[R] Mysterious seg fault.

[Eric Berger]

Hi Rolf,
When faced with such a situation I take the following approach which often
helps.
Use the same setup that caused the seg fault (you need a reproducible
problem.)
Start your R session using valgrind. e.g. in linux I do:

$ valgrind R

Assuming that a seg fault still occurs then valgrind should provide info as
to where.

HTH,
Eric


On Sun, Aug 12, 2018 at 5:13 AM, Peter Langfelder <
peter.langfelder using gmail.com> wrote:

> Segfaults are not always repeatable. You may have an undefined pointer that
> sometime points into unreachable or unallocated memory, causing a segfault,
> and sometimes may point into valid memory, without causing a segfault.
>
> You may want to read
> https://cran.r-project.org/doc/manuals/r-release/R-exts.
> html#Checking-memory-access
> for tips on how to diagnose such problems.
>
> HTH,
>
> Peter
>
> On Sat, Aug 11, 2018 at 2:13 PM Rolf Turner <r.turner using auckland.ac.nz>
> wrote:
>
> >
> > I am getting a seg fault from a package that I am working on, and I am
> > totally flummoxed by it.  The fault presumably arises from dynamically
> > loaded Fortran code, but I'm damned if I can see where the error lies.
> >
> > In an effort to diagnose the problem I created a "non-package" version
> > of the code.  That is, I copied all the *.R files and *.f file into a
> > new directory.  In that directory I created a *.so file using
> > R CMD SHLIB.
> >
> > In the R code I removed all the "PACKAGE=" lines from the calls to
> > .Fortran() and put in appropriate dyn.load() calls.
> >
> > I then started R in this new "clean" directory and sourced all of the
> > *.R files.
> >
> > I then issued the command that produces the seg fault when run under the
> > aegis of the package.  The command ran without a murmur of complaint.
> > WTF?
> >
> > Can anyone suggest a reason why a seg fault might arise when the code is
> > run in the context of a package, but not when it is run in "standalone
> > mode"?
> >
> > I have checked and rechecked my init.c file --- which is the only thing
> > that I can think of that might create a difference --- and cannot find
> > any discrepancy between the declarations in the init.c file and the
> > Fortran code.
> >
> > The package is a bit complicated, so giving more detail would be
> > cumbersome.  Also I have no idea what aspects of detail would be
> > relevant.  If anyone would like more info, feel free to ask.
> >
> > I would really appreciate it if someone could give me some suggestions
> > before I go *completely* mad!
> >
> > cheers,
> >
> > Rolf Turner
> >
> > --
> > Technical Editor ANZJS
> > Department of Statistics
> > University of Auckland
> > Phone: +64-9-373-7599 ext. 88276
> >
> > ______________________________________________
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> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
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>
> ______________________________________________
> R-help using 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.
>

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