Problem installing rgeos
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. Roger
HTH 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 PNNL
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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