[R-sig-Geo] Issues installing rgeos on linux server

[Matthew Simpson]

I'm installing some spatial packages on a linux server and due to
university constraints, cannot install anything using a package manager.
I've managed to get rgdal installed successfully, but rgeos is causing
problems.

I've installed the geos library already, but when I attempt to install
rgeos within R, it complains that that it cannot run C compiled programs.

I've also tried downloading the tarball myself and running R CMD check, and
it gives me the same complaint.

I've successfully reinstalled Rcpp from source, but that seemed to do
nothing.

Below is: 1) the console input from the attempted installation, 2) shell
output from running R CMD check, and 3) my sessionInfo()

Any help would be appreciated.

Matt

1) Here is the result of attempted installation: (note: removing type =
"source" changes nothing):

> install.packages("rgeos", type = "source",
+         configure.args =
"--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",
+         repos = "https://cloud.r-project.org")
Installing package into ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
Content type 'application/x-gzip' length 257486 bytes (251 KB)
==================================================
downloaded 251 KB

* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
configure: CC: /usr/bin/gcc -std=gnu99
configure: CXX: /usr/bin/g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... no
configure: svn revision: 546
configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
checking geos-config exists... yes
checking geos-config executable... yes
checking geos-config usability... yes
configure: GEOS version: 3.7.0dev
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... /usr/bin/gcc -std=gnu99
checking whether the C compiler works... yes
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/RtmppP5J2b/R.INSTALL236bb22fea27c/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 ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3/rgeos’

The downloaded source packages are in
        ‘/tmp/RtmpwkU04N/downloaded_packages’
Warning message:
In install.packages("rgeos", type = "source", configure.args =
"--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",  :
  installation of package ‘rgeos’ had non-zero exit status

2) Here's the result from running R CMD check:

R CMD check
--install-args='--configure-args=--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config'
rgeos_0.3-23.tar.gz
* using log directory ‘/group/stsn/src/test/rgeos.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rgeos/DESCRIPTION’ ... OK
* this is package ‘rgeos’ version ‘0.3-23’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rgeos’ can be installed ... ERROR
Installation failed.
See ‘/group/stsn/src/test/rgeos.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/group/stsn/src/test/rgeos.Rcheck/00check.log’
for details.

cat /group/stsn/src/test/rgeos.Rcheck/00install.out
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
configure: CC: /usr/bin/gcc -std=gnu99
configure: CXX: /usr/bin/g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... no
configure: svn revision: 546
configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
checking geos-config exists... yes
checking geos-config executable... yes
checking geos-config usability... yes
configure: GEOS version: 3.7.0dev
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... /usr/bin/gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in
`/group/stsn/src/test/rgeos.Rcheck/00_pkg_src/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 ‘/group/stsn/src/test/rgeos.Rcheck/rgeos’

3) And here's my session info:

 sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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