(PR#7826) [Rd] segfault during build of 2.1.0 on RH9;
print.POSIXct
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Apr 30 12:16:58 CEST 2005
I've now tested our one remaining RH9 system (built from the sources), and
that behaves exactly as FC3.
Something is wrong with Jskud at jskud.com's system or its build, not RH9 nor
R generically.
I've put a workaround in R-patched, but ultimately cycles in inheritance
are always possible and the expressions/ppsize limits are there to catch
those.
On Sat, 30 Apr 2005 ripley at stats.ox.ac.uk wrote:
> 1) Why did you submit this *twice*, as PR#7826 and PR#7827? Please don't
> be so careless of the volunteers' time.
>
> 2) > print.POSIXct
> function (x, ...)
> {
> print(format(x, usetz = TRUE, ...), ...)
> invisible(x)
> }
>
> is definitely *not* implicated. (Use of ... in two places is correct.)
>
> 3) On FC3:
>
>> unusual_and_faults
> Error: protect(): protection stack overflow
>> format(unusual_and_faults)
> Error: protect(): protection stack overflow
>> as.POSIXlt(unusual_and_faults)
> Error: protect(): protection stack overflow
>
> which is what should happen. It looks like RH9 has an inadequate stack
> size for the new recursion limits of R 2.1.0. This is nothing whatsoever
> to do with print.POSIXct.
>
> The problem is in fact in c.POSIXct which is not checking its arguments.
>
>
> On Sat, 30 Apr 2005 Jskud at jskud.com wrote:
>
>> In attempting to build R using
>>
>> rpmbuild --rebuild R-2.1.0-0.fdr.2.fc3.src.rpm
>>
>> on a fairly up-to-date RedHat 9 system (that is, with patches installed
>> through May 1 2004), it failed at the make check-all step.
>>
>> The problem was reproducible by going into the tests directory and
>>
>> make test-Segfault
>>
>> The last lines of the saved file no-segfault.Rout.fail are
>>
>>>> ## c.POSIXct :
>>>> f <- get("c.POSIXct", pos = 'package:base')
>>>> f()
>>> character(0)
>>>> f(NULL)
>>> character(0)
>>>> f(,NULL)
>>> Error in lapply(list(...), unclass) : argument is missing, with no default
>>>> f(NULL,NULL)
>>> character(0)
>>>> f(list())
>>> character(0)
>>>> f(l0)
>>> character(0)
>>
>> I was able to reproduce the problem (a segfault) as the following simple
>> transcript demonstrates:
>>
>> LC_ALL=C SRCDIR=. R_DEFAULT_PACKAGES= ../bin/R --vanilla
>>
>> R : Copyright 2005, The R Foundation for Statistical Computing
>> Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for a HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> > unusual_but_ok <- c.POSIXlt(character(0))
>> > unusual_but_ok
>> character(0)
>> > unusual_and_faults <- c.POSIXct(character(0))
>> > unusual_and_faults
>> Segmentation fault
>>
>> Running this test program under gdb, we find that we're running off the
>> end of the stack, with 4222 stack frames showing -- apparently in an
>> infinite recursion -- "as.character" shows up every 69 function calls:
>>
>> #64 0x080ea1ef in Rf_usemethod (generic=0x81c8b12 "as.character", obj=0x0, call=0x85a04f4,
>> args=0x8af8b00, rho=0x8af8b70, callrho=0x8af8b70, defrho=0x829d4c0, ans=0xbff042b8)
>> at objects.c:328
>>
>> #133 0x080ea1ef in Rf_usemethod (generic=0x81c8b12 "as.character", obj=0x0, call=0x85a04f4,
>> args=0x8af35f0, rho=0x8af3660, callrho=0x8af3660, defrho=0x829d4c0, ans=0xbff08538)
>> at objects.c:328
>>
>> #202 0x080ea1ef in Rf_usemethod (generic=0x81c8b12 "as.character", obj=0x0, call=0x85a04f4,
>> args=0x8aeca08, rho=0x8aeca78, callrho=0x8aeca78, defrho=0x829d4c0, ans=0xbff0c7b8)
>> at objects.c:328
>>
>> #271 0x080ea1ef in Rf_usemethod (generic=0x81c8b12 "as.character", obj=0x0, call=0x85a04f4,
>> args=0x8ae7514, rho=0x8ae7584, callrho=0x8ae7584, defrho=0x829d4c0, ans=0xbff10a38)
>> at objects.c:328
>>
>> #340 0x080ea1ef in Rf_usemethod (generic=0x81c8b12 "as.character", obj=0x0, call=0x85a04f4,
>> args=0x8ade4c0, rho=0x8ade530, callrho=0x8ade530, defrho=0x829d4c0, ans=0xbff14cb8)
>> at objects.c:328
>>
>> So it would seem that *printing* the unusual POSIXct value is suspect.
>> Looking at a R-1.8.1 install, we find these definitions in base/R/base:
>>
>> print.POSIXct <- function(x, ...)
>> {
>> print(format(x, usetz=TRUE), ...)
>> invisible(x)
>> }
>>
>> print.POSIXlt <- function(x, ...)
>> {
>> print(format(x, usetz=TRUE), ...)
>> invisible(x)
>> }
>>
>> However, looking at the 2.1.0 src file
>> R-2.1.0/src/library/base/R/datetime.R, we find
>>
>> print.POSIXct <- function(x, ...)
>> {
>> print(format(x, usetz=TRUE, ...), ...)
>> invisible(x)
>> }
>>
>> print.POSIXlt <- function(x, ...)
>> {
>> print(format(x, usetz=TRUE), ...)
>> invisible(x)
>> }
>>
>> Note the suspicious definition of print.POSIXct using *two* sets of
>> ellipses, and that the print.POSIXct and print.POSIXlt definitions no
>> longer match.
>>
>> /Jskud
>>
>> --please do not edit the information below--
>>
>> Version:
>> platform = i686-pc-linux-gnu
>> arch = i686
>> os = linux-gnu
>> system = i686, linux-gnu
>> status =
>> major = 2
>> minor = 1.0
>> year = 2005
>> month = 04
>> day = 18
>> language = R
>>
>> []
>>
>> ______________________________________________
>> R-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> 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, UK Fax: +44 1865 272595
>
> ______________________________________________
> R-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
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, UK Fax: +44 1865 272595
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