[Rd] segfault during build of 2.1.0 on RH9;
print.POSIXct implicated (PR#7826)
Jskud at Jskud.com
Jskud at Jskud.com
Sat Apr 30 09:04:03 CEST 2005
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
[]
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