library fails to load in linux

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]]