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

[Wall, Wade A ERDC-RDE-CERL-IL CIV]

I had trouble installing gdal and proj4 as well, but not trouble installing rgdal. 

Is the path to proj4 and the proj4 library in your path? I put it in my .bashrc and it worked okay.

export LD_LIBRARY_PATH=/pathTobin/bin/proj4/lib:$LD_LIBRARY_PATH
export PATH==/pathTobin/bin/proj4/bin:$PATH

HTH,
Wade

-----Original Message-----
From: R-sig-Geo [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of Ryan Runquist
Sent: Monday, June 19, 2017 9:34 AM
To: r-sig-geo at r-project.org
Subject: [R-sig-Geo] Problem with Proj when loading 'rgdal' on Super Computer Facility

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 'Blockedhttps://mirror.las.iastate.edu/CRAN/src/contrib/rgdal_1Blocked.
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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