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] quantile and IQR do not check for numeric input (PR#13631)
This report follows the post http://tolstoy.newcastle.edu.au/R/e6/devel/09/03/0760.html where it is shown that quantile() and IQR() do not work as documented. In fact they do not check for numeric input even if the documentation says = : ?quantile x numeric vectors whose sample quantiles are wanted. Missing values are ignored. ?IQR x a numeric vector. quantile(factor(1:9)) 0% 25% 50% 75% 100% 13579 Levels: 1 2 3 4 5 6 7 8 9 IQR(factor(1:9)) [1] 4 R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status alpha major 2 minor 9.0 year 2009 month 03 day26 svn rev48224 language R version.string R version 2.9.0 alpha (2009-03-26 r48224) -- __ Simone Giannerini Dipartimento di Scienze Statistiche Paolo Fortunati Universita' di Bologna Via delle belle arti 41 - 40126 =A0Bologna, =A0ITALY Tel: +39 051 2098262 =A0Fax: +39 051 232153 http://www2.stat.unibo.it/giannerini/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] quantile and IQR do not check for numeric input (PR#13631)
On Mon, 30 Mar 2009 sgianner...@gmail.com wrote: This report follows the post http://tolstoy.newcastle.edu.au/R/e6/devel/09/03/0760.html where it is shown that quantile() and IQR() do not work as documented. Nothing of the sort is shown! The thread argued that methods for these functions for ordered factors would be useful. In fact they do not check for numeric input even if the documentation says = : ?quantile x numeric vectors whose sample quantiles are wanted. Missing values are ignored. ?IQR x a numeric vector. The documentation says that you are not allowed to pass anything except a numeric vector to quantile() and IQR(). It doesn't, for example, say you can pass an arbitrary vector that will be checked to see if it is numeric. If you have code that passes a factor to IQR(), the bug is in that code. On the other hand, as someone else has since reported, the 'missing values are ignored' statement in ?quantile is wrong (or at least incomplete). -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] quantile and IQR do not check for numeric input (PR#13631)
On 3/30/2009 7:50 AM, Thomas Lumley wrote: On Mon, 30 Mar 2009 sgianner...@gmail.com wrote: This report follows the post http://tolstoy.newcastle.edu.au/R/e6/devel/09/03/0760.html where it is shown that quantile() and IQR() do not work as documented. Nothing of the sort is shown! The thread argued that methods for these functions for ordered factors would be useful. In fact they do not check for numeric input even if the documentation says = : ?quantile x numeric vectors whose sample quantiles are wanted. Missing values are ignored. ?IQR x a numeric vector. The documentation says that you are not allowed to pass anything except a numeric vector to quantile() and IQR(). It doesn't, for example, say you can pass an arbitrary vector that will be checked to see if it is numeric. If you have code that passes a factor to IQR(), the bug is in that code. On the other hand, as someone else has since reported, the 'missing values are ignored' statement in ?quantile is wrong (or at least incomplete). I think that statement was wrong, and I fixed it last night, but then didn't get it committed. The commit will make it into 2.9 and R-devel today. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] quantile and IQR do not check for numeric input (PR#13631)
Dear Thomas, On Mon, Mar 30, 2009 at 1:50 PM, Thomas Lumley tlum...@u.washington.edu wrote: On Mon, 30 Mar 2009 sgianner...@gmail.com wrote: This report follows the post http://tolstoy.newcastle.edu.au/R/e6/devel/09/03/0760.html where it is shown that quantile() and IQR() do not work as documented. Nothing of the sort is shown! The thread argued that methods for these functions for ordered factors would be useful. in the original thread I initiated the matters were two (at least in my intention) 1. quantile() and IQR() do not check for numeric input whereas median() has a check (for a factor input). This has nothing to deal with ordered factors 2. the opportunity of having methods for ordered factors for quantile() and the like. If, for some reason, you think that it is ok to have such check for median but not for quantile and IQR then take this as a wishlist. BTW also var() and the like do not check for factor input while mean() has the check. x - factor(letters[1:9]) x [1] a b c d e f g h i Levels: a b c d e f g h i mean(x) [1] NA Warning message: In mean.default(x) : argument is not numeric or logical: returning NA var(x) [1] 7.5 Regards Simone In fact they do not check for numeric input even if the documentation says = : ?quantile x numeric vectors whose sample quantiles are wanted. Missing values are ignored. ?IQR x a numeric vector. The documentation says that you are not allowed to pass anything except a numeric vector to quantile() and IQR(). It doesn't, for example, say you can pass an arbitrary vector that will be checked to see if it is numeric. If you have code that passes a factor to IQR(), the bug is in that code. On the other hand, as someone else has since reported, the 'missing values are ignored' statement in ?quantile is wrong (or at least incomplete). -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.edu University of Washington, Seattle -- __ Simone Giannerini Dipartimento di Scienze Statistiche Paolo Fortunati Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153 http://www2.stat.unibo.it/giannerini/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] duplicated fails to rise correct errors (PR#13632)
Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48242 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (129.241.110.161) In the following code: duplicated(data.frame(), incomparables=NA) # Error in if (!is.logical(incomparables) || incomparables) .NotYetUsed(incomparables != FALSE) : # missing value where TRUE/FALSE needed the raised error is clearly not the one intended to be raised. ?duplicated says: incomparables: a vector of values that cannot be compared. 'FALSE' is a special value, meaning that all values can be compared, and may be the only value accepted for methods other than the default. It will be coerced internally to the same type as 'x'. (...) Values in 'incomparables' will never be marked as duplicated. This is intended to be used for a fairly small set of values and will not be efficient for a very large set. However, in duplicated.data.frame (which is called when duplicated is applied to a data frame, as above) the parameter 'incomparables' is defunct. The documentation fails to explain this, and it might be a good idea to improve it. In the code for duplicated.data.frame there is an attempt to intercept any use of the parameter 'incomparables' with a value other than FALSE and to raise an appropriate error, but this attempt fails with, e.g., incomparables=NA. Incidentally, the attempt to intercept incomparables != FALSE fails completely (i.e., the call to duplicated succeeds) with certain inputs: duplicated(data.frame(logical=c(TRUE, TRUE)), incomparables=c(FALSE, TRUE)) # [1] FALSE TRUE while duplicated(c(TRUE, TRUE), incomparables=c(FALSE, TRUE)) # [1] FALSE FALSE Regards, vQ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] duplicated fails to rise correct errors (PR#13632)
the bug seems to have a trivial solution; as far as i can see, it suffices to
replace
if (!is.logical(incomparables) || incomparables)
with
if(!identical(incomparables, FALSE))
in all its occurrences in src/library/base/R/duplicated.R
attached is a patch created, successfully tested and installed on Ubuntu 8.04
Linux 32 bit as follows:
svn co https://svn.r-project.org/R/trunk trunk
cd trunk
# edit src/library/base/R/duplicated.R
svn diff duplicated.R.diff
svn revert -R src
patch -p0 duplicated.R.diff
tools/rsync-recommended
./configure
make
make check
and now
duplicated(data.frame(), incomparables=NA)
# error: argument 'incomparables != FALSE' is not used (yet)
regards,
vQ
waclaw.marcin.kusnierc...@idi.ntnu.no wrote:
Full_Name: Wacek Kusnierczyk
Version: 2.8.0 and 2.10.0 r48242
OS: Ubuntu 8.04 Linux 32 bit
Submission from: (NULL) (129.241.110.161)
In the following code:
duplicated(data.frame(), incomparables=NA)
# Error in if (!is.logical(incomparables) || incomparables)
.NotYetUsed(incomparables != FALSE) :
# missing value where TRUE/FALSE needed
the raised error is clearly not the one intended to be raised.
?duplicated says:
incomparables: a vector of values that cannot be compared. 'FALSE' is a
special value, meaning that all values can be compared, and
may be the only value accepted for methods other than the
default. It will be coerced internally to the same type as
'x'.
(...)
Values in 'incomparables' will never be marked as duplicated. This
is intended to be used for a fairly small set of values and will
not be efficient for a very large set.
However, in duplicated.data.frame (which is called when duplicated is applied
to
a data frame, as above) the parameter 'incomparables' is defunct. The
documentation fails to explain this, and it might be a good idea to improve
it.
In the code for duplicated.data.frame there is an attempt to intercept any use
of the parameter 'incomparables' with a value other than FALSE and to raise an
appropriate error, but this attempt fails with, e.g., incomparables=NA.
Incidentally, the attempt to intercept incomparables != FALSE fails completely
(i.e., the call to duplicated succeeds) with certain inputs:
duplicated(data.frame(logical=c(TRUE, TRUE)), incomparables=c(FALSE, TRUE))
# [1] FALSE TRUE
while
duplicated(c(TRUE, TRUE), incomparables=c(FALSE, TRUE))
# [1] FALSE FALSE
Regards,
vQ
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---
Wacek Kusnierczyk, MD PhD
Email: w...@idi.ntnu.no
Phone: +47 73591875, +47 72574609
Department of Computer and Information Science (IDI)
Faculty of Information Technology, Mathematics and Electrical Engineering (IME)
Norwegian University of Science and Technology (NTNU)
Sem Saelands vei 7, 7491 Trondheim, Norway
Room itv303
Bioinformatics Gene Regulation Group
Department of Cancer Research and Molecular Medicine (IKM)
Faculty of Medicine (DMF)
Norwegian University of Science and Technology (NTNU)
Laboratory Center, Erling Skjalgsons gt. 1, 7030 Trondheim, Norway
Room 231.05.060
---
Index: src/library/base/R/duplicated.R
===
--- src/library/base/R/duplicated.R (revision 48242)
+++ src/library/base/R/duplicated.R (working copy)
@@ -25,7 +25,7 @@
duplicated.data.frame - function(x, incomparables = FALSE, fromLast = FALSE, ...)
{
-if(!is.logical(incomparables) || incomparables)
+if (!identical(incomparables, FALSE))
.NotYetUsed(incomparables != FALSE)
duplicated(do.call(paste, c(x, sep=\r)), fromLast = fromLast)
}
@@ -33,7 +33,7 @@
duplicated.matrix - duplicated.array -
function(x, incomparables = FALSE , MARGIN = 1L, fromLast = FALSE, ...)
{
-if(!is.logical(incomparables) || incomparables)
+if (!identical(incomparables, FALSE))
.NotYetUsed(incomparables != FALSE)
ndim - length(dim(x))
if (length(MARGIN) ndim || any(MARGIN ndim))
@@ -67,7 +67,7 @@
unique.data.frame - function(x, incomparables = FALSE, fromLast = FALSE, ...)
{
-if(!is.logical(incomparables) || incomparables)
+if (!identical(incomparables, FALSE))
.NotYetUsed(incomparables != FALSE)
x[!duplicated(x, fromLast = fromLast), , drop = FALSE]
}
@@ -75,7 +75,7 @@
unique.matrix - unique.array -
function(x, incomparables = FALSE , MARGIN = 1, fromLast = FALSE, ...)
{
-if(!is.logical(incomparables) || incomparables)
+if (!identical(incomparables, FALSE))
.NotYetUsed(incomparables != FALSE)
ndim - length(dim(x))
if (length(MARGIN) 1L || any(MARGIN ndim))
Re: [Rd] if does not covert raw to logical (PR#13630)
Thank you, Wacek,
for
Wacek Kusnierczyk w...@idi.ntnu.no
on Sun, 29 Mar 2009 22:40:11 +0200 (CEST) writes:
Full_Name: Wacek Kusnierczyk
Version: 2.8.0 and 2.10.0 r48242
OS: Ubuntu 8.04 Linux 32 bit
Submission from: (NULL) (80.202.30.36)
The following raises an error:
if (as.raw(1)) 1
# error: unimplemented type 'raw' in 'asLogical'
However, ?'if' says:
Arguments:
cond: A length-one logical vector that is not 'NA'. Conditions of
length greater than one are accepted with a warning, but only
the first element is used. Other types are coerced to
logical if possible, ignoring any class.
and the help page does not mention raw type arguments to 'if' at all.
The error above is in clear contradiction to the documentation. This
might be a
flaw in the documentation, but the following succeeds:
ifelse(raw(1), 1, 0)
# 1
which suggests that the error above is a bug (i.e., the implementation
fails to
convert raw to logical).
The same problem involves 'while':
while(as.raw(1)) break
# error: unimplemented type 'raw' in 'asLogical'
indeed, it was pretty straightforward hard to implement the missing case in
asLogical(.) and I will commit my patch to the sources tomorrow
{being busy otherwise for the rest of today}.
Note that the raw data type has been a newish addition to R a
while ago though, and if you find further cases where
such raw objects do not work as documented,
we'd gladly accept further such reports.
Regards,
Martin Maechler, ETH Zurich
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Re: [Rd] Gamma funtion(s) bug
On 30-Mar-09 18:40:03, Kjetil Halvorsen wrote: With R 2.8.1 on ubuntu I get: gamma(-1) [1] NaN Warning message: In gamma(-1) : NaNs produced lgamma(-1) [1] Inf Warning message: value out of range in 'lgamma' Is'nt the first one right, and the second one (lgamma) should also be NaN? Kjetil That is surely correct! Since lim[x-(-1)+] gamma(x) = +Inf, while lim[x-(-1)-] gamma(x) = -Inf, at gamma(-1) one cannot choose between +Inf and -Inf, so surely is is NaN. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 30-Mar-09 Time: 19:55:33 -- XFMail -- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] if does not covert raw to logical (PR#13630)
Martin Maechler wrote:
Thank you, Wacek,
happy to serve.
(...)
indeed, it was pretty straightforward hard to implement the missing case in
asLogical(.) and I will commit my patch to the sources tomorrow
{being busy otherwise for the rest of today}.
thanks!
Note that the raw data type has been a newish addition to R a
while ago though, and if you find further cases where
such raw objects do not work as documented,
we'd gladly accept further such reports.
yes, i'll keep sniffing.
best,
vQ
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Re: [Rd] Gamma funtion(s) bug
On 3/30/2009 2:55 PM, (Ted Harding) wrote: On 30-Mar-09 18:40:03, Kjetil Halvorsen wrote: With R 2.8.1 on ubuntu I get: gamma(-1) [1] NaN Warning message: In gamma(-1) : NaNs produced lgamma(-1) [1] Inf Warning message: value out of range in 'lgamma' Is'nt the first one right, and the second one (lgamma) should also be NaN? Kjetil That is surely correct! Since lim[x-(-1)+] gamma(x) = +Inf, while lim[x-(-1)-] gamma(x) = -Inf, at gamma(-1) one cannot choose between +Inf and -Inf, so surely is is NaN. But lgamma(x) is log(abs(gamma(x))), so it looks okay to me. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Gamma funtion(s) bug
On 30-Mar-09 20:37:51, Duncan Murdoch wrote: On 3/30/2009 2:55 PM, (Ted Harding) wrote: On 30-Mar-09 18:40:03, Kjetil Halvorsen wrote: With R 2.8.1 on ubuntu I get: gamma(-1) [1] NaN Warning message: In gamma(-1) : NaNs produced lgamma(-1) [1] Inf Warning message: value out of range in 'lgamma' Is'nt the first one right, and the second one (lgamma) should also be NaN? Kjetil That is surely correct! Since lim[x-(-1)+] gamma(x) = +Inf, while lim[x-(-1)-] gamma(x) = -Inf, at gamma(-1) one cannot choose between +Inf and -Inf, so surely is is NaN. But lgamma(x) is log(abs(gamma(x))), so it looks okay to me. Duncan Murdoch Oops, yes! That's what comes of talking off the top of my head (I don't think I've ever had occasion to evaluate lgamma(x) for negative x, so never consciously checked in ?lgamma). Thanks, Duncan! Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 30-Mar-09 Time: 22:28:52 -- XFMail -- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Possible bug in summary.survfit - 'scale' argument ignored?
Hi all, Using: R version 2.8.1 Patched (2009-03-07 r48068) on OSX (10.5.6) with survival version: Version:2.35-3 Date: 2009-02-10 I get the following using the first example in ?summary.survfit: summary( survfit( Surv(futime, fustat)~1, data=ovarian)) Call: survfit(formula = Surv(futime, fustat) ~ 1, data = ovarian) time n.risk n.event survival std.err lower 95% CI upper 95% CI 59 26 10.962 0.03770.8901.000 115 25 10.923 0.05230.8261.000 156 24 10.885 0.06270.7701.000 268 23 10.846 0.07080.7180.997 329 22 10.808 0.07730.6700.974 353 21 10.769 0.08260.6230.949 365 20 10.731 0.08700.5790.923 431 17 10.688 0.09190.5290.894 464 15 10.642 0.09650.4780.862 475 14 10.596 0.09990.4290.828 563 12 10.546 0.10320.3770.791 638 11 10.497 0.10510.3280.752 summary( survfit( Surv(futime, fustat)~1, data=ovarian), scale = 365.25) Call: survfit(formula = Surv(futime, fustat) ~ 1, data = ovarian) time n.risk n.event survival std.err lower 95% CI upper 95% CI 59 26 10.962 0.03770.8901.000 115 25 10.923 0.05230.8261.000 156 24 10.885 0.06270.7701.000 268 23 10.846 0.07080.7180.997 329 22 10.808 0.07730.6700.974 353 21 10.769 0.08260.6230.949 365 20 10.731 0.08700.5790.923 431 17 10.688 0.09190.5290.894 464 15 10.642 0.09650.4780.862 475 14 10.596 0.09990.4290.828 563 12 10.546 0.10320.3770.791 638 11 10.497 0.10510.3280.752 Of course the time periods in the second output should be scaled to years, that is (time / 365.25). I noted this today running some Sweave code, but not sure when the actual change in behavior occurred. I can replicate the same behavior on a Windows machine here as well, so this is not OSX specific. Regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] external equiv to R_serialize()?
I'm trying to efficiently allow conversion of R objects to PostgreSQL bytea (raw binary) datatype within PL/R for persistent storage in Postgres tables. I have found R_serialize() which looks like what I need, -- e.g. R_serialize(object, NULL, FALSE, NULL) -- except that it is marked attribute_hidden. Is there some other externally available interface that I can use? Thanks, Joe __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
