>>>>> Jan van der Laan <rh...@eoos.dds.nl>
>>>>> on Fri, 6 Oct 2017 12:13:39 +0200 writes:
> It is actually model.matrix that crashes, not glm. Same
> crash occurs with e.g. lm.
> model.matrix(dob_mon ~ dob_day*dob_mon, data = tab)
> also crashes R.
Yes, segmentation fault.
It only happens when these are *logical* variables, not, e.g., when
transformed to integer.
The C code in src/library/stats/src/model.c tries to eliminate
occurances of the LHS of the formula from the RHS when building
the model matrix and it does work fine in the integer case.
Part of the culprit code may be this (from line 717),
with the isLogical(.) which in our case, shifts the pointer by
1 in the call to firstfactor() :
int adj = isLogical(var_i)?1:0;
// avoid overflow of jstart * nn PR#15578
firstfactor(&rx[jstart * nn], n, jnext - jstart,
REAL(contrast), nrows(contrast),
ncols(contrast), INTEGER(var_i)+adj);
then in firstfactor(), we see the segfault (when running R with
'-d gdb') :
> model.matrix(dob_mon ~ dob_day*dob_mon, data = tab)
Program received signal SIGSEGV, Segmentation fault.
0x00007fffeafa76b5 in firstfactor (ncx=0, v=0x5c3b37c, ncc=1, nrc=2,
c=0x5c90008,
nrx=8, x=0x5cbf150) at ../../../../../R/src/library/stats/src/model.c:252
252 else xj[i] = cj[v[i]-1];
Missing separate debuginfos, .................
(gdb) list
247 for (int j = 0; j < ncc; j++) {
248 xj = &x[j * (R_xlen_t)nrx];
249 cj = &c[j * (R_xlen_t)nrc];
250 for (int i = 0; i < nrx; i++)
251 if(v[i] == NA_INTEGER) xj[i] = NA_REAL;
252 else xj[i] = cj[v[i]-1];
253 }
254 }
255
and indeed in the debugger, i=7 and v[i] is "outside", v[]
being of length 7, hence indexed 0:6.
> Jan
> On 06-10-17 12:08, Jan van der Laan wrote:
>>
>> The following code crashes R (I know I shouldn't try to
>> estimate such a model; this was a bug in some code of
>> mine). I also tried with R-devel; same result.
>>
>>
>> tab <- structure(list(dob_day = c(FALSE, FALSE, FALSE,
>> FALSE, TRUE, TRUE, TRUE, TRUE), dob_mon = c(FALSE, FALSE,
>> TRUE, TRUE, FALSE, FALSE, TRUE, TRUE), dob_year =
>> c(FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE), n
>> = c(1489634L, 17491L, 134985L, 1639L, 47892L, 611L,
>> 4365L, 750L), pred1 = c(1488301, 18187, 135605, 1657,
>> 48547, 593, 4423, 54)), .Names = c("dob_day", "dob_mon",
>> "dob_year", "n", "pred1"), row.names = c(NA, -8L), class
>> = "data.frame")
>>
>> m <- glm(dob_mon ~ dob_day*dob_mon, data = tab, family =
>> binomial())
>>
>>
>> The crash doesn't when the variables are added just as
>> main effects (dob_day+dob_mon): this results in a warning
>> and the removal of dob_mon from the formula.
>>
>> --
>>
>> Jan
>>
>>
>>
>> > R.version _ platform
>> x86_64-pc-linux-gnu arch x86_64 os
>> linux-gnu system x86_64, linux-gnu status
>> major 3 minor 4.1 year 2017
>> month 06 day 30 svn rev 72865
>> language R version.string R version 3.4.1
>> (2017-06-30) nickname Single Candle
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
