: pack2
Version: 0.0.1
Date: 12 Jan 2009
Title: pack2 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack2
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack2: NAMESPACE --
import(pack1)
exportPattern(^[^\\.])
--- pack2: posix.R --
testPosix = function() {
z = as.POSIXct(testPosixVal)
print(z)
print(class(z))
z
}
-- test code to run from global env, showing problems ---
require(pack2)
## use as.POSIXct imported into pack2 from pack1 to do the
conversion in
the fun
testPosix()
#~ [1] 2009-01-13 15:29:50 UTC
#~ [1] POSIXt POSIXct
#~ [1] 2009-01-13 15:29:50 UTC
## now try using it directly from the global env (pack1 was not
explicitly loaded)
as.POSIXct(pack1::testPosixVal)
#~ Error in as.POSIXct.default(pack1::testPosixVal) :
#~ do not know how to convert 'pack1::testPosixVal' to
class POSIXlt
## now require pack1 explicitly and try again
require(pack1)
as.POSIXct(pack1::testPosixVal)
#~ [1] 2009-01-13 15:29:50 UTC
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667
Re: [Rd] particulars of importing/loading libraries
So essentially I guess it would be nice to have a way of reexporting
everything in
get(imports,env=pack2:::.__NAMESPACE__.)
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: 13 January 2009 16:31
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
Hi Oleg --
Sklyar, Oleg (London) oskl...@maninvestments.com writes:
Dear List:
Sorry for posting maybe a trivial question, but I have a basic
understanding problem. If I have say pack1 and pack2, two R
packages,
and pack2 depends on and imports pack1 fully (as in the
code below), is
there a way to make all the functionality of pack1 available for the
global and other environments (not only for the functions
called from
withing pack2) by loading pack2 only? I thought if pack2
depends on and
imports pack1 and essentially reexports everything, one
should get the
full functionality simply by loading pack2. This does not
seem to be the
case or I am missing something trivial in my NAMESPACE/DESCRIPTION
files?
I think that exportPattern does a simple ls() on the environment of
the package name space. The imported symbols are not defined in that
environment, but (I think) in a variable .__NAMESPACE__. and so are
not discovered. Arguably, exportPattern (and friends) should be
smarter. Pragmatically, you need to re-export imported symbols
explicitly. I haven't worked this through entirely, and could be
wrong...
Martin
If this is documented in Writing R Extensions, I would be
thankful for a
page number and maybe a quick fix in my example below as so
far I have
not been able to find a clear explanation.
The problem can be illustrated by the following simple
example (this is
a simple code for 2 packages, pack1 and pack2; plus an example).
Thank you for your replies.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
--- pack1: DESCRIPTION --
Package: pack1
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack1
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack1: NAMESPACE --
import(methods)
exportPattern(^[^\\.])
exportClasses(posixTime)
exportMethods(as.POSIXct)
--- pack1: posix.R --
setClass(posixTime, numeric)
setGeneric(as.POSIXct)
setMethod(as.POSIXct, signature(x=posixTime),
function(x, tz) {
z = x...@.data
attr(z,class) = c(POSIXt, POSIXct)
attr(z,tzone) = UTC
z
}
)
testPosixVal = new(posixTime, as.numeric(Sys.time()))
--- pack2: DESCRIPTION
Package: pack2
Version: 0.0.1
Date: 12 Jan 2009
Title: pack2 to test S3/S4 methods compatibility
Author: Oleg Sklyar
Depends: R (= 2.7.1), methods
Maintainer: Oleg Sklyar oskl...@maninvestments.com
Description: pack2
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no
--- pack2: NAMESPACE --
import(pack1)
exportPattern(^[^\\.])
--- pack2: posix.R --
testPosix = function() {
z = as.POSIXct(testPosixVal)
print(z)
print(class(z))
z
}
-- test code to run from global env, showing problems ---
require(pack2)
## use as.POSIXct imported into pack2 from pack1 to do the
conversion in
the fun
testPosix()
#~ [1] 2009-01-13 15:29:50 UTC
#~ [1] POSIXt POSIXct
#~ [1] 2009-01-13 15:29:50 UTC
## now try using it directly from the global env (pack1 was not
explicitly loaded)
as.POSIXct(pack1::testPosixVal)
#~ Error in as.POSIXct.default(pack1::testPosixVal) :
#~ do not know how to convert 'pack1::testPosixVal' to
class POSIXlt
## now require pack1 explicitly and try again
require(pack1)
as.POSIXct(pack1::testPosixVal)
#~ [1] 2009-01-13 15:29:50 UTC
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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
**
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Re: [Rd] handling a matrix and .C
You should not have started with R/C API without reading this (first
link in google): Writing R Extensions. For your particular question
you want pages 72+ and sections 5.9.3 and 5.9.4, possibly further as
well
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Wilm Schumacher
Sent: 24 November 2008 18:59
To: r-devel@r-project.org
Subject: [Rd] handling a matrix and .C
Hello R-devel,
I want to write extensions for R in C (maybe C++ and Fortran
later) and it works fine, but there is one problem, which I
cannot solve (in my view).
I want to handle a matrix from R in C. For arrays there is
as.double(...), but nothing for a matrix.
I searched a while, but didn't find something.
Last I looked at the source code of e1071 and of the core
itself and recognized (I hope I understood this), that you
(and the e1071 people) use as.double() and give .C an
array and one have to parse the matrix again in the C function.
This sounds a little complicate. Isn't there another way? A
more adapted way?
Greetings
Wilm
ps: I joined the R-devel list, but didn't get an confirmation
mail. I hope this is normal
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[Rd] POSIXlt getting sec element at 60 when converting from POSIXct
In some cases rounding problems lead to creation of logically incorrect
times in POSIXlt when converting from POSIXct.
## everything works fine for the following values:
x = c(1223972160.0, 1223982660.0, 1223994660.)
## adding 0s for the epoch
x = x + as.POSIXct(1970-01-01 00:00) -
as.numeric(as.POSIXct(1970-01-01 00:00))
x
## [1] 2008-10-14 09:16:00 BST 2008-10-14 12:11:00 BST
## [3] 2008-10-14 15:31:00 BST
Now, numbers that look the same but originate from some calculations
lead to the following weirdness in POSIXlt. Sorry you will not be able
to reproduce as it is impossible to reproduce the same rounding:
as.character(as.numeric(t1))
[1] 1223972160.0 1223982660.0 1223994660.0
class(t1)
[1] POSIXt POSIXct
## here we get a second less due to rounding errors somewhere, not too
bad
t1
[1] 2008-10-14 09:15:59 BST 2008-10-14 12:10:59 BST
[3] 2008-10-14 15:30:59 BST
t2 = as.POSIXlt(t1)
t2
[1] 2008-10-14 09:15:59 BST 2008-10-14 12:10:59 BST
[3] 2008-10-14 15:30:59 BST
## however here we do get a real problem
t2$sec
[1] 60 60 60
## and here as well
format(t2, %Y-%m-%d %H:%M:%OS3)
[1] 2008-10-14 09:15:60.000 2008-10-14 12:10:60.000
[3] 2008-10-14 15:30:60.000
format(t1, %Y-%m-%d %H:%M:%OS3)
[1] 2008-10-14 09:15:60.000 2008-10-14 12:10:60.000
[3] 2008-10-14 15:30:60.000
Everything is back to normal with applying round (we are anyway limited
to 15 digits):
t3 = round(as.numeric(t1),5) + .origin
t3
[1] 2008-10-14 09:16:00 BST 2008-10-14 12:11:00 BST
[3] 2008-10-14 15:31:00 BST
sessionInfo()
R version 2.9.0 Under development (unstable) (2008-09-30 r46585)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] splines stats graphics utils datasets grDevices methods
[8] base
other attached packages:
[1] AHLFinance_0.1.54 AHLDBConn_0.2.3ROracle_0.5-9 DBI_0.2-4
[5] RODBC_1.2-3AHLNagLib_0.1.3AHLCalendar_0.2.59
AHLBase_0.1.25
loaded via a namespace (and not attached):
[1] tools_2.9.0
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
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Re: [Rd] Extract method for a new class
You will need to define several for different combinations of i and j
types e.g. ANY,missing; ANY,ANY; missing,ANY or possibly for types like
integer, character and logical more or less in the following way:
setMethod([, signature(x=haplogList, i=ANY,j=ANY),
function(x, i, j, ..., drop=TRUE) {
## do whatever you want here; your class is not derived
from a list
## so we cannot use NextMethod
}
)
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Coster, Albart
Sent: 19 September 2008 16:00
To: r-devel@r-project.org
Subject: [Rd] Extract method for a new class
Dear list,
I am trying to write a package for simulating meioses in R.
We defined a class 'haplotype' which contains the basic units
of our simulation:
setClass(haplotype,representation(snp = numeric,qtl = list,
hID = numeric,phID0 =
numeric,phID1 = numeric),
prototype = list(hID =
0,phID0 = NaN,phID1 = NaN))
In addition, we define a class 'haploList', which is just a
list of haplotypes:
setClass(haploList,contains = list,representation(genDist
= numeric,roundDec = integer))
Most things work fine, but when subsetting a haploList object
an object of class list is returned. I realize that I need to
write a function for subsetting this new object, and tried to
find the code for '[.listof' or something similar could not
find it, probably due to a suboptimal understanding of how it
is organized.
My question is, how could I define a extraction function for
my new class that uses all the existing functionality of the
Extract function for list?
Thanks in advance,
Albart Coster
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[Rd] 'xtfrm' performance (influences 'order' performance) in R devel
Hello everybody,
it looks like the presense of some (do know know which) S4 methods for a
given S4 class degrades the performance of xtfrm (used in 'order' in new
R-devel) by a factor of millions. This is for classes that ARE derived
from numeric directly and thus should be quite trivial to convert to
numeric.
Consider the following example:
setClass(TimeDateBase,
representation(numeric, mode=character),
prototype(mode=posix)
)
setClass(TimeDate,
representation(TimeDateBase, tzone=character),
prototype(tzone=London)
)
x = new(TimeDate, 1220966224 + runif(1e5))
system.time({ z = order(x) })
## system.time({ z = order(x) })
## user system elapsed
## 0.048 0.000 0.048
getClass(TimeDate)
## Class TimeDate
## Slots:
## Name: .Data tzone mode
## Class: numeric character character
## Extends:
## Class TimeDateBase, directly
## Class numeric, by class TimeDateBase, distance 2
## Class vector, by class TimeDateBase, distance 3
Now, if I load a library that not only defines these same classes, but
also a bunch of methods for those, then I have the following result:
library(AHLCalendar)
x = now() + runif(1e5) ## just random times in POSIXct format
x[1:5]
## TimeDate [posix] object in 'Europe/London' of length 5:
## [1] 2008-09-09 14:19:35.218 2008-09-09 14:19:35.672
## [3] 2008-09-09 14:19:35.515 2008-09-09 14:19:35.721
## [5] 2008-09-09 14:19:35.657
system.time({ z = order(x) })
Enter a frame number, or 0 to exit
1: system.time({
2: order(x)
3: lapply(z, function(x) if (is.object(x)) xtfrm(x) else x)
4: FUN(X[[1]], ...)
5: xtfrm(x)
6: xtfrm.default(x)
7: as.vector(rank(x, ties.method = min, na.last = keep))
8: rank(x, ties.method = min, na.last = keep)
9: switch(ties.method, average = , min = , max =
.Internal(rank(x[!nas], ties.
10: .gt(c(1220966375.21811, 1220966375.67217, 1220966375.51470,
1220966375.7211
11: x[j]
12: x[j]
Selection: 0
Timing stopped at: 47.618 13.791 66.478
At the same time:
system.time({ z = as.numeric(x) }) ## same as [EMAIL PROTECTED]
## user system elapsed
## 0.001 0.000 0.001
The only difference between the two is that I have the following methods
defined for TimeDate (full listing below).
Any idea why this could be happenning. And yes, it is down to xtfrm
function, 'order' was just a place where the problem occured. Should
xtfrm function be smarter with respect to classes that are actually
derived from 'numeric'?
showMethods(class=TimeDate)
Function: + (package base)
e1=TimeDate, e2=TimeDate
e1=TimeDate, e2=numeric
(inherited from: e1=TimeDateBase, e2=numeric)
Function: - (package base)
e1=TimeDate, e2=TimeDate
Function: Time (package AHLCalendar)
x=TimeDate
Function: TimeDate (package AHLCalendar)
x=TimeDate
Function: TimeDate- (package AHLCalendar)
x=TimeSeries, value=TimeDate
Function: TimeSeries (package AHLCalendar)
x=data.frame, ts=TimeDate
x=matrix, ts=TimeDate
x=numeric, ts=TimeDate
Function: [ (package base)
x=TimeDate, i=POSIXt, j=missing
x=TimeDate, i=Time, j=missing
x=TimeDate, i=TimeDate, j=missing
x=TimeDate, i=integer, j=missing
(inherited from: x=TimeDateBase, i=ANY, j=missing)
x=TimeDate, i=logical, j=missing
(inherited from: x=TimeDateBase, i=ANY, j=missing)
x=TimeSeries, i=TimeDate, j=missing
x=TimeSeries, i=TimeDate, j=vector
Function: [- (package base)
x=TimeDate, i=ANY, j=ANY, value=ANY
x=TimeDate, i=ANY, j=ANY, value=numeric
x=TimeDate, i=missing, j=ANY, value=ANY
x=TimeDate, i=missing, j=ANY, value=numeric
Function: add (package AHLCalendar)
x=TimeDate
Function: addMonths (package AHLCalendar)
x=TimeDate
Function: addYears (package AHLCalendar)
x=TimeDate
Function: align (package AHLCalendar)
x=TimeDate, to=character
x=TimeDate, to=missing
Function: as.POSIXct (package base)
x=TimeDate
Function: as.POSIXlt (package base)
x=TimeDate
Function: coerce (package methods)
from=TimeDate, to=TimeDateBase
Function: coerce- (package methods)
from=TimeDate, to=numeric
Function: dates (package AHLCalendar)
x=TimeDate
Function: format (package base)
x=TimeDate
Function: fxFwdDate (package AHLCalendar)
x=TimeDate, country=character
Function: fxSettleDate (package AHLCalendar)
x=TimeDate, country=character
Function: holidays (package AHLCalendar)
x=TimeDate
Function: index (package AHLCalendar)
x=TimeDate, y=POSIXt
x=TimeDate, y=Time
x=TimeDate, y=TimeDate
Function: initialize (package methods)
.Object=TimeDate
(inherited from: .Object=ANY)
Function: leapYear (package AHLCalendar)
x=TimeDate
Function: mday (package AHLCalendar)
x=TimeDate
Function: mode (package base)
x=TimeDate
(inherited from: x=TimeDateBase)
Function: mode- (package base)
x=TimeDate, value=character
(inherited from: x=TimeDateBase, value=character)
Function: month (package AHLCalendar)
x=TimeDate
Function: pretty (package base)
x=TimeDate
Function: prettyFormat (package AHLCalendar)
x=TimeDate, munit=character
x=TimeDate,
Re: [Rd] 'xtfrm' performance (influences 'order' performance) in R devel
Thanks for a quick reply, I was thinking of [ methods myself, but there
are so many of them. I only tested [(x=TimeDate,i=TimeDate,j=missing),
which is a completely non-standard one. It did not seem to have any
effect though.
I was thinking of writing the 'order' method and will experiment with
getting the one for xtfrm. However, it seems reasonable for the default
xtfrm to check if the object is inherited from a vector and in that case
simply returning the .Data slot? This would solve this and similar cases
immediately:
if (inherits(x,vector)) return(as.vector([EMAIL PROTECTED]))
BTW, generally, xtfrm.default calls 'rank' and it is not clear why rank
should work for a generic S4 object... this is essentially where the
problem is.
On a side note, a week ago I submitted a patch for the plot.default to
Rd, but nobody reacted (I checked the most recent patched and devel as
well) -- it is really an ugly bug (e.g
plot(1:5,1:5,xlim=c(-10,10),ylim=c(-8,3)) ) and the trivial patch fixes
it. Would be grateful if somebody from R-core checks it up. Meanwhile I
patch the graphics library before compiling R, which is not the best
solution. Here is the patch for src/library/graphics/plot.R
70,71c70,71
localAxis(if(is.null(y)) xy$x else x, side = 1, ...)
localAxis(if(is.null(y)) x else y, side = 2, ...)
---
localAxis(xlim, side = 1, ...)
localAxis(ylim, side = 2, ...)
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: 09 September 2008 15:11
To: Sklyar, Oleg (London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance (influences 'order'
performance) in R devel
No definitive answers, but here are a few observations.
In the call to order() code, I notice that you have dropped
into the branch
if (any(unlist(lapply(z, is.object
where the alternative in your case would seem to have been
going directly to the internal code.
You can consider a method for xtfrm(), which would help but
won't get you completely back to a trivial computation.
Alternatively, order() should be eligible for the new
mechanism of defining methods for
(Individual existing methods may not be the issue, and one
can't infer anything definite from the evidence given, but a
plausible culprit is the [ method. Because [] expressions
appear so often, it's always chancy to define a nontrivial
method for this function.)
John
Sklyar, Oleg (London) wrote:
Hello everybody,
it looks like the presense of some (do know know which)
S4 methods for a
given S4 class degrades the performance of xtfrm (used
in 'order' in new
R-devel) by a factor of millions. This is for classes
that ARE derived
from numeric directly and thus should be quite trivial
to convert to
numeric.
Consider the following example:
setClass(TimeDateBase,
representation(numeric, mode=character),
prototype(mode=posix)
)
setClass(TimeDate,
representation(TimeDateBase, tzone=character),
prototype(tzone=London)
)
x = new(TimeDate, 1220966224 + runif(1e5))
system.time({ z = order(x) })
## system.time({ z = order(x) })
## user system elapsed
## 0.048 0.000 0.048
getClass(TimeDate)
## Class TimeDate
## Slots:
## Name: .Data tzone mode
## Class: numeric character character
## Extends:
## Class TimeDateBase, directly
## Class numeric, by class TimeDateBase, distance 2
## Class vector, by class TimeDateBase, distance 3
Now, if I load a library that not only defines these
same classes, but
also a bunch of methods for those, then I have the
following result:
library(AHLCalendar)
x = now() + runif(1e5) ## just random times in POSIXct format
x[1:5]
## TimeDate [posix] object in 'Europe/London' of length 5:
## [1] 2008-09-09 14:19:35.218 2008-09-09 14:19:35.672
## [3] 2008-09-09 14:19:35.515 2008-09-09 14:19:35.721
## [5] 2008-09-09 14:19:35.657
system.time({ z = order(x) })
Enter a frame number, or 0 to exit
1: system.time({
2: order(x)
3: lapply(z, function(x) if (is.object(x)) xtfrm(x) else x)
4: FUN(X[[1]], ...)
5: xtfrm(x)
6: xtfrm.default(x)
7: as.vector(rank(x, ties.method = min, na.last = keep))
8: rank(x, ties.method = min, na.last = keep)
9: switch(ties.method, average = , min = , max =
.Internal(rank(x[!nas], ties.
10: .gt(c(1220966375.21811
Re: [Rd] 'xtfrm' performance (influences 'order' performance) in R devel
Ha, defined xtfrm for TimeDate, works instantly (xtfrm is already a
method). However, it won't be taken up by order as it is not in the
imported namespace, so order falls back to xtfrm.default.
Moreover, defining order (which is not a method unfortunately, *any
chance of changing this*?):
setGeneric(order)
setMethod(order, TimeDate,
function (..., na.last = TRUE, decreasing = FALSE)
order(list(...)[EMAIL PROTECTED],na.last=na.last,
decreasing=decreasing))
does not help either as it won't be taken up, order still calls the
default one, what am I doing wrong?
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: 09 September 2008 15:11
To: Sklyar, Oleg (London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance (influences 'order'
performance) in R devel
No definitive answers, but here are a few observations.
In the call to order() code, I notice that you have dropped
into the branch
if (any(unlist(lapply(z, is.object
where the alternative in your case would seem to have been
going directly to the internal code.
You can consider a method for xtfrm(), which would help but
won't get you completely back to a trivial computation.
Alternatively, order() should be eligible for the new
mechanism of defining methods for
(Individual existing methods may not be the issue, and one
can't infer anything definite from the evidence given, but a
plausible culprit is the [ method. Because [] expressions
appear so often, it's always chancy to define a nontrivial
method for this function.)
John
Sklyar, Oleg (London) wrote:
Hello everybody,
it looks like the presense of some (do know know which)
S4 methods for a
given S4 class degrades the performance of xtfrm (used
in 'order' in new
R-devel) by a factor of millions. This is for classes
that ARE derived
from numeric directly and thus should be quite trivial
to convert to
numeric.
Consider the following example:
setClass(TimeDateBase,
representation(numeric, mode=character),
prototype(mode=posix)
)
setClass(TimeDate,
representation(TimeDateBase, tzone=character),
prototype(tzone=London)
)
x = new(TimeDate, 1220966224 + runif(1e5))
system.time({ z = order(x) })
## system.time({ z = order(x) })
## user system elapsed
## 0.048 0.000 0.048
getClass(TimeDate)
## Class TimeDate
## Slots:
## Name: .Data tzone mode
## Class: numeric character character
## Extends:
## Class TimeDateBase, directly
## Class numeric, by class TimeDateBase, distance 2
## Class vector, by class TimeDateBase, distance 3
Now, if I load a library that not only defines these
same classes, but
also a bunch of methods for those, then I have the
following result:
library(AHLCalendar)
x = now() + runif(1e5) ## just random times in POSIXct format
x[1:5]
## TimeDate [posix] object in 'Europe/London' of length 5:
## [1] 2008-09-09 14:19:35.218 2008-09-09 14:19:35.672
## [3] 2008-09-09 14:19:35.515 2008-09-09 14:19:35.721
## [5] 2008-09-09 14:19:35.657
system.time({ z = order(x) })
Enter a frame number, or 0 to exit
1: system.time({
2: order(x)
3: lapply(z, function(x) if (is.object(x)) xtfrm(x) else x)
4: FUN(X[[1]], ...)
5: xtfrm(x)
6: xtfrm.default(x)
7: as.vector(rank(x, ties.method = min, na.last = keep))
8: rank(x, ties.method = min, na.last = keep)
9: switch(ties.method, average = , min = , max =
.Internal(rank(x[!nas], ties.
10: .gt(c(1220966375.21811, 1220966375.67217, 1220966375.51470,
1220966375.7211
11: x[j]
12: x[j]
Selection: 0
Timing stopped at: 47.618 13.791 66.478
At the same time:
system.time({ z = as.numeric(x) }) ## same as [EMAIL PROTECTED]
## user system elapsed
## 0.001 0.000 0.001
The only difference between the two is that I have the
following methods
defined for TimeDate (full listing below).
Any idea why this could be happenning. And yes, it is
down to xtfrm
function, 'order' was just a place where the problem
occured. Should
xtfrm function be smarter with respect to classes that
are actually
derived from 'numeric'?
showMethods(class=TimeDate
Re: [Rd] 'xtfrm' performance (influences 'order' performance) in R devel
In fact it all comes back to 'rank', which uses 'order(x[!nas])'
internally. Surprisingly one does not get an infinite recursion: rank -
order - xtfrm - rank - ...
This is obviously only one of possible outcomes, yet it seems to be
happening. Previous implementation of order did not have a reference to
xtfrm and thus would not cause this infinite loop
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sklyar,
Oleg (London)
Sent: 09 September 2008 15:49
To: John Chambers
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance (influences 'order'
performance) in R devel
Ha, defined xtfrm for TimeDate, works instantly (xtfrm is already a
method). However, it won't be taken up by order as it is not in the
imported namespace, so order falls back to xtfrm.default.
Moreover, defining order (which is not a method unfortunately, *any
chance of changing this*?):
setGeneric(order)
setMethod(order, TimeDate,
function (..., na.last = TRUE, decreasing = FALSE)
order(list(...)[EMAIL PROTECTED],na.last=na.last,
decreasing=decreasing))
does not help either as it won't be taken up, order still calls the
default one, what am I doing wrong?
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: 09 September 2008 15:11
To: Sklyar, Oleg (London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance (influences 'order'
performance) in R devel
No definitive answers, but here are a few observations.
In the call to order() code, I notice that you have dropped
into the branch
if (any(unlist(lapply(z, is.object
where the alternative in your case would seem to have been
going directly to the internal code.
You can consider a method for xtfrm(), which would help but
won't get you completely back to a trivial computation.
Alternatively, order() should be eligible for the new
mechanism of defining methods for
(Individual existing methods may not be the issue, and one
can't infer anything definite from the evidence given, but a
plausible culprit is the [ method. Because [] expressions
appear so often, it's always chancy to define a nontrivial
method for this function.)
John
Sklyar, Oleg (London) wrote:
Hello everybody,
it looks like the presense of some (do know know which)
S4 methods for a
given S4 class degrades the performance of xtfrm (used
in 'order' in new
R-devel) by a factor of millions. This is for classes
that ARE derived
from numeric directly and thus should be quite trivial
to convert to
numeric.
Consider the following example:
setClass(TimeDateBase,
representation(numeric, mode=character),
prototype(mode=posix)
)
setClass(TimeDate,
representation(TimeDateBase, tzone=character),
prototype(tzone=London)
)
x = new(TimeDate, 1220966224 + runif(1e5))
system.time({ z = order(x) })
## system.time({ z = order(x) })
## user system elapsed
## 0.048 0.000 0.048
getClass(TimeDate)
## Class TimeDate
## Slots:
## Name: .Data tzone mode
## Class: numeric character character
## Extends:
## Class TimeDateBase, directly
## Class numeric, by class TimeDateBase, distance 2
## Class vector, by class TimeDateBase, distance 3
Now, if I load a library that not only defines these
same classes, but
also a bunch of methods for those, then I have the
following result:
library(AHLCalendar)
x = now() + runif(1e5) ## just random times in POSIXct format
x[1:5]
## TimeDate [posix] object in 'Europe/London' of length 5:
## [1] 2008-09-09 14:19:35.218 2008-09-09 14:19:35.672
## [3] 2008-09-09 14:19:35.515 2008-09-09 14:19:35.721
## [5] 2008-09-09 14:19:35.657
system.time({ z = order(x) })
Enter a frame number, or 0 to exit
1: system.time({
2: order(x)
3: lapply(z, function(x) if (is.object(x)) xtfrm(x) else x)
4: FUN(X[[1]], ...)
5: xtfrm(x)
6: xtfrm.default(x)
7: as.vector(rank(x, ties.method = min, na.last = keep))
8: rank(x, ties.method = min, na.last = keep)
9: switch(ties.method, average = , min = , max =
.Internal(rank(x[!nas], ties.
10: .gt(c(1220966375.21811, 1220966375.67217, 1220966375.51470,
1220966375.7211
11: x[j]
12: x[j
Re: [Rd] 'xtfrm' performance (influences 'order' performance) in R devel
Aha, it works if I do
setGeneric(order, signature=...)
However the problem with that is that it generates a warning which I
cannot suppress on install:
Creating a generic for order in package AHLCalendar
(the supplied definition differs from and overrides the implicit
generic in package base: Signatures differ: (...), (na.last,
decreasing))
and it generates a warning about masking order from base on load:
AHLCalendar [0.2.42] (9 Sep 2008). ?AHLCalendar or
vignette('AHLCalendar') to get started
Attaching package: 'AHLCalendar'
The following object(s) are masked from package:base :
order
The package exports (excerpt):
exportPattern(^[^\\.])
exportMethods(order)
The reason for these messages is that the signature is different and I
particularly dislike the masking thing (as I cannot predict if it leads
to other problems somewhere). As I understand the current dotsMethods
does not allow mixing dots and other types, so I cannot really define a
matching signature. Is that right? Is there a way around it?
As for the rest, yes, I meant generic and it works nicely for xtfrm. But
as I wrote later, the problem is in 'rank' and rank is not generic so
defining a method would not help in calling a different implementation.
Thanks,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: 09 September 2008 16:42
To: Sklyar, Oleg (London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance (influences 'order'
performance) in R devel
Sklyar, Oleg (London) wrote:
Ha, defined xtfrm for TimeDate, works instantly (xtfrm
is already a
method). However, it won't be taken up by order as it
is not in the
imported namespace, so order falls back to xtfrm.default.
By method you mean generic? xtfrm is an S3 generic. I'm
not clear what happens if you define an S3 method for it.
Yes, there is a problem defining an S4 generic it would be
good to deal with that. Nontrivial, however.
Moreover, defining order (which is not a method
unfortunately, *any
chance of changing this*?):
setGeneric(order)
setMethod(order, TimeDate,
function (..., na.last = TRUE, decreasing = FALSE)
order(list(...)[EMAIL PROTECTED],na.last=na.last,
decreasing=decreasing))
does not help either as it won't be taken up, order
still calls the
default one, what am I doing wrong?
I'm skeptical that this is true. I did a simple example:
setClass(foo, contains = numeric, representation(flag =
logical))
[1] foo
xx = new(foo, rnorm(5))
setGeneric(order, sig = ...)
Creating a generic for order in package .GlobalEnv
(the supplied definition differs from and overrides the
implicit generic in package base: Signatures differ:
(...), (na.last, decreasing))
[1] order
setMethod(order, foo, function (..., na.last = TRUE,
decreasing = FALSE){message(Method called); order([EMAIL PROTECTED])})
[1] order
order(xx)
Method called
[1] 2 4 3 1 5
You do need to be calling order() directly from one of your
functions, and have it in your namespace, if your package has one.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
[EMAIL PROTECTED]
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: 09 September 2008 15:11
To: Sklyar, Oleg (London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] 'xtfrm' performance
(influences 'order'
performance) in R devel
No definitive answers, but here are a few observations.
In the call to order() code, I notice that you
have dropped
into the branch
if (any(unlist(lapply(z, is.object
where the alternative in your case would seem
to have been
going directly to the internal code.
You can consider a method for xtfrm(), which
would help but
won't get you completely back to a trivial
computation.
Alternatively, order() should be eligible for the new
mechanism of defining methods for
(Individual existing methods may not be the
issue, and one
can't infer anything definite from the evidence
given, but a
plausible culprit is the [ method. Because
[] expressions
appear so often, it's always chancy to define a
nontrivial
method for this function.)
John
[Rd] incorrect ticks in plot(with xlim/ylim) and matplot in R2.7.2, R2.8.0
Dear Martin,
I understand the reasons behind PDF removal, but I actually added a
description of the problem with R2.7+ before... (I cannot select which
email client I use in the office).
Now the problem remains and here is the illustration. The reason for
setting xlim beyond the data range can be e.g. that more data are added
afterwards:
plot(c(-5,5),1:2, xlim=c(-10,10))
R2.6.1 outputs X axis ticks correctly as in:
+--- (-10) - (-5) - (0) - (5) - (10)
---+
R2.8.0 and R2.7.2 patched output X-axis ticks incorrectly as in the
following illustration (well, the ticks are correct, but the plots are
ugly because ticks do not cover the whole range requested):
+- (-6) - (-4) - (-2) - (0) - (2) - (4) - (6)
--+
Also, try the following code in R2.6.1 and R2.7+:
m = matrix(c(-0.033, 0.009, 0.064, 0.050, 0.097,
-0.008, 0.037, 0.070, 0.060, 0.077,
-0.027, 0.051, 0.060, 0.106, 0.049,
-0.068, -0.009, 0.095, 0.091, 0.125,
-0.065, 0.013, 0.062, 0.111, 0.080), ncol=5, byrow=TRUE)
plot(c(-5,5),c(0,10),xlim=c(-10,10),ylim=c(-5,15))
x11(); matplot(m)
Here are the seesionInfo's:
-
R version 2.8.0 Under development (unstable) (2008-08-05 r46234)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-
R version 2.7.2 Patched (2008-08-26 r46442)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-
R version 2.6.1 (2007-11-26)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
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[Rd] patch for graphics/R/plot.R that fixes incorrect tick positions
As I haven't got any replies to my earlier posts about incorrect tick
positions in plot and matplot, here is the simplest patch to correct
this issue (it fixes both plot with xlim/ylim and matplot). The plot.R
was unchanged between 2.7 and current R-devel. It would be great if the
patch could be (tested and) applied to both the current patched and the
current devel versions.
70,71c70,71
localAxis(if(is.null(y)) xy$x else x, side = 1, ...)
localAxis(if(is.null(y)) x else y, side = 2, ...)
---
localAxis(xlim, side = 1, ...)
localAxis(ylim, side = 2, ...)
It works fine with y given or y NULL, which was an issue before when the
above is.null test was introduced about half a year ago to avoid
conversion to double and thus dropping custom Axis methods. The patched
version was tested with custom time/date Axis methods and works fine, as
well as it works fine with POSIXct objects.
Thanks,
Oleg
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
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[Rd] ugly plots with xlim/ylim exceeding data range (changed since R2.6.1)
The behaviour of the plot function when used with xlim/ylim and the matplot function as in the following simple example changed between R2.6.1 and 2.7.0+ producing ugly plots in the new versions. In case of plot it looks like the pretty function is called with wrong arguments (i.e. range of supplied data rather than values of xlim and ylim): m = matrix(c(-0.033, 0.009, 0.064, 0.050, 0.097, -0.008, 0.037, 0.070, 0.060, 0.077, -0.027, 0.051, 0.060, 0.106, 0.049, -0.068, -0.009, 0.095, 0.091, 0.125, -0.065, 0.013, 0.062, 0.111, 0.080), ncol=5, byrow=TRUE) pdf(sprintf(R2.%s_SVN_%s.pdf, version$minor, version$svn rev)) plot(c(-5,5),c(0,10),xlim=c(-10,10),ylim=c(-5,15)) matplot(m) dev.off() I attached three PDFs with the outputs from R2.6.1 (43537) (which I consider to be correct), R2.7.2 patched (46442) and R2.8.0 (46234). Just in case PDFs are removed by the mail server here is the description of the problem: the one from R2.6.1 plots the axes correctly putting ticks along the whole axis range even if the data fits just the part of the range; the ones from 2.7.2 and 2.8.0 put ticks just for the part of the axis range. In case of plot they cover the range of the data, but with the requested xlim and ylim they should cover the range of those, and in case of matplot the range of ticks does not cover the range of data at all. Here are the seesionInfo's: - R version 2.8.0 Under development (unstable) (2008-08-05 r46234) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base - R version 2.7.2 Patched (2008-08-26 r46442) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base - R version 2.6.1 (2007-11-26) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 Dr Oleg Sklyar Technology Group Man Investments Ltd +44 (0)20 7144 3803 [EMAIL PROTECTED] ** The contents of this email are for the named addressee(s) only. It contains information which may be confidential and privileged. If you are not the intended recipient, please notify the sender immediately, destroy this email and any attachments and do not otherwise disclose or use them. Email transmission is not a secure method of communication and Man Investments cannot accept responsibility for the completeness or accuracy of this email or any attachments. Whilst Man Investments makes every effort to keep its network free from viruses, it does not accept responsibility for any computer virus which might be transferred by way of this email or any attachments. This email does not constitute a request, offer, recommendation or solicitation of any kind to buy, subscribe, sell or redeem any investment instruments or to perform other such transactions of any kind. Man Investments reserves the right to monitor, record and retain all electronic communications through its network to ensure the integrity of its systems, for record keeping and regulatory purposes. Visit us at: www.maninvestments.com ** __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] showMethods(plot, printTo=FALSE) fails if printTo set to FALSE
Hi everybody,
any idea why showMethods fails with the following error when printTo is
set to false, i.e. to return the output as a character vector. It works
fine if printTo is left default as seen below. The behaviour is
consistent for any method I tried. stdin() generally works fine on this
system, at least when checked with: x = readLines().
Thanks,
Oleg
x = showMethods(plot, printTo=FALSE)
Error in cat(file = printTo, sep = , ...) :
cannot switch output to stdin
Enter a frame number, or 0 to exit
1: showMethods(plot, printTo = FALSE)
2: .showMethodsTable(fdef, includeDefs, inherited, classes = classes,
showEmpt
3: doFun(f, p)
4: cf(Function: , func, (package , pkg, )\n)
5: cat(file = printTo, sep = , ...)
Selection: 0
x = showMethods(plot)
Function: plot (package graphics)
x=ANY, y=ANY
x=SimResults, y=SimResults
x=SimResults, y=missing
x=TimeDateBase, y=character
x=TimeDateBase, y=data.frameOrMatrix
x=TimeDateBase, y=missing
x=TimeSeries, y=missing
sessionInfo()
R version 2.8.0 Under development (unstable) (2008-08-05 r46234)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] datasets splines utils stats graphics grDevices methods
[8] base
other attached packages:
## 64bit RHEL 5
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
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Re: [Rd] showMethods(plot, printTo=FALSE) fails if printTo set to FALSE
Thanks for a good tip.
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: 20 August 2008 13:29
To: Sklyar, Oleg (London)
Cc: [EMAIL PROTECTED]
Subject: Re: [Rd] showMethods(plot, printTo=FALSE) fails if
printTo set to FALSE
On Wed, 20 Aug 2008, Sklyar, Oleg (London) wrote:
Hi everybody,
any idea why showMethods fails with the following error
when printTo is
set to false, i.e. to return the output as a character
vector. It works
fine if printTo is left default as seen below. The behaviour is
consistent for any method I tried. stdin() generally works
fine on this
system, at least when checked with: x = readLines().
Thanks,
Oleg
x = showMethods(plot, printTo=FALSE)
Error in cat(file = printTo, sep = , ...) :
cannot switch output to stdin
This has coerced FALSE to 0, which is connection stdin(). You cannot
write to stdin.
I see no sign that printTo = FALSE has been implemented. You
could use a
text connection, e.g.
con - textConnection(NULL, open=w)
x - showMethods(plot, printTo=con)
textConnectionValue(con)
close(con)
Enter a frame number, or 0 to exit
1: showMethods(plot, printTo = FALSE)
2: .showMethodsTable(fdef, includeDefs, inherited, classes
= classes,
showEmpt
3: doFun(f, p)
4: cf(Function: , func, (package , pkg, )\n)
5: cat(file = printTo, sep = , ...)
Selection: 0
x = showMethods(plot)
Function: plot (package graphics)
x=ANY, y=ANY
x=SimResults, y=SimResults
x=SimResults, y=missing
x=TimeDateBase, y=character
x=TimeDateBase, y=data.frameOrMatrix
x=TimeDateBase, y=missing
x=TimeSeries, y=missing
sessionInfo()
R version 2.8.0 Under development (unstable) (2008-08-05 r46234)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] datasets splines utils stats graphics
grDevices methods
[8] base
other attached packages:
## 64bit RHEL 5
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] Clash between 'Cairo' and 'EBImage' packages on Windows
EBImage is dynamically linked against GTK, which includes cairo
libraries, so those are installed along with GTK. Cairo seems to be
statically linking to libcairo.dll.a. I would assume that if it is
linked statically it should not get confused with a shared library
present elsewhere in the path, but it looks like it does. I have no
solution for that because unlike Cairo I cannot not statically link
EBImage to GTK as it is not one library that I need, but a bunch of
those.
On Linux you won't get this problem as it uses the same centrally
installed Cairo library.
In a way it would be better, if Cairo relied on the gladewin32.sf.net
which normally provides GTK (and thus cairo libraries) for Windows and
linked dynamically, but probably to simplify user installations the
developers wanted to avoid this.
There is not much I can do now about this, but I will follow the thread
if anybody comes up with an idea to change the code if possible
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Henrik Bengtsson
Sent: 19 July 2008 19:26
To: R-devel
Subject: [Rd] Clash between 'Cairo' and 'EBImage' packages on Windows
Hi,
on Windows XP Pro with R version 2.7.1 Patched (2008-06-27
r46012) the 'Cairo' and the 'EBImage' packages does not play
well together.
Loading EBImage before Cairo cause the following to happen:
# Rterm --vanilla
library(EBImage);
library(Cairo)
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library
'C:/PROGRA~1/R/R-2.7.1pat/library/Cairo/libs/Cai
ro.dll':
LoadLibrary failure: The specified procedure could not be found.
Error : .onLoad failed in 'loadNamespace' for 'Cairo'
Error: package/namespace load failed for 'Cairo'
with a dialog titled 'Rterm.exe - Entry Point Not Found'
saying 'The procedure entry point cairo_pdf_surface_create
could not be located in the dynamic link library libcairo-2.dll'.
Loading the packages in the reverse order works, but the
Rterm seems unstable, e.g. calling q() immediately after will
exit the R session without questions:
# Rterm --vanilla
library(Cairo)
library(EBImage)
q()
[Immediately back to the command line].
I cannot reproduce the problem on R v2.7.1 on Ubuntu Hardy.
sessionInfo()
R version 2.7.1 Patched (2008-06-27 r46012)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MON ETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] EBImage_2.4.0 Cairo_1.4-2
Cheers
Henrik
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Re: [Rd] Clash between 'Cairo' and 'EBImage' packages on Windows
Thanks fot the response. I will try to recompile EBImage with the newest
GTK and would advise Henrik to update the GTK to the latest one as it
should be backward compatible.
As for where it is posted, it is not a BioC only issue either and too
technical for R-help, so I would rather support Henrik on posting it
here. But please take my apollogies if it is not too appropriate to have
it on R-devel.
Best,
Oleg
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: 21 July 2008 11:29
To: Sklyar, Oleg (London)
Cc: Henrik Bengtsson; R-devel
Subject: Re: [Rd] Clash between 'Cairo' and 'EBImage'
packages on Windows
On Mon, 21 Jul 2008, Sklyar, Oleg (London) wrote:
EBImage is dynamically linked against GTK, which includes cairo
libraries, so those are installed along with GTK. Cairo seems to be
statically linking to libcairo.dll.a. I would assume that if it is
That is an import library, so it is actually linked to
libcairo-2.dll, which it ships.
linked statically it should not get confused with a shared library
present elsewhere in the path, but it looks like it does. I have no
solution for that because unlike Cairo I cannot not statically link
EBImage to GTK as it is not one library that I need, but a bunch of
those.
On Linux you won't get this problem as it uses the same centrally
installed Cairo library.
In a way it would be better, if Cairo relied on the
gladewin32.sf.net
which normally provides GTK (and thus cairo libraries) for
Windows and
linked dynamically, but probably to simplify user installations the
developers wanted to avoid this.
It _is_ using dynamic loading, or there would be no conflict.
From the names, it looks very like that it is using a DLL
from gladewin32.
The real issue looks rather like a versioning problem, that
the cairo libraries installed as part of GTK and used by
EBImage are way too old (cairo_pdf_surface_create was added
at cairo 1.2, and cairo is at 1.6.4).
So updating to the current GTK distribution may be all that
is needed (and Henrik could also try replacing your GTK's
libcairo-2.dll by that distributed with Cairo).
There is not much I can do now about this, but I will follow the
thread if anybody comes up with an idea to change the code
if possible
The Cairo package (which ships DLLs) could rename them, as R
itself does where it builds its own versions. Or it could
link statically (if that works, which it does not for e.g.
package XML).
I don't really understand why this was posted to R-devel: it
is not an R issue.
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Henrik
Bengtsson
Sent: 19 July 2008 19:26
To: R-devel
Subject: [Rd] Clash between 'Cairo' and 'EBImage' packages
on Windows
Hi,
on Windows XP Pro with R version 2.7.1 Patched (2008-06-27
r46012) the 'Cairo' and the 'EBImage' packages does not play
well together.
Loading EBImage before Cairo cause the following to happen:
# Rterm --vanilla
library(EBImage);
library(Cairo)
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library
'C:/PROGRA~1/R/R-2.7.1pat/library/Cairo/libs/Cai
ro.dll':
LoadLibrary failure: The specified procedure could not be found.
Error : .onLoad failed in 'loadNamespace' for 'Cairo'
Error: package/namespace load failed for 'Cairo'
with a dialog titled 'Rterm.exe - Entry Point Not Found'
saying 'The procedure entry point cairo_pdf_surface_create
could not be located in the dynamic link library libcairo-2.dll'.
Loading the packages in the reverse order works, but the
Rterm seems unstable, e.g. calling q() immediately after will
exit the R session without questions:
# Rterm --vanilla
library(Cairo)
library(EBImage)
q()
[Immediately back to the command line].
I cannot reproduce the problem on R v2.7.1 on Ubuntu Hardy.
sessionInfo()
R version 2.7.1 Patched (2008-06-27 r46012)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MON ETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets
methods base
other attached packages:
[1] EBImage_2.4.0 Cairo_1.4-2
Cheers
Henrik
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R
