Re: [Rd] Possible bug in POSIX classes for R 2.11.0?

Duncan Murdoch Sat, 01 May 2010 04:11:56 -0700

On 30/04/2010 12:46 PM, Lester Wollman wrote:

To the R development team;


I found an unusual behavior in zoo when I upgraded to R 2.11.0 - it abruptly 
terminated when I performed certain operations on large zoo objects.  I sent an 
e-mail to Achim Zeileis and he said this was a potential bug that I should 
report to the R development team.  The details are given below in the thread 
below.  Basically, I can crash R with this code:

library(zoo)
x <- runif(140000, 2009, 2010)
x <- as.yearmon(x)
table(x)

This will not crash with a vector of size 130000.

Achim got it to crash with the following code that did not use zoo:

x <- rep(as.Date("1970-01-01"), 140000)
y <- as.POSIXlt(x)
z <- format(y, "%d")

I did find a work around, so this is no longer an immediate problem for me, but 
it would be better if the problem didn't exist in the first place.  Thank you 
for your help.

Have you tried R-patched? This looks like a bug that was fixed thererecently. See


https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14267

for details.

Duncan Murdoch

Lester Wollman
Corporate Statistician
Symmetricom, Inc.
lwoll...@symmetricom.com



-----Original Message-----

From: Achim Zeileis [mailto:achim.zeil...@uibk.ac.at]Sent: Thursday, April 29, 2010 1:16 PM

To: Lester Wollman
Subject: Re: Unusual behavior of zoo and R2.11.0 - simple operation on large 
zoo object crashes R

Lester,

thanks for the report. The problem does not seem to be in "zoo" but in thenew POSIX classes and/or their their coercion from "Date".


The following should reproduce your crash:

x <- rep(as.Date("1970-01-01"), 140000)
y <- as.POSIXlt(x)
z <- format(y, "%d")

The reason is probably that R-core changed the internals of all the POSIXstuff. Furthermore, this problem appears to be fixed in 2.12.0 (thecurrent devel version). Maybe you can ask on R-devel whether this is aknow issue (my guess is that it is).


Thanks for the report && best wishes,
Z

On Thu, 29 Apr 2010, Lester Wollman wrote:

Achim,

I found unusual behavior, or even possibly a bug,  in zoo.  When I run the
code below, R crashes.  There is no error message,  R simply exits with no
warning.

library(zoo)

x <- runif(140000, 2009, 2010)     # Random days in 2009

x <- as.yearmon(x)                 # This works

table(x)                           #  This crashes. print(x) also crashes R. 
summary(x) does not

However, if I change the number of random dates to 130000, there is no
problem.

I have been using zoo for a few years with no problems,  including using
code similar to the one above.  I did just upgrade to R 2.11.0 and this is
my first use of zoo for a large vector since the upgrade.

I cannot tell if the problem is with zoo or R or my machine.  I tried

installing zoo from CRAN instead of R-Forge, but that did not help.Increasing the memory limit to 3G did not help either.

I attached relevant (and irrelevant) system information below.  I am using R
with Tinn-R and Tinn-R loads some packages (Hmisc, R2HTML, etc.)

Thank you for your help.

Lester Wollman

Corporate Statistician

Symmetricom, Inc.

lwoll...@symmetricom.com

sessionInfo()

R version 2.11.0 (2010-04-22)

i386-pc-mingw32

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C                           LC_TIME=English_United

States.1252

attached base packages:

[1] grDevices datasets splines graphics stats tcltk utilsmethods base

other attached packages:

[1] svSocket_0.9-48 TinnR_1.0.3 R2HTML_2.0.0 Hmisc_3.7-0survival_2.35-8

loaded via a namespace (and not attached):

[1] cluster_1.12.3 grid_2.11.0    lattice_0.18-5 svMisc_0.9-57

System Information:

Windows XP Professional Version 2002 Service Pack 3

Computer Information:

Dell with Intel CPU

T2600 @ 2.16 GHz, 1G of RAM

zoo information

packageDescription("zoo")

Package: zoo

Version: 1.6-3

Date: 2010-02-22

Title: Z's ordered observations

Author: Achim Zeileis, Gabor Grothendieck, Felix Andrews

Maintainer: Achim Zeileis <achim.zeil...@r-project.org>

Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series of numeric
vectors/matrices and factors. zoo's key design goals are independence of a
particular index/date/time class and consistency with ts and base R by
providing methods to extend standard generics.

Depends: R (>= 2.10.0), stats

Suggests: coda, chron, DAAG, fCalendar, fSeries, fts, its, lattice,
strucchange, timeDate, timeSeries, tis, tseries, xts

Imports: stats, utils, graphics, grDevices, lattice (>= 0.18-1)

LazyLoad: yes

License: GPL-2

URL: http://R-Forge.R-project.org/projects/zoo/

Repository: R-Forge

Repository/R-Forge/Project: zoo

Repository/R-Forge/Revision: 688

Date/Publication: 2010-03-20 02:29:04

Packaged: 2010-03-20 21:59:26 UTC; rforge

Built: R 2.11.0; ; 2010-03-22 14:03:33 UTC; windows

-- File: C:/PROGRA~1/STATIS~1/R2110/library/zoo/Meta/package.rds


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Re: [Rd] Possible bug in POSIX classes for R 2.11.0?

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