Issues installing rgeos on linux server

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Issues installing rgeos on linux server

Matthew Simpson
I'm installing some spatial packages on a linux server and due to
university constraints, cannot install anything using a package manager.
I've managed to get rgdal installed successfully, but rgeos is causing
problems.

I've installed the geos library already, but when I attempt to install
rgeos within R, it complains that that it cannot run C compiled programs.

I've also tried downloading the tarball myself and running R CMD check, and
it gives me the same complaint.

I've successfully reinstalled Rcpp from source, but that seemed to do
nothing.

Below is: 1) the console input from the attempted installation, 2) shell
output from running R CMD check, and 3) my sessionInfo()

Any help would be appreciated.

Matt

1) Here is the result of attempted installation: (note: removing type =
"source" changes nothing):

> install.packages("rgeos", type = "source",
+         configure.args =
"--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",
+         repos = "https://cloud.r-project.org")
Installing package into ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
Content type 'application/x-gzip' length 257486 bytes (251 KB)
==================================================
downloaded 251 KB

* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
configure: CC: /usr/bin/gcc -std=gnu99
configure: CXX: /usr/bin/g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... no
configure: svn revision: 546
configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
checking geos-config exists... yes
checking geos-config executable... yes
checking geos-config usability... yes
configure: GEOS version: 3.7.0dev
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... /usr/bin/gcc -std=gnu99
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... configure: error: in
`/tmp/RtmppP5J2b/R.INSTALL236bb22fea27c/rgeos':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ‘rgeos’
* removing ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3/rgeos’

The downloaded source packages are in
        ‘/tmp/RtmpwkU04N/downloaded_packages’
Warning message:
In install.packages("rgeos", type = "source", configure.args =
"--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",  :
  installation of package ‘rgeos’ had non-zero exit status

2) Here's the result from running R CMD check:

R CMD check
--install-args='--configure-args=--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config'
rgeos_0.3-23.tar.gz
* using log directory ‘/group/stsn/src/test/rgeos.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rgeos/DESCRIPTION’ ... OK
* this is package ‘rgeos’ version ‘0.3-23’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rgeos’ can be installed ... ERROR
Installation failed.
See ‘/group/stsn/src/test/rgeos.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/group/stsn/src/test/rgeos.Rcheck/00check.log’
for details.

cat /group/stsn/src/test/rgeos.Rcheck/00install.out
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
configure: CC: /usr/bin/gcc -std=gnu99
configure: CXX: /usr/bin/g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... no
configure: svn revision: 546
configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
checking geos-config exists... yes
checking geos-config executable... yes
checking geos-config usability... yes
configure: GEOS version: 3.7.0dev
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... /usr/bin/gcc -std=gnu99
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... configure: error: in
`/group/stsn/src/test/rgeos.Rcheck/00_pkg_src/rgeos':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ‘rgeos’
* removing ‘/group/stsn/src/test/rgeos.Rcheck/rgeos’

3) And here's my session info:

 sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

        [[alternative HTML version deleted]]

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Re: Issues installing rgeos on linux server

Roger Bivand
Administrator
On Tue, 20 Jun 2017, Matthew Simpson wrote:

> I'm installing some spatial packages on a linux server and due to
> university constraints, cannot install anything using a package manager.
> I've managed to get rgdal installed successfully, but rgeos is causing
> problems.
>
> I've installed the geos library already, but when I attempt to install
> rgeos within R, it complains that that it cannot run C compiled programs.

Could you please say how you installed GEOS? Could you try out geos-config
with each of the settings? Do you need 3.7.0dev (I haven't tried this as a
source of difficulty as it seems implausible, but neither rgeos nor sf
need bleeding edge functionality from GEOS)? Could you try to install sf
from source (it also uses GEOS)? Is this the GEOS geos-config -m library
bug (probably not)? Unpacking rgeos, running ./configure in the package
root, I see (Fedora 25, R 3.4.0):

$ ./configure
configure: CC: gcc
configure: CXX: g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... yes
configure: svn revision: 547
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.6.1
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with libgeos_c... yes
configure: PKG_CPPFLAGS:  -I/usr/local/include
configure: PKG_LIBS:  -L/usr/local/lib -lgeos -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars

but you fail about half-way down at the standard croos-compilation test.
For rgdal/configure - you said your rgdal install on the same system
succeeded, I see:

...
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
...

What do you see (just running ./configure in the package root)?

Roger

>
> I've also tried downloading the tarball myself and running R CMD check, and
> it gives me the same complaint.
>
> I've successfully reinstalled Rcpp from source, but that seemed to do
> nothing.
>
> Below is: 1) the console input from the attempted installation, 2) shell
> output from running R CMD check, and 3) my sessionInfo()
>
> Any help would be appreciated.
>
> Matt
>
> 1) Here is the result of attempted installation: (note: removing type =
> "source" changes nothing):
>
>> install.packages("rgeos", type = "source",
> +         configure.args =
> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",
> +         repos = "https://cloud.r-project.org")
> Installing package into ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3’
> (as ‘lib’ is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
> Content type 'application/x-gzip' length 257486 bytes (251 KB)
> ==================================================
> downloaded 251 KB
>
> * installing *source* package ‘rgeos’ ...
> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
> configure: CC: /usr/bin/gcc -std=gnu99
> configure: CXX: /usr/bin/g++
> configure: rgeos: 0.3-23
> checking for /usr/bin/svnversion... no
> configure: svn revision: 546
> configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
> checking geos-config exists... yes
> checking geos-config executable... yes
> checking geos-config usability... yes
> configure: GEOS version: 3.7.0dev
> checking geos version at least 3.2.0... yes
> checking geos-config clibs... yes
> checking for gcc... /usr/bin/gcc -std=gnu99
> 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... configure: error: in
> `/tmp/RtmppP5J2b/R.INSTALL236bb22fea27c/rgeos':
> configure: error: cannot run C compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details
> ERROR: configuration failed for package ‘rgeos’
> * removing ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3/rgeos’
>
> The downloaded source packages are in
>        ‘/tmp/RtmpwkU04N/downloaded_packages’
> Warning message:
> In install.packages("rgeos", type = "source", configure.args =
> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",  :
>  installation of package ‘rgeos’ had non-zero exit status
>
> 2) Here's the result from running R CMD check:
>
> R CMD check
> --install-args='--configure-args=--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config'
> rgeos_0.3-23.tar.gz
> * using log directory ‘/group/stsn/src/test/rgeos.Rcheck’
> * using R version 3.3.1 (2016-06-21)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘rgeos/DESCRIPTION’ ... OK
> * this is package ‘rgeos’ version ‘0.3-23’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘rgeos’ can be installed ... ERROR
> Installation failed.
> See ‘/group/stsn/src/test/rgeos.Rcheck/00install.out’ for details.
> * DONE
>
> Status: 1 ERROR
> See
>  ‘/group/stsn/src/test/rgeos.Rcheck/00check.log’
> for details.
>
> cat /group/stsn/src/test/rgeos.Rcheck/00install.out
> * installing *source* package ‘rgeos’ ...
> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
> configure: CC: /usr/bin/gcc -std=gnu99
> configure: CXX: /usr/bin/g++
> configure: rgeos: 0.3-23
> checking for /usr/bin/svnversion... no
> configure: svn revision: 546
> configure: geos-config set to /group/stsn/shared_libs/geos/bin/geos-config
> checking geos-config exists... yes
> checking geos-config executable... yes
> checking geos-config usability... yes
> configure: GEOS version: 3.7.0dev
> checking geos version at least 3.2.0... yes
> checking geos-config clibs... yes
> checking for gcc... /usr/bin/gcc -std=gnu99
> 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... configure: error: in
> `/group/stsn/src/test/rgeos.Rcheck/00_pkg_src/rgeos':
> configure: error: cannot run C compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details
> ERROR: configuration failed for package ‘rgeos’
> * removing ‘/group/stsn/src/test/rgeos.Rcheck/rgeos’
>
> 3) And here's my session info:
>
> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
--
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
_______________________________________________
R-sig-Geo mailing list
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https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Issues installing rgeos on linux server

Matthew Simpson
Thank you, this was very helpful. It turned out the issue was that I was
using the development version - I had cloned the github repository and
installed from there. Downloading the tarball for the latest stable release
solved the problem. I went ahead and did the same thing for GDAL and proj.4
and reinstalled rgdal just to be safe. And sure enough, before reinstalling
rgdal was complaining about missing proj_defs.dat, even though it existed
in the proj.4/share folder. But now it's working just fine.

For posterity, my full commands to get GEOS, GDAL, proj.4, rgdal, and rgeos
installed from source on a linux server (CentOS 7.3.1611) are below.

cd /path/to/src/geos/
wget http://download.osgeo.org/geos/geos-3.6.1.tar.bz2
tar -vxjf geos-3.6.1.tar.bz2
cd geos-3.6.1
./configure --prefix=/path/to/install/geos
make
make check
make install

cd /path/to/src/gdal
wget http://download.osgeo.org/gdal/2.2.0/gdal-2.2.0.tar.gz
tar -xvzf gdal-2.2.0.tar.gz
cd gdal-2.2.0
./autogen.sh
./configure --prefix=/path/to/install/gdal
make
## there is no make check
make install

cd /path/to/src/proj.4/
wget http://download.osgeo.org/proj/proj-4.9.3.tar.gz
tar -xvzf proj-4.9.3.tar.gz
cd proj-4.9.3
./configure --prefix=/path/to/install/proj.4
make
make check
make install

echo 'export
PATH=/path/to/install/gdal/bin:/path/to/install/proj.4/bin:/path/to/install/geos/bin:$PATH'
>> ~/.bash_profile
echo 'export
LD_LIBRARY_PATH=/path/to/install/gdal/lib:/path/to/install/proj.4/lib:/path/to/install/geos/lib:$LD_LIBRARY_PATH'
>> ~/.bash_profile
. ~/.bash_profile

## in R run:
## need this installed from source to prevent some compiler issues that
would cause R to segfault if rgdal was loaded and you tried to install
certain packages
install.packages("Rcpp", type = "source", repos = "
https://cloud.r-project.org")

install.packages("rgdal", type = "source", repos = "
https://cloud.r-project.org",
configure.args = "--with-proj-include=/path/to/install/proj.4/include
--with-proj-lib=/path/to/install/proj.4/lib
--with-proj-share=/path/to/install/proj.4/share/proj
--with-gdal-config=/path/to/install/gdal/bin/gdal-config")

install.packages("rgeos", type = "source", repos = "
https://cloud.r-project.org",
         configure.args =
"--with-geos-config=/path/to/install/geos/bin/geos-config")


Note that --with-proj-share=/path/to/install/proj.4/share did NOT work.


On Tue, Jun 20, 2017 at 4:26 AM, Roger Bivand <[hidden email]> wrote:

> On Tue, 20 Jun 2017, Matthew Simpson wrote:
>
> I'm installing some spatial packages on a linux server and due to
>> university constraints, cannot install anything using a package manager.
>> I've managed to get rgdal installed successfully, but rgeos is causing
>> problems.
>>
>> I've installed the geos library already, but when I attempt to install
>> rgeos within R, it complains that that it cannot run C compiled programs.
>>
>
> Could you please say how you installed GEOS? Could you try out geos-config
> with each of the settings? Do you need 3.7.0dev (I haven't tried this as a
> source of difficulty as it seems implausible, but neither rgeos nor sf need
> bleeding edge functionality from GEOS)? Could you try to install sf from
> source (it also uses GEOS)? Is this the GEOS geos-config -m library bug
> (probably not)? Unpacking rgeos, running ./configure in the package root, I
> see (Fedora 25, R 3.4.0):
>
> $ ./configure
> configure: CC: gcc
> configure: CXX: g++
> configure: rgeos: 0.3-23
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 547
> checking for geos-config... /usr/local/bin/geos-config
> checking geos-config usability... yes
> configure: GEOS version: 3.6.1
> checking geos version at least 3.2.0... yes
> checking geos-config clibs... yes
> checking for gcc... 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 gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/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 geos_c.h usability... yes
> checking geos_c.h presence... yes
> checking for geos_c.h... yes
> checking geos: linking with libgeos_c... yes
> configure: PKG_CPPFLAGS:  -I/usr/local/include
> configure: PKG_LIBS:  -L/usr/local/lib -lgeos -L/usr/local/lib -lgeos_c
> configure: creating ./config.status
> config.status: creating src/Makevars
>
> but you fail about half-way down at the standard croos-compilation test.
> For rgdal/configure - you said your rgdal install on the same system
> succeeded, I see:
>
> ...
> checking for gcc... 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 gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> ...
>
> What do you see (just running ./configure in the package root)?
>
> Roger
>
>
>> I've also tried downloading the tarball myself and running R CMD check,
>> and
>> it gives me the same complaint.
>>
>> I've successfully reinstalled Rcpp from source, but that seemed to do
>> nothing.
>>
>> Below is: 1) the console input from the attempted installation, 2) shell
>> output from running R CMD check, and 3) my sessionInfo()
>>
>> Any help would be appreciated.
>>
>> Matt
>>
>> 1) Here is the result of attempted installation: (note: removing type =
>> "source" changes nothing):
>>
>> install.packages("rgeos", type = "source",
>>>
>> +         configure.args =
>> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",
>> +         repos = "https://cloud.r-project.org")
>> Installing package into ‘/home/msimpson/R/x86_64-pc-li
>> nux-gnu-library/3.3’
>> (as ‘lib’ is unspecified)
>> trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
>> Content type 'application/x-gzip' length 257486 bytes (251 KB)
>> ==================================================
>> downloaded 251 KB
>>
>> * installing *source* package ‘rgeos’ ...
>> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
>> configure: CC: /usr/bin/gcc -std=gnu99
>> configure: CXX: /usr/bin/g++
>> configure: rgeos: 0.3-23
>> checking for /usr/bin/svnversion... no
>> configure: svn revision: 546
>> configure: geos-config set to /group/stsn/shared_libs/geos/b
>> in/geos-config
>> checking geos-config exists... yes
>> checking geos-config executable... yes
>> checking geos-config usability... yes
>> configure: GEOS version: 3.7.0dev
>> checking geos version at least 3.2.0... yes
>> checking geos-config clibs... yes
>> checking for gcc... /usr/bin/gcc -std=gnu99
>> 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... configure: error: in
>> `/tmp/RtmppP5J2b/R.INSTALL236bb22fea27c/rgeos':
>> configure: error: cannot run C compiled programs.
>> If you meant to cross compile, use `--host'.
>> See `config.log' for more details
>> ERROR: configuration failed for package ‘rgeos’
>> * removing ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3/rgeos’
>>
>> The downloaded source packages are in
>>        ‘/tmp/RtmpwkU04N/downloaded_packages’
>> Warning message:
>> In install.packages("rgeos", type = "source", configure.args =
>> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",  :
>>  installation of package ‘rgeos’ had non-zero exit status
>>
>> 2) Here's the result from running R CMD check:
>>
>> R CMD check
>> --install-args='--configure-args=--with-geos-config=/group/
>> stsn/shared_libs/geos/bin/geos-config'
>> rgeos_0.3-23.tar.gz
>> * using log directory ‘/group/stsn/src/test/rgeos.Rcheck’
>> * using R version 3.3.1 (2016-06-21)
>> * using platform: x86_64-pc-linux-gnu (64-bit)
>> * using session charset: UTF-8
>> * checking for file ‘rgeos/DESCRIPTION’ ... OK
>> * this is package ‘rgeos’ version ‘0.3-23’
>> * checking package namespace information ... OK
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking if there is a namespace ... OK
>> * checking for executable files ... OK
>> * checking for hidden files and directories ... OK
>> * checking for portable file names ... OK
>> * checking for sufficient/correct file permissions ... OK
>> * checking whether package ‘rgeos’ can be installed ... ERROR
>> Installation failed.
>> See ‘/group/stsn/src/test/rgeos.Rcheck/00install.out’ for details.
>> * DONE
>>
>> Status: 1 ERROR
>> See
>>  ‘/group/stsn/src/test/rgeos.Rcheck/00check.log’
>> for details.
>>
>> cat /group/stsn/src/test/rgeos.Rcheck/00install.out
>> * installing *source* package ‘rgeos’ ...
>> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
>> configure: CC: /usr/bin/gcc -std=gnu99
>> configure: CXX: /usr/bin/g++
>> configure: rgeos: 0.3-23
>> checking for /usr/bin/svnversion... no
>> configure: svn revision: 546
>> configure: geos-config set to /group/stsn/shared_libs/geos/b
>> in/geos-config
>> checking geos-config exists... yes
>> checking geos-config executable... yes
>> checking geos-config usability... yes
>> configure: GEOS version: 3.7.0dev
>> checking geos version at least 3.2.0... yes
>> checking geos-config clibs... yes
>> checking for gcc... /usr/bin/gcc -std=gnu99
>> 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... configure: error: in
>> `/group/stsn/src/test/rgeos.Rcheck/00_pkg_src/rgeos':
>> configure: error: cannot run C compiled programs.
>> If you meant to cross compile, use `--host'.
>> See `config.log' for more details
>> ERROR: configuration failed for package ‘rgeos’
>> * removing ‘/group/stsn/src/test/rgeos.Rcheck/rgeos’
>>
>> 3) And here's my session info:
>>
>> sessionInfo()
>> R version 3.3.1 (2016-06-21)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> --
> 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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Re: Issues installing rgeos on linux server

edzer
Would it be helpful if we kept a docker file somewhere, that shows how
to install rgeos/rgdal with custom installed libraries? For sf, I
maintain one here:

https://github.com/edzer/sfr/tree/master/inst/docker/custom

On 20/06/17 22:35, Matthew Simpson wrote:

> Thank you, this was very helpful. It turned out the issue was that I was
> using the development version - I had cloned the github repository and
> installed from there. Downloading the tarball for the latest stable release
> solved the problem. I went ahead and did the same thing for GDAL and proj.4
> and reinstalled rgdal just to be safe. And sure enough, before reinstalling
> rgdal was complaining about missing proj_defs.dat, even though it existed
> in the proj.4/share folder. But now it's working just fine.
>
> For posterity, my full commands to get GEOS, GDAL, proj.4, rgdal, and rgeos
> installed from source on a linux server (CentOS 7.3.1611) are below.
>
> cd /path/to/src/geos/
> wget http://download.osgeo.org/geos/geos-3.6.1.tar.bz2
> tar -vxjf geos-3.6.1.tar.bz2
> cd geos-3.6.1
> ./configure --prefix=/path/to/install/geos
> make
> make check
> make install
>
> cd /path/to/src/gdal
> wget http://download.osgeo.org/gdal/2.2.0/gdal-2.2.0.tar.gz
> tar -xvzf gdal-2.2.0.tar.gz
> cd gdal-2.2.0
> ./autogen.sh
> ./configure --prefix=/path/to/install/gdal
> make
> ## there is no make check
> make install
>
> cd /path/to/src/proj.4/
> wget http://download.osgeo.org/proj/proj-4.9.3.tar.gz
> tar -xvzf proj-4.9.3.tar.gz
> cd proj-4.9.3
> ./configure --prefix=/path/to/install/proj.4
> make
> make check
> make install
>
> echo 'export
> PATH=/path/to/install/gdal/bin:/path/to/install/proj.4/bin:/path/to/install/geos/bin:$PATH'
>>> ~/.bash_profile
> echo 'export
> LD_LIBRARY_PATH=/path/to/install/gdal/lib:/path/to/install/proj.4/lib:/path/to/install/geos/lib:$LD_LIBRARY_PATH'
>>> ~/.bash_profile
> . ~/.bash_profile
>
> ## in R run:
> ## need this installed from source to prevent some compiler issues that
> would cause R to segfault if rgdal was loaded and you tried to install
> certain packages
> install.packages("Rcpp", type = "source", repos = "
> https://cloud.r-project.org")
>
> install.packages("rgdal", type = "source", repos = "
> https://cloud.r-project.org",
> configure.args = "--with-proj-include=/path/to/install/proj.4/include
> --with-proj-lib=/path/to/install/proj.4/lib
> --with-proj-share=/path/to/install/proj.4/share/proj
> --with-gdal-config=/path/to/install/gdal/bin/gdal-config")
>
> install.packages("rgeos", type = "source", repos = "
> https://cloud.r-project.org",
>          configure.args =
> "--with-geos-config=/path/to/install/geos/bin/geos-config")
>
>
> Note that --with-proj-share=/path/to/install/proj.4/share did NOT work.
>
>
> On Tue, Jun 20, 2017 at 4:26 AM, Roger Bivand <[hidden email]> wrote:
>
>> On Tue, 20 Jun 2017, Matthew Simpson wrote:
>>
>> I'm installing some spatial packages on a linux server and due to
>>> university constraints, cannot install anything using a package manager.
>>> I've managed to get rgdal installed successfully, but rgeos is causing
>>> problems.
>>>
>>> I've installed the geos library already, but when I attempt to install
>>> rgeos within R, it complains that that it cannot run C compiled programs.
>>>
>>
>> Could you please say how you installed GEOS? Could you try out geos-config
>> with each of the settings? Do you need 3.7.0dev (I haven't tried this as a
>> source of difficulty as it seems implausible, but neither rgeos nor sf need
>> bleeding edge functionality from GEOS)? Could you try to install sf from
>> source (it also uses GEOS)? Is this the GEOS geos-config -m library bug
>> (probably not)? Unpacking rgeos, running ./configure in the package root, I
>> see (Fedora 25, R 3.4.0):
>>
>> $ ./configure
>> configure: CC: gcc
>> configure: CXX: g++
>> configure: rgeos: 0.3-23
>> checking for /usr/bin/svnversion... yes
>> configure: svn revision: 547
>> checking for geos-config... /usr/local/bin/geos-config
>> checking geos-config usability... yes
>> configure: GEOS version: 3.6.1
>> checking geos version at least 3.2.0... yes
>> checking geos-config clibs... yes
>> checking for gcc... 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 gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -E
>> checking for grep that handles long lines and -e... /usr/bin/grep
>> checking for egrep... /usr/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 geos_c.h usability... yes
>> checking geos_c.h presence... yes
>> checking for geos_c.h... yes
>> checking geos: linking with libgeos_c... yes
>> configure: PKG_CPPFLAGS:  -I/usr/local/include
>> configure: PKG_LIBS:  -L/usr/local/lib -lgeos -L/usr/local/lib -lgeos_c
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>>
>> but you fail about half-way down at the standard croos-compilation test.
>> For rgdal/configure - you said your rgdal install on the same system
>> succeeded, I see:
>>
>> ...
>> checking for gcc... 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 gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -E
>> ...
>>
>> What do you see (just running ./configure in the package root)?
>>
>> Roger
>>
>>
>>> I've also tried downloading the tarball myself and running R CMD check,
>>> and
>>> it gives me the same complaint.
>>>
>>> I've successfully reinstalled Rcpp from source, but that seemed to do
>>> nothing.
>>>
>>> Below is: 1) the console input from the attempted installation, 2) shell
>>> output from running R CMD check, and 3) my sessionInfo()
>>>
>>> Any help would be appreciated.
>>>
>>> Matt
>>>
>>> 1) Here is the result of attempted installation: (note: removing type =
>>> "source" changes nothing):
>>>
>>> install.packages("rgeos", type = "source",
>>>>
>>> +         configure.args =
>>> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",
>>> +         repos = "https://cloud.r-project.org")
>>> Installing package into ‘/home/msimpson/R/x86_64-pc-li
>>> nux-gnu-library/3.3’
>>> (as ‘lib’ is unspecified)
>>> trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
>>> Content type 'application/x-gzip' length 257486 bytes (251 KB)
>>> ==================================================
>>> downloaded 251 KB
>>>
>>> * installing *source* package ‘rgeos’ ...
>>> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
>>> configure: CC: /usr/bin/gcc -std=gnu99
>>> configure: CXX: /usr/bin/g++
>>> configure: rgeos: 0.3-23
>>> checking for /usr/bin/svnversion... no
>>> configure: svn revision: 546
>>> configure: geos-config set to /group/stsn/shared_libs/geos/b
>>> in/geos-config
>>> checking geos-config exists... yes
>>> checking geos-config executable... yes
>>> checking geos-config usability... yes
>>> configure: GEOS version: 3.7.0dev
>>> checking geos version at least 3.2.0... yes
>>> checking geos-config clibs... yes
>>> checking for gcc... /usr/bin/gcc -std=gnu99
>>> 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... configure: error: in
>>> `/tmp/RtmppP5J2b/R.INSTALL236bb22fea27c/rgeos':
>>> configure: error: cannot run C compiled programs.
>>> If you meant to cross compile, use `--host'.
>>> See `config.log' for more details
>>> ERROR: configuration failed for package ‘rgeos’
>>> * removing ‘/home/msimpson/R/x86_64-pc-linux-gnu-library/3.3/rgeos’
>>>
>>> The downloaded source packages are in
>>>        ‘/tmp/RtmpwkU04N/downloaded_packages’
>>> Warning message:
>>> In install.packages("rgeos", type = "source", configure.args =
>>> "--with-geos-config=/group/stsn/shared_libs/geos/bin/geos-config",  :
>>>  installation of package ‘rgeos’ had non-zero exit status
>>>
>>> 2) Here's the result from running R CMD check:
>>>
>>> R CMD check
>>> --install-args='--configure-args=--with-geos-config=/group/
>>> stsn/shared_libs/geos/bin/geos-config'
>>> rgeos_0.3-23.tar.gz
>>> * using log directory ‘/group/stsn/src/test/rgeos.Rcheck’
>>> * using R version 3.3.1 (2016-06-21)
>>> * using platform: x86_64-pc-linux-gnu (64-bit)
>>> * using session charset: UTF-8
>>> * checking for file ‘rgeos/DESCRIPTION’ ... OK
>>> * this is package ‘rgeos’ version ‘0.3-23’
>>> * checking package namespace information ... OK
>>> * checking package dependencies ... OK
>>> * checking if this is a source package ... OK
>>> * checking if there is a namespace ... OK
>>> * checking for executable files ... OK
>>> * checking for hidden files and directories ... OK
>>> * checking for portable file names ... OK
>>> * checking for sufficient/correct file permissions ... OK
>>> * checking whether package ‘rgeos’ can be installed ... ERROR
>>> Installation failed.
>>> See ‘/group/stsn/src/test/rgeos.Rcheck/00install.out’ for details.
>>> * DONE
>>>
>>> Status: 1 ERROR
>>> See
>>>  ‘/group/stsn/src/test/rgeos.Rcheck/00check.log’
>>> for details.
>>>
>>> cat /group/stsn/src/test/rgeos.Rcheck/00install.out
>>> * installing *source* package ‘rgeos’ ...
>>> ** package ‘rgeos’ successfully unpacked and MD5 sums checked
>>> configure: CC: /usr/bin/gcc -std=gnu99
>>> configure: CXX: /usr/bin/g++
>>> configure: rgeos: 0.3-23
>>> checking for /usr/bin/svnversion... no
>>> configure: svn revision: 546
>>> configure: geos-config set to /group/stsn/shared_libs/geos/b
>>> in/geos-config
>>> checking geos-config exists... yes
>>> checking geos-config executable... yes
>>> checking geos-config usability... yes
>>> configure: GEOS version: 3.7.0dev
>>> checking geos version at least 3.2.0... yes
>>> checking geos-config clibs... yes
>>> checking for gcc... /usr/bin/gcc -std=gnu99
>>> 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... configure: error: in
>>> `/group/stsn/src/test/rgeos.Rcheck/00_pkg_src/rgeos':
>>> configure: error: cannot run C compiled programs.
>>> If you meant to cross compile, use `--host'.
>>> See `config.log' for more details
>>> ERROR: configuration failed for package ‘rgeos’
>>> * removing ‘/group/stsn/src/test/rgeos.Rcheck/rgeos’
>>>
>>> 3) And here's my session info:
>>>
>>> sessionInfo()
>>> R version 3.3.1 (2016-06-21)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: CentOS Linux 7 (Core)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> 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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Edzer Pebesma
Institute for Geoinformatics  (ifgi),  University of Münster
Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081
Journal of Statistical Software:   http://www.jstatsoft.org/
Computers & Geosciences:   http://elsevier.com/locate/cageo/


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