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

[Shaun Walbridge]

Try passing the configure arguments to the command directly to rproj:

install.packages('rgdal', configure.args = '--with-proj-include=/correct/proj4/include --with-proj-lib=/correct/proj4/lib --with-proj-share=/correct/proj4/share')

On 6/19/17, 10:33 AM, "R-sig-Geo on behalf of Ryan Runquist" <r-sig-geo-bounces at r-project.org on behalf of rdbrunquist at gmail.com> wrote:

    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://urldefense.proofpoint.com/v2/url?u=https-3A__mirror.las.iastate.edu_CRAN_src_contrib_rgdal-5F1&d=DwIGaQ&c=n6-cguzQvX_tUIrZOS_4Og&r=YFaRLkcUCdDkLrpTbNOUV9J1CwYBCTMwgm5tdQkRSm4&m=SJ8UGKdbyg0VNXfUCOOVJNKZJSQbEZ1KRCyHR_oEtC8&s=sqbCt8BPZes79H33y7aSpNnE5tALDJOhMfpOybZ4e7c&e= .
    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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