[R-sig-Geo] Problem with Proj when loading 'rgdal' on Super Computer Facility

[Ryan Runquist]

Hello,

I am working on manipulating some spatial data and performing SDMs on
invasive species. I have been using R and the package 'rgdal' to do some of
these analyses.

On my own computer, Mac OSX 10.12.2 running R 3.3.3, I have had not
problems installing 'rgdal', loading the library, and using the functions.

However, we are starting to work on the UMN MSI facility and we are having
problems installing 'rgdal' on their Linux supercomputing cluster.

In order to install this package, we have to load the GDAL library and the
PROJ4 library in Linux. We have not had any problems loading their GDAL
module and accessing the libraries. They work fine for 'rgeos'. However, we
are having problems with the PROJ module.

When we run 'install.packages('rgdal')', the installation process begins,
but it stalls when it checks for "'pj_init_plus' in -lproj", and then
fails.

We have been working with someone at MSI to remedy this problem. They are
able to see that the file does in fact exist and don't know why 'rgdal' is
having problems locating it.

So far, we have tried different versions of PROJ (Proj 4.4.9, Proj 4.9.2,
Proj 4.9.3_gcc4.8.2 - meaning it was compiled with gcc 4.8.2) and they have
complied PROJ with GCC 4.8.2 instead of their default complier. They also
tried to compile it with  GCC 6.3, but that failed with a complier error.

I have copied the full error message below.

Sincerely,

Ryan



> install.packages("rgdal")
Installing package into ‘/panfs/roc/groups/7/moeller/rbriscoe/R/x86_64-pc-
linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/rgdal_1.
2-7.tar.gz'
Content type 'application/x-gzip' length 1653897 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: CC: /panfs/roc/msisoft/gcc/6.1.0/bin/gcc
configure: CXX: /panfs/roc/msisoft/gcc/6.1.0/bin/g++
configure: rgdal: 1.2-7
checking for /usr/bin/svnversion... yes
configure: svn revision: 660
checking for gdal-config... /panfs/roc/msisoft/gdal/2.0.1/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.0.1
checking GDAL version >= 1.6.3... yes
checking for gcc... /panfs/roc/msisoft/gcc/6.1.0/bin/gcc
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... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /panfs/roc/msisoft/gcc/6.1.0/bin/gcc accepts -g... yes
checking for /panfs/roc/msisoft/gcc/6.1.0/bin/gcc option to accept ISO
C89... none needed
checking how to run the C preprocessor... /panfs/roc/msisoft/gcc/6.1.0/b
in/gcc
-E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... yes
checking GDAL: /soft/gdal/2.0.1/share/gdal/pcs.csv readable... yes
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... no
configure: error: libproj not found in standard or given locations.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/panfs/roc/groups/7/moeller/rbriscoe/R/x86_64-pc-
linux-gnu-library/3.3/rgdal’

The downloaded source packages are in
‘/tmp/RtmpBVhI5E/downloaded_packages’
Warning message:
In install.packages("rgdal") :
  installation of package ‘rgdal’ had non-zero exit status

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