[R-sig-Geo] cannot install rgeos

[Martin Ivanov]

Dear Prof. Pebesma,

sp and proj4 install just fine. I am having trouble with rgeos and rgdal.
I try to install rgdal with:

  install.packages(pkgs="rgdal", 
configure.args=c("LDFLAGS=-L/home-link/epaiv01/system/usr/lib64","PKG_CPPFLAGS=-I/home-link/epaiv01/system/usr/include", 
"PKG_LIBS=-L/home-link/epaiv01/system/usr/lib64", 
"--with-gdal-config=/home-link/epaiv01/system/usr/bin/gdal-config", 
"--with-proj-lib=/home-link/epaiv01/system/usr/lib64", 
"--with-proj-include=/home-link/epaiv01/system/usr/include"), type="source")

it seems to compile ok, but at the testing whether the package can be 
loaded it complains:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object 
'/lustre/home/zdv/ep/epaiv01/R/x86_64-unknown-linux-gnu-library/2.15/rgdal/libs/rgdal.so':
   /usr/java/default/jre/../lib/amd64/libstdc++.so.6: version 
`GLIBCXX_3.4.14' not found (required by 
/home-link/epaiv01/system/usr/lib64/libgdal.so.1)
Error: loading failed
Execution halted
ERROR: loading failed
* removing 
â/lustre/home/zdv/ep/epaiv01/R/x86_64-unknown-linux-gnu-library/2.15/rgdalâ

Is it possible that the compilation within R uses different compiler 
than the one I loaded in the
bash environment with:
module load compiler/gnu/4.5 ?
It seems to me that it is can be the case. How can I tell R to use 
exactly the gnu/4.5 compiler
and not something else?

Best regards,

Martin


On 08/18/2012 05:11 PM, Edzer Pebesma wrote:
> Hi,
>
> To me, this looks like an error in your gcc setup. Have you searched for
> the error message you get? Do other packages, such as sp, install fine?
>
> On 08/18/2012 04:06 PM, Martin Ivanov wrote:
>> Dear R users,
>>
>> I am having immense trouble trying to install the rgeos package on a
>> Linux cluster. I have installed geos locally in the directory
>> /home-link/epaiv01/system.
>>
>> The command
>> install.packages(pkgs="rgeos",
>> configure.args=c("LDFLAGS=-L/home-link/epaiv01/system/usr/lib64","PKG_CPPFLAGS=-I/home-link/epaiv01/system/usr/include",
>> "PKG_LIBS=-L/home-link/epaiv01/system/usr/lib64",
>> "--with-geos-config=/home-link/epaiv01/system/usr/bin/geos-config"))
>>
>> fails with the complaint:
>> checking for C compiler default output file name... configure: error: C
>> compiler cannot create executables
>> See `config.log' for more details.
>> ERROR: configuration failed for package ârgeosâ
>> * removing
>> â/lustre/home/zdv/ep/epaiv01/R/x86_64-unknown-linux-gnu-library/2.15/rgeosâ
>>
>> Oddly, if I get *into* the rgeos directory after unpacking it, and run:
>> LDFLAGS=-L/home-link/epaiv01/system/usr/lib64
>> PKG_CPPFLAGS=-I/home-link/epaiv01/system/usr/include
>> PKG_LIBS=-L/home-link/epaiv01/system/usr/lib64 ./configure
>> --with-geos-config=/home-link/epaiv01/system/usr/bin/geos-config
>>
>> the configure phase passes normally. I am attaching the two log files,
>> which are identical until the command :
>>
>> configure:1761: gcc -std=gnu99 -march=core2 -O3 -I/usr/local/include
>> -I/home-link/epaiv01/system/usr/include
>> -I/home-link/epaiv01/system/usr/include -L/home-link/epaiv01/syste
>> m/usr/lib64 conftest.c  -L/home-link/epaiv01/system/usr/lib64
>> -L/home-link/epaiv01/system/usr/lib64 -lgeos
>> -L/home-link/epaiv01/system/usr/lib64 -lgeos_c >&5
>>
>> which in the failed configure complains that:
>>
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::basic_ostream<char, std::char_traits<char> >&
>> std::__ostream_insert<char, std::char_traits<char> >
>> (std::basic_ostream<char, std::char_traits<char> >&, char const*,
>> long)@GLIBCXX_3.4.9'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::_List_node_base::_M_unhook()@GLIBCXX_3.4.14'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::basic_ostream<char, std::char_traits<char> >&
>> std::basic_ostream<char, std::char_traits<char> >::_
>> M_insert<void const*>(void const*)@GLIBCXX_3.4.9'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::ctype<char>::_M_widen_init() const at GLIBCXX_3.4.11'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::basic_ostream<char, std::char_traits<char> >&
>> std::basic_ostream<char, std::char_traits<char> >::_
>> M_insert<unsigned long>(unsigned long)@GLIBCXX_3.4.9'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::basic_ostream<char, std::char_traits<char> >&
>> std::basic_ostream<char, std::char_traits<char> >::_
>> M_insert<double>(double)@GLIBCXX_3.4.9'
>> /home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference to
>> `std::_List_node_base::_M_hook(std::_List_node_base*)@GLIBCXX_3.4.14'
>>
>>
>> I am really at a loss. I have no clue whatsoever what to try any further.
>> Any suggestions will be appreciated.
>> Best regards,
>>
>> -- 
>> Dr. Martin Ivanov
>> Eberhard-Karls-Universität Tübingen
>> Mathematisch-Naturwissenschaftliche Fakultät
>> Fachbereich Geowissenschaften
>> Water & Earth System Science (WESS)
>> Keplerstraße 17, 72074 Tübingen, Deutschland
>> Tel. +4970712975023
>>
>>
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>


-- 
Dr. Martin Ivanov
Eberhard-Karls-Universität Tübingen
Mathematisch-Naturwissenschaftliche Fakultät
Fachbereich Geowissenschaften
Water & Earth System Science (WESS)
Keplerstraße 17, 72074 Tübingen, Deutschland
Tel. +4970712975023