[R-sig-Geo] Problem installing rgeos

Roger Bivand Roger.Bivand at nhh.no
Tue Aug 4 15:25:06 CEST 2015

On Tue, 4 Aug 2015, chris english wrote:

> Scott:
> I found this discussion that chokes at the same point as yours on:
> http://unix.stackexchange.com/questions/50151/getting-newer-version-of-geos-than-what-is-available-in-debian-repositories
> I don't know that it will be applicable. Why don't you post your
> sessionInfo() as this may be useful to others in the future.  Which version
> of GEOS do you have installed?

The problem is almost certainly that the platform build train (compilers 
and libraries) which underlie all the other programs have been updated, as 
Chris has suggested (and we still do not know the OS version or output of 
sessionInfo()). This is neither a GEOS nor an rgeos problem. Most likely 
the C and C++ libraries have changed, leading to a need to re-install an 
unknown number of downstream components.

I suggest checking that you can install Rcpp from source (to test the 
build train). If there are problems, you should correct these first, by 
bringing your build train into reasonable order.

If you can, re-install GEOS from source (to freshen up its dependencies on 
the C and C++ libraries) and only when GEOS passes make check itself 
(ourside R), proceed to install rgeos. If you download the R source 
tarball of rgeos, and run R CMD check on it, you will get a full test of 
its state. Following R CMD INSTALL, this should then work.


> Chris
> On Mon, Aug 3, 2015 at 10:34 AM, Waichler, Scott R <Scott.Waichler at pnnl.gov>
> wrote:
>> Thanks for the suggestions, but I think what I need is help tracking down
>> what the exact error is in the compilation.  Let me try again with the part
>> of the output describing the error:
>>> install.packages("rgeos", dependencies = F, repos = "
>> http://cran.fhcrc.org/")
>> . . .
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... configure: error: in
>> `/tmp/RtmpUjYUle/R.INSTALL41c15690b9e1/rgeos':
>> configure: error: cannot run C compiled programs.
>> If you meant to cross compile, use `--host'.
>> See `config.log' for more details
>> ERROR: configuration failed for package 'rgeos'
>> * removing '/files3/R/R-3.2.1_install/lib64/R/library/rgeos'
>> It says I should refer to config.log for more details.  The only
>> config.log file I can find in the directory tree is the one for geos, which
>> I installed a couple of years ago, and did not give me problems with
>> previous installations of rgeos under earlier releases of R.  In case there
>> is a clue, here is the output in that config.log around the cross compile
>> message:
>> configure:3682: result:
>> configure:3704: checking whether we are cross compiling
>> configure:3712: gcc -o conftest    conftest.c  >&5
>> configure:3716: $? = 0
>> configure:3723: ./conftest
>> Is there a config.log for the attempted rgeos installation?  Where would I
>> find it?
>>> You're build is failing pretty early in the configuration process which
>>> suggests you are missing some tools in your development
>>> environment.  The latest geos was found. Was that a binary or built from
>>> source?  If from source you have the necessary tools in your dev
>>> environment and it may merely be a function of dropping the depends in
>>> you install.packages call....
>> Rgeos was built from source.
>> Thanks,
>> Scott Waichler
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Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no

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