[R-sig-Geo] library fails to load in linux

[Esa Östring]

Hi,

Seems to me that this is a safety mechanism during compilation 
(FORTIFY_SOURCE) built into recent Fedora and Ubuntu distributions, to 
detect SW run time memory corruption.

See:
https://wiki.ubuntu.com/Security/Features
and https://idea.popcount.org/2013-08-15-fortify_source/

I suspect that this problem has nothing to do with VM:s, but I have no 
facts to support that claim.

br, Esa Östring, Data Scientist

On 25/06/15 12:16, chris english wrote:
> http://r.789695.n4.nabble.com/Re-RGtk2-on-linux-quot-stack-smashing-detected-quot-td920903.html
>
> googling the error message suggests pointers to external resources and
> since these instances are VM's,
> it is likely either the VM or underlying hardware if these are linux guest
> on windows/iOS host.
>
> HTH-
> chris
>
> On Thu, Jun 25, 2015 at 4:20 AM, Rolf Turner <r.turner at auckland.ac.nz>
> wrote:
>
>> On 25/06/15 18:49, Harold-Jeffrey Ship wrote:
>>
>>   Hi Rolf. Thank you for your quick response!
>>> I had tried using install.packages, and just now tried the method you
>>> suggested (R CMD INSTALL spatstat_1.42-1.tar.gz) with the same results.
>>>
>>> By the way, we have the same problem when we try on RHEL 6.4 on a
>>> different machine with R 3.2.0. I should mention that both of these are
>>> VM's.
>>>
>> But was this on the same *physical* machine?  There *might* be some
>> hardware (???) induced problem.  I'm clutching at straws here.
>>
>>   I can send you the entire stack trace if it will help.
>> Hmm.  Dunno if it will *help* --- I'm puzzled at the moment --- but I
>> guess it can't hurt, so yes, please do send the stack trace.
>>
>> Is there anyone out there on the R-sig-Geo list running Ubuntu 12.4
>> "Precise"?  If so could you try downloading the spatstat tarball and
>> installing from source, and let me know what happens?
>>
>> Has anyone ever seen an error message about "stack smashing" (?!?!?!)
>> before?  Anyone have any idea what this *means*?
>>
>> cheers,
>>
>> Rolf Turner
>>
>>
>>   Rolf Turner <r.turner at auckland.ac.nz> wrote on 06/25/2015 01:23:18 AM:
>>>   > From: Rolf Turner <r.turner at auckland.ac.nz>
>>>   > To: Harold-Jeffrey Ship/Haifa/IBM at IBMIL
>>>   > Cc: r-sig-geo at r-project.org, Adrian Baddeley
>>> <adrian.baddeley at uwa.edu.au>
>>>   > Date: 06/25/2015 01:23 AM
>>>   > Subject: Re: [R-sig-Geo] library fails to load in linux
>>>   >
>>>   >
>>>   > How did you effect the installation command?  Did you use
>>>   >
>>>   >      install.packages(.....)
>>>   >
>>>   > from the R command line?  Or did you use a precompiled Ubuntu binary?
>>> Or
>>>   > ....?
>>>   >
>>>   > When I do
>>>   >
>>>   >      install.packages("spatstat", <etc.>)
>>>   >
>>>   > from the R command line, under my antiquated Fedora system, it installs
>>>   > with no problems.
>>>   >
>>>   > Have you tried downloading the tarball and installing from source, i.e.
>>>   >
>>>   >      R CMD INSTALL spatstat_1.42-1.tar.gz
>>>   >
>>>   > ???
>>>   >
>>>   > We need more detail.  If there really is a problem, we need to get to
>>>   > the bottom of it.
>>>   >
>>>   > You might possibly get more help on the R-sig-Debian list; please keep
>>>   > us informed of developments.
>>>   >
>>>   > cheers,
>>>   >
>>>   > Rolf Turner
>>>   >
>>>   > On 25/06/15 01:39, Harold-Jeffrey Ship wrote:
>>>   > > I have Ubuntu 12.04 Precise. I just installed R and want to install
>>>   > > spatstat. This is the R information:
>>>   > >
>>>   > > R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
>>>   > > Copyright (C) 2015 The R Foundation for Statistical Computing
>>>   > > Platform: x86_64-pc-linux-gnu (64-bit)
>>>   > >
>>>   > > When I try to install spatstat things look fine at first until it
>>> tries to
>>>   > > verify the installation by loading the library. It crashes, with
>>> the below
>>>   > > error message (snipped).
>>>   > > Any help would be greatly appreciated!
>>>   > >
>>>   > > installing to
>>> /home/harold/R/x86_64-pc-linux-gnu-library/3.2/spatstat/libs
>>>   > > ** R
>>>   > > ** data
>>>   > > *** moving datasets to lazyload DB
>>>   > > ** demo
>>>   > > ** inst
>>>   > > ** byte-compile and prepare package for lazy loading
>>>   > > ** help
>>>   > > *** installing help indices
>>>   > > ** building package indices
>>>   > > ** installing vignettes
>>>   > > ** testing if installed package can be loaded
>>>   > > *** stack smashing detected ***: /usr/lib/R/bin/exec/R terminated
>>>   > > ======= Backtrace: =========
>>>   > > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f3895976e57]
>>>   > > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x7f3895976e20]
>>>   > > /usr/lib/R/lib/libR.so(+0xc9825)[0x7f3895f11825]
>>>   > >    [[alternative HTML version deleted]]
>>>
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