Hi all,
I ran into a segfault while playing with dates.
$ R --no-init-file
...
> library(lubridate);
d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL;
d$zone=""; d
Attaching package: ?lubridate?
The following object is masked from ?package:base?:
date
Warning message:
package ?lubridate? was built under R version 3.4.0
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: format.POSIXlt(x, usetz = TRUE)
2: format(x, usetz = TRUE)
3: print(format(x, usetz = TRUE), ...)
4: print.POSIXlt(x)
5: function (x, ...) UseMethod("print")(x)
Possible actions:
...
Hope I'm not doing something illegal...
Thanks,
Frederick
On Tue, Dec 6, 2016 at 6:37 AM, <frederik at ofb.net> wrote:> Hi all, > > I ran into a segfault while playing with dates. > > $ R --no-init-file > ... > > library(lubridate); d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL; d$zone=""; d >If you're asking about a bug in R, you should provide a *minimal* reproducible example (i.e. one without any package dependencies). This has nothing to do with lubridate, so you can reproduce the behavior with: d <- as.POSIXlt(Sys.time()) d$zone <- NULL d$zone <- "" d> Attaching package: ?lubridate? > > The following object is masked from ?package:base?: > > date > > Warning message: > package ?lubridate? was built under R version 3.4.0 > > *** caught segfault *** > address (nil), cause 'unknown' > > Traceback: > 1: format.POSIXlt(x, usetz = TRUE) > 2: format(x, usetz = TRUE) > 3: print(format(x, usetz = TRUE), ...) > 4: print.POSIXlt(x) > 5: function (x, ...) UseMethod("print")(x) > > Possible actions: > ... > > Hope I'm not doing something illegal... >You are. You're changing the internal structure of a POSIXlt object by re-ordering the list elements. You should not expect a malformed POSIXlt object to behave as if it's correctly formed. You can see it's malformed by comparing it's unclass()'d output. d <- as.POSIXlt(Sys.time()) unclass(d) # valid POSIXlt object d$zone <- NULL d$zone <- "" unclass(d) # your malformed POSIXlt object> Thanks, > > Frederick > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com R/Finance 2016 | www.rinfinance.com
Hi Joshua, Thank you for minimizing my test case.> > Hope I'm not doing something illegal... > > > You are. You're changing the internal structure of a POSIXlt object > by re-ordering the list elements. You should not expect a malformed > POSIXlt object to behave as if it's correctly formed. You can see > it's malformed by comparing it's unclass()'d output. > > d <- as.POSIXlt(Sys.time()) > unclass(d) # valid POSIXlt object > d$zone <- NULL > d$zone <- "" > unclass(d) # your malformed POSIXlt objectI don't know if these questions are not already obvious, but: 1. Is there a reasonable way to fail more elegantly when a user makes this mistake? 2. Should we update the documentation for POSIXlt to warn people that the optional "zone" list element must precede the optional "gmtoff" list element, in cases where both are present? Thanks, Frederick
frederik at ofb.net
2016-Dec-06 17:27 UTC
[Rd] ok to segfault with POSIXlt zone=NULL zone=""?
Hi all, Here's a more minimal version of my earlier bug report (thanks, Joshua Ulrich): d=as.POSIXlt(Sys.time()); d$zone=NULL; d$zone=""; d I got some helpful, if glib, feedback from Joshua that the segfault may be caused by the changing of the order of the list elements in 'd' (representing the "internal structure" of the POSIXlt object). He seems to think that it's OK for R to segfault - I was wondering if someone else could lend a second opinion. My understanding is that we should try to avoid segfaulting as a way of handling errors, if only because they become much more difficult to debug when the R session is forced to quit. I don't know exactly which line is causing the bug, but looking at the code for do_formatPOSIXlt in "src/main/datetime.c", it seems that there would not be a huge performance penalty to add an extra sanity check to prevent this from occurring. Thank you, Frederick On Tue, Dec 06, 2016 at 04:37:20AM -0800, frederik at ofb.net wrote:> Hi all, > > I ran into a segfault while playing with dates. > > $ R --no-init-file > ... > > library(lubridate); d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL; d$zone=""; d > > Attaching package: ?lubridate? > > The following object is masked from ?package:base?: > > date > > Warning message: > package ?lubridate? was built under R version 3.4.0 > > *** caught segfault *** > address (nil), cause 'unknown' > > Traceback: > 1: format.POSIXlt(x, usetz = TRUE) > 2: format(x, usetz = TRUE) > 3: print(format(x, usetz = TRUE), ...) > 4: print.POSIXlt(x) > 5: function (x, ...) UseMethod("print")(x) > > Possible actions: > ... > > Hope I'm not doing something illegal... > > Thanks, > > Frederick > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
I agree this is a bug; R should never segfault. I wouldn't call it a high priority one, since you can avoid the problem by not messing with R's internal structures. It's unlikely to get fixed unless someone posts it as a bug report to bugs.r-project.org (because low priority bugs reported only on mailing lists get forgotten). So please post a minimal example there, possibly accompanied with a patch. If you don't have an account, you can write to me privately and I'll set one up for you. (We no longer allow people to create their own accounts because of abuse by spammers.) Duncan Murdoch On 06/12/2016 12:27 PM, frederik at ofb.net wrote:> Hi all, > > Here's a more minimal version of my earlier bug report (thanks, Joshua > Ulrich): > > d=as.POSIXlt(Sys.time()); d$zone=NULL; d$zone=""; d > > I got some helpful, if glib, feedback from Joshua that the segfault > may be caused by the changing of the order of the list elements in 'd' > (representing the "internal structure" of the POSIXlt object). > > He seems to think that it's OK for R to segfault - I was wondering if > someone else could lend a second opinion. My understanding is that we > should try to avoid segfaulting as a way of handling errors, if only > because they become much more difficult to debug when the R session is > forced to quit. > > I don't know exactly which line is causing the bug, but looking at the > code for do_formatPOSIXlt in "src/main/datetime.c", it seems that > there would not be a huge performance penalty to add an extra sanity > check to prevent this from occurring. > > Thank you, > > Frederick > > On Tue, Dec 06, 2016 at 04:37:20AM -0800, frederik at ofb.net wrote: >> Hi all, >> >> I ran into a segfault while playing with dates. >> >> $ R --no-init-file >> ... >> > library(lubridate); d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL; d$zone=""; d >> >> Attaching package: ?lubridate? >> >> The following object is masked from ?package:base?: >> >> date >> >> Warning message: >> package ?lubridate? was built under R version 3.4.0 >> >> *** caught segfault *** >> address (nil), cause 'unknown' >> >> Traceback: >> 1: format.POSIXlt(x, usetz = TRUE) >> 2: format(x, usetz = TRUE) >> 3: print(format(x, usetz = TRUE), ...) >> 4: print.POSIXlt(x) >> 5: function (x, ...) UseMethod("print")(x) >> >> Possible actions: >> ... >> >> Hope I'm not doing something illegal... >> >> Thanks, >> >> Frederick >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
>>>>> Joshua Ulrich <josh.m.ulrich at gmail.com> >>>>> on Tue, 6 Dec 2016 09:51:16 -0600 writes:> On Tue, Dec 6, 2016 at 6:37 AM, <frederik at ofb.net> wrote: >> Hi all, >> >> I ran into a segfault while playing with dates. >> >> $ R --no-init-file >> ... >> > library(lubridate); d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL; d$zone=""; d >> > If you're asking about a bug in R, you should provide a *minimal* > reproducible example (i.e. one without any package dependencies). > This has nothing to do with lubridate, so you can reproduce the > behavior with: > d <- as.POSIXlt(Sys.time()) > d$zone <- NULL > d$zone <- "" > d [..........] >> Hope I'm not doing something illegal... >> > You are. You're changing the internal structure of a POSIXlt object > by re-ordering the list elements. You should not expect a malformed > POSIXlt object to behave as if it's correctly formed. You can see > it's malformed by comparing it's unclass()'d output. > d <- as.POSIXlt(Sys.time()) > unclass(d) # valid POSIXlt object > d$zone <- NULL > d$zone <- "" > unclass(d) # your malformed POSIXlt object Indeed, really illegal, i.e. "against the law" ... ;-) Thank you, Joshua! Still, if R segfaults without the user explicitly calling .Call(), .Internal() or similar -- as here -- we usually acknowledge there *is* a bug in R .. even if it is only triggered by a users "illegal" messing around. an MRE for the above, where I really only re-order the "internal" list: d <- as.POSIXlt("2016-12-06"); dz <- d$zone; d$zone <- NULL; d$zone <- dz; f <- format(d)> *** caught segfault *** > address 0x80000020, cause 'memory not mapped'> Traceback: > 1: format.POSIXlt(d) > 2: format(d)The current code is "optimized for speed" (not perfectly), and a patch should hopefully address the C code. Note that a smaller MRE -- which does *not* re-order, but just invalidate the time zone is d <- as.POSIXlt("2016-12-06"); d$zone <- 1; f <- format(d) ------ I have now committed a "minimal" patch (to the C code) which for the above two cases gives a sensible error rather than a seg.fault : > d <- as.POSIXlt("2016-12-06"); d$zone <- 1 ; f <- format(d) Error in format.POSIXlt(d) : invalid 'zone' component in "POSIXlt" structure > d <- as.POSIXlt("2016-12-06"); dz <- d$zone; d$zone <- NULL; d$zone <- dz; f <- format(d) Error in format.POSIXlt(d) : invalid 'zone' component in "POSIXlt" structure > I guess that it should still be possible to produce a segfault with invalid 'POSIXlt' structures though. Martin
I got a similar result from R-Studio 1.0.44 with
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.3.2
> d <- as.POSIXlt(Sys.time())
> d$zone <- NULL
> d$zone <- ""
: "R Session Aborted. R encountered a fatal error. The session was
terminated. Start New Session".
I got essentially the same result with R 3.3.1. Then I installed
3.3.2 and got the above.
Spencer Graves
On 12/6/2016 11:27 AM, frederik at ofb.net wrote:> Hi all,
>
> Here's a more minimal version of my earlier bug report (thanks, Joshua
> Ulrich):
>
> d=as.POSIXlt(Sys.time()); d$zone=NULL; d$zone=""; d
>
> I got some helpful, if glib, feedback from Joshua that the segfault
> may be caused by the changing of the order of the list elements in
'd'
> (representing the "internal structure" of the POSIXlt object).
>
> He seems to think that it's OK for R to segfault - I was wondering if
> someone else could lend a second opinion. My understanding is that we
> should try to avoid segfaulting as a way of handling errors, if only
> because they become much more difficult to debug when the R session is
> forced to quit.
>
> I don't know exactly which line is causing the bug, but looking at the
> code for do_formatPOSIXlt in "src/main/datetime.c", it seems that
> there would not be a huge performance penalty to add an extra sanity
> check to prevent this from occurring.
>
> Thank you,
>
> Frederick
>
> On Tue, Dec 06, 2016 at 04:37:20AM -0800, frederik at ofb.net wrote:
>> Hi all,
>>
>> I ran into a segfault while playing with dates.
>>
>> $ R --no-init-file
>> ...
>> > library(lubridate);
d=as.POSIXlt(floor_date(Sys.time(),"year")); d$zone=NULL;
d$zone=""; d
>>
>> Attaching package: ?lubridate?
>>
>> The following object is masked from ?package:base?:
>>
>> date
>>
>> Warning message:
>> package ?lubridate? was built under R version 3.4.0
>>
>> *** caught segfault ***
>> address (nil), cause 'unknown'
>>
>> Traceback:
>> 1: format.POSIXlt(x, usetz = TRUE)
>> 2: format(x, usetz = TRUE)
>> 3: print(format(x, usetz = TRUE), ...)
>> 4: print.POSIXlt(x)
>> 5: function (x, ...) UseMethod("print")(x)
>>
>> Possible actions:
>> ...
>>
>> Hope I'm not doing something illegal...
>>
>> Thanks,
>>
>> Frederick
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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