[Rd] Using response variable in interaction as explanatory variable in glm crashes R
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
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Re: [Rd] Using response variable in interaction as explanatory variable in glm crashes R
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.
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
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[Rd] SIGSEGV during startup
Hi,
This problem started as of r73472 ("Merged in the rest of the basic
ALTREP framework."); I tested r73471 and it did not exist.
I'm building R devel on Ubuntu 16.04.3 LTS (64-bit), with the following flags:
CC="gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer"
CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
and using
configure --with-valgrind-instrumentation=2
Running 'make' builds the R binary, but R fails to start. So 'make'
ultimately fails when trying to install sysdata.rda during the tools
package build. Here is the traceback:
make[5]: Leaving directory '/home/josh/R/R-build/src/library/tools/src'
make[4]: Leaving directory '/home/josh/R/R-build/src/library/tools'
make[4]: Entering directory '/home/josh/R/R-build/src/library/tools'
installing 'sysdata.rda'
ASAN:SIGSEGV
=
==3543==ERROR: AddressSanitizer: SEGV on unknown address
0x (pc 0x0043b2f2 bp 0x7ffeb5fdc670 sp 0x7ffeb5fdc660
T0)
#0 0x43b2f1 in ALTVEC_DATAPTR ../../../R-svn/src/main/altrep.c:305
#1 0x6b1068 in DATAPTR ../../../R-svn/src/include/Rinlinedfuns.h:105
#2 0x6b1068 in GetNewPage ../../../R-svn/src/main/memory.c:908
#3 0x6b5284 in Rf_allocVector3 ../../../R-svn/src/main/memory.c:2514
#4 0x654a49 in Rf_allocVector ../../../R-svn/src/include/Rinlinedfuns.h:514
#5 0x654a49 in Rf_mkTrue ../../../R-svn/src/main/gram.c:4164
#6 0x6b616c in Rf_InitMemory ../../../R-svn/src/main/memory.c:2137
#7 0x69186a in setup_Rmainloop ../../../R-svn/src/main/main.c:842
#8 0x694488 in Rf_mainloop ../../../R-svn/src/main/main.c:1088
#9 0x41e398 in main ../../../R-svn/src/main/Rmain.c:29
#10 0x7f9d71f4182f in __libc_start_main
(/lib/x86_64-linux-gnu/libc.so.6+0x2082f)
#11 0x41fbe8 in _start (/home/josh/R/R-build/bin/exec/R+0x41fbe8)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV ../../../R-svn/src/main/altrep.c:305
ALTVEC_DATAPTR
==3543==ABORTING
../../../../R-svn/share/make/basepkg.mk:150: recipe for target 'sysdata' failed
make[4]: *** [sysdata] Error 1
make[4]: Leaving directory '/home/josh/R/R-build/src/library/tools'
Makefile:30: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/home/josh/R/R-build/src/library/tools'
Makefile:36: recipe for target 'R' failed
make[2]: *** [R] Error 1
make[2]: Leaving directory '/home/josh/R/R-build/src/library'
Makefile:28: recipe for target 'R' failed
make[1]: *** [R] Error 1
make[1]: Leaving directory '/home/josh/R/R-build/src'
Makefile:60: recipe for target 'R' failed
make: *** [R] Error 1
The context around memory.c:908 is below, and suggests the issue
manifests with the combination of the ALTREP framework and valgrind
instrumentation level >1.
#if VALGRIND_LEVEL > 1
if (NodeClassSize[node_class] > 0)
VALGRIND_MAKE_MEM_NOACCESS(DATAPTR(s),
NodeClassSize[node_class]*sizeof(VECREC));
#endif
--
Joshua Ulrich | about.me/joshuaulrich
FOSS Trading | www.fosstrading.com
R/Finance 2017 | www.rinfinance.com
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Re: [Rd] SIGSEGV during startup
Thanks -- should be resolved now.
Best,
luke
On Fri, 6 Oct 2017, Joshua Ulrich wrote:
Hi,
This problem started as of r73472 ("Merged in the rest of the basic
ALTREP framework."); I tested r73471 and it did not exist.
I'm building R devel on Ubuntu 16.04.3 LTS (64-bit), with the following flags:
CC="gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer"
CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
and using
configure --with-valgrind-instrumentation=2
Running 'make' builds the R binary, but R fails to start. So 'make'
ultimately fails when trying to install sysdata.rda during the tools
package build. Here is the traceback:
make[5]: Leaving directory '/home/josh/R/R-build/src/library/tools/src'
make[4]: Leaving directory '/home/josh/R/R-build/src/library/tools'
make[4]: Entering directory '/home/josh/R/R-build/src/library/tools'
installing 'sysdata.rda'
ASAN:SIGSEGV
=
==3543==ERROR: AddressSanitizer: SEGV on unknown address
0x (pc 0x0043b2f2 bp 0x7ffeb5fdc670 sp 0x7ffeb5fdc660
T0)
#0 0x43b2f1 in ALTVEC_DATAPTR ../../../R-svn/src/main/altrep.c:305
#1 0x6b1068 in DATAPTR ../../../R-svn/src/include/Rinlinedfuns.h:105
#2 0x6b1068 in GetNewPage ../../../R-svn/src/main/memory.c:908
#3 0x6b5284 in Rf_allocVector3 ../../../R-svn/src/main/memory.c:2514
#4 0x654a49 in Rf_allocVector ../../../R-svn/src/include/Rinlinedfuns.h:514
#5 0x654a49 in Rf_mkTrue ../../../R-svn/src/main/gram.c:4164
#6 0x6b616c in Rf_InitMemory ../../../R-svn/src/main/memory.c:2137
#7 0x69186a in setup_Rmainloop ../../../R-svn/src/main/main.c:842
#8 0x694488 in Rf_mainloop ../../../R-svn/src/main/main.c:1088
#9 0x41e398 in main ../../../R-svn/src/main/Rmain.c:29
#10 0x7f9d71f4182f in __libc_start_main
(/lib/x86_64-linux-gnu/libc.so.6+0x2082f)
#11 0x41fbe8 in _start (/home/josh/R/R-build/bin/exec/R+0x41fbe8)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV ../../../R-svn/src/main/altrep.c:305
ALTVEC_DATAPTR
==3543==ABORTING
../../../../R-svn/share/make/basepkg.mk:150: recipe for target 'sysdata' failed
make[4]: *** [sysdata] Error 1
make[4]: Leaving directory '/home/josh/R/R-build/src/library/tools'
Makefile:30: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/home/josh/R/R-build/src/library/tools'
Makefile:36: recipe for target 'R' failed
make[2]: *** [R] Error 1
make[2]: Leaving directory '/home/josh/R/R-build/src/library'
Makefile:28: recipe for target 'R' failed
make[1]: *** [R] Error 1
make[1]: Leaving directory '/home/josh/R/R-build/src'
Makefile:60: recipe for target 'R' failed
make: *** [R] Error 1
The context around memory.c:908 is below, and suggests the issue
manifests with the combination of the ALTREP framework and valgrind
instrumentation level >1.
#if VALGRIND_LEVEL > 1
if (NodeClassSize[node_class] > 0)
VALGRIND_MAKE_MEM_NOACCESS(DATAPTR(s),
NodeClassSize[node_class]*sizeof(VECREC));
#endif
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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