On 2015-01-29 12:42, Duncan Murdoch wrote:
On 29/01/2015 6:24 AM, Göran Broström wrote:
Hello,
A weird thing happened to me while I was playing around in the R console
with a data frame ('fert'). The finale was
-----------------------------------------------------
> with(fert[fert$parity == 4, ], table(age, event))
event
age 0 1 2
(14,20] 0 0 0
(20,25] 6 43 41
(25,30] 57 565 513
(30,35] 121 719 686
(35,40] 165 309 317
(40,45] 156 45 29
(45,50] 13 0 0
> fit1 <- coxph(Surv(exit - enter, event > 0.5) ~ strata(age) + civst +
birthdate, data = fert[fert$parity == 0, ])
*** Error in `/usr/local/lib/R/bin/exec/R': corrupted double-linked
list: 0x0000000004f1aa40 ***
Aborted
------------------------------------------------------
There was no .Rhistory file left (and my memory is too short) so I
cannot reproduce it, but what is a "double-linked list"?
That message likely comes from the C runtime library glibc, not directly
from R. It says that the memory being managed by C has been corrupted,
presumably by an out of bounds write sometime earlier. (This might
conceivably happen if an object had been cleaned up by the R memory
manager then referred to later, but that usually gives a different error.)
If you can make it reproducible we could track it down, but it's much
harder without that. You could try running your code under valgrind if
you know how to do that (or want to read the manual and learn).
I ran
$ R -d "valgrind --leak-check=full --show-reachable=yes -v" -f koll.R 2> ojd
on koll.R:
load("fert.rda")
library(eha)
fert$age <- cut(fert$enter, c(15, 20, 25, 30, 35, 40, 45, 50))
fert$age <- cut(fert$enter, c(14, 20, 25, 30, 35, 40, 45, 50))
fit <- coxreg(Surv(exit - enter, event > 0.5) ~ strata(age) + civst +
birthdate, data = fert[fert$parity == 0, ])
fit1 <- coxph(Surv(exit - enter, event > 0.5) ~ strata(age) + civst +
birthdate, data = fert[fert$parity == 0, ])
summary(fit1)
which produced an output of 22765 lines. A quick scan of them showed
nothing in particular, except:
(lines 50 - 54):
--29802-- .. CRC mismatch (computed 1fb85af8 wanted 2e9e3c16)
--29802-- object doesn't have a symbol table
==29802== WARNING: new redirection conflicts with existing -- ignoring it
--29802-- old: 0x04019ca0 (strlen ) R-> (0000.0)
0x38068331 ???
--29802-- new: 0x04019ca0 (strlen ) R-> (2007.0)
0x04c2e1a0 strlen
and, at the end:
==29802== LEAK SUMMARY:
==29802== definitely lost: 0 bytes in 0 blocks
==29802== indirectly lost: 0 bytes in 0 blocks
==29802== possibly lost: 0 bytes in 0 blocks
==29802== still reachable: 39,088,272 bytes in 13,280 blocks
==29802== suppressed: 0 bytes in 0 blocks
==29802==
==29802== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==29802== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
(should this go to R-devel? I could try harder to provoke the error.)
Göran
Duncan Murdoch
This is on Ubuntu 14.10 with R built from source.
> sessionInfo()
R version 3.1.2 Patched (2014-12-08 r67137)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] eha_2.4-2 survival_2.37-7
loaded via a namespace (and not attached):
[1] tools_3.1.2
Göran
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______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.