Problem with Proj when loading 'rgdal' on Super Computer Facility

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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

        [[alternative HTML version deleted]]

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Re: 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" <[hidden email] on behalf of [hidden email]> 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
   
    [[alternative HTML version deleted]]
   
    _______________________________________________
    R-sig-Geo mailing list
    [hidden email]
    https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dgeo&d=DwIGaQ&c=n6-cguzQvX_tUIrZOS_4Og&r=YFaRLkcUCdDkLrpTbNOUV9J1CwYBCTMwgm5tdQkRSm4&m=SJ8UGKdbyg0VNXfUCOOVJNKZJSQbEZ1KRCyHR_oEtC8&s=K2N5LvwRn4RSLJNVBjbxQyBFejL-jaD1fky4cOX6WwU&e= 

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Re: Problem with Proj when loading 'rgdal' on Super Computer Facility

Thierry Onkelinx
In reply to this post by Ryan Runquist
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 <[hidden email]>:

> 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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

        [[alternative HTML version deleted]]

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Re: Problem with Proj when loading 'rgdal' on Super Computer Facility

Wall, Wade A ERDC-RDE-CERL-IL CIV
In reply to this post by Ryan Runquist
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:[hidden email]] On Behalf Of Ryan Runquist
Sent: Monday, June 19, 2017 9:34 AM
To: [hidden email]
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

        [[alternative HTML version deleted]]

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Re: Problem with Proj when loading 'rgdal' on Super Computer Facility

Roger Bivand
Administrator
In reply to this post by Shaun Walbridge
On Mon, 19 Jun 2017, Shaun Walbridge wrote:

> 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')

Thanks, Shaun! My reply when approached off-list initially, was:

"Did you consider reading the help file of install.packages? Did you
consider unpacking the source tarball of rgdal and running ./configure
--help and reading the README file, also at:

https://r-forge.r-project.org/scm/viewvc.php/pkg/inst/README?view=markup&roo
t=rgdal

or

library(rgdal)
file.show(system.file("README", package="rgdal"))

which details configure arguments, which tell the install system where to
find external dependencies.

You also typically need each core to have access to the same external
dependencies, so you may wish to build GDAL, etc. static, so that the
rgdal.so in the package that you build from source is self-contained, that
is your choice."

Installing on clusters can be a problem, so choosing the static route is
actually more predictable, but is quite a lot of work the first time
round. The build scripts for the Windows sf and rgdal binary package
external dependencies at for example:

https://github.com/rwinlib/gdal2/blob/master/build64.sh

give a flavour - you will probably only need a subset of drivers. If you
build such a static binary package, it will protect you from missing
dependencies on the nodes, at the cost of few drivers and a big shared
object. If the nodes are the homogeneous, this route should be robust.
Does anyone have recent experience of a static install under Linux (build
GDAL and its dependencies, and PROJ4, static only)?

Roger


>
> On 6/19/17, 10:33 AM, "R-sig-Geo on behalf of Ryan Runquist" <[hidden email] on behalf of [hidden email]> 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
>    â€˜/tmp/RtmpBVhI5E/downloaded_packages’
>    Warning message:
>    In install.packages("rgdal") :
>      installation of package ‘rgdal’ had non-zero exit status
>
>     [[alternative HTML version deleted]]
>
>    _______________________________________________
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>
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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