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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