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

[Thierry Onkelinx]

Dear Ryan,

You **first** need to install the dependencies of rgdal.

sudo apt-get update && sudo apt-get install libgdal-dev libproj-dev

Then you should be able to install rgdal.

For more details google "rgdal install linux"

Best regards,


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2017-06-19 16:33 GMT+02:00 Ryan Runquist <rdbrunquist at gmail.com>:

> 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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