[R-sig-Geo] Issues installing rgeos on linux server
Matthew Simpson
themattsimpson at gmail.com
Tue Jun 20 22:35:35 CEST 2017
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 <Roger.Bivand at nhh.no> 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
>>
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>>
>> _______________________________________________
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>> R-sig-Geo at r-project.org
>> 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: Roger.Bivand at nhh.no
> 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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