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Dear R users,<br>
<br>
I am having immense trouble trying to install the rgeos package on a
<br>
Linux cluster. I have installed geos locally in the directory
/home-link/epaiv01/system.<br>
<br>
The command <br>
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"))<br>
<br>
fails with the complaint:<br>
checking for C compiler default output file name... configure:
error: C compiler cannot create executables<br>
See `config.log' for more details.<br>
ERROR: configuration failed for package ârgeosâ<br>
* removing
â/lustre/home/zdv/ep/epaiv01/R/x86_64-unknown-linux-gnu-library/2.15/rgeosâ<br>
<br>
Oddly, if I get <b>into</b> the rgeos directory after unpacking it,
and run:<br>
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<br>
<br>
the configure phase passes normally. I am attaching the two log
files,<br>
which are identical until the command :<br>
<br>
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<br>
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<br>
<br>
which in the failed configure complains that:<br>
<br>
/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> ><br>
(std::basic_ostream<char, std::char_traits<char> >&,
char const*, <a class="moz-txt-link-abbreviated" href="mailto:long)@GLIBCXX_3.4.9">long)@GLIBCXX_3.4.9</a>'<br>
/home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference
to `std::_List_node_base::_M_unhook()@GLIBCXX_3.4.14'<br>
/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>
>::_<br>
M_insert<void const*>(void <a class="moz-txt-link-abbreviated" href="mailto:const*)@GLIBCXX_3.4.9">const*)@GLIBCXX_3.4.9</a>'<br>
/home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference
to `std::ctype<char>::_M_widen_init() <a class="moz-txt-link-abbreviated" href="mailto:const@GLIBCXX_3.4.11">const@GLIBCXX_3.4.11</a>'<br>
/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>
>::_<br>
M_insert<unsigned long>(unsigned <a class="moz-txt-link-abbreviated" href="mailto:long)@GLIBCXX_3.4.9">long)@GLIBCXX_3.4.9</a>'<br>
/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>
>::_<br>
M_insert<double>(<a class="moz-txt-link-abbreviated" href="mailto:double)@GLIBCXX_3.4.9">double)@GLIBCXX_3.4.9</a>'<br>
/home-link/epaiv01/system/usr/lib64/libgeos.so: undefined reference
to
`std::_List_node_base::_M_hook(<a class="moz-txt-link-abbreviated" href="mailto:std::_List_node_base*)@GLIBCXX_3.4.14">std::_List_node_base*)@GLIBCXX_3.4.14</a>'<br>
<br>
<br>
I am really at a loss. I have no clue whatsoever what to try any
further.<br>
Any suggestions will be appreciated.<br>
Best regards,<br>
<br>
<pre class="moz-signature" cols="72">--
Dr. Martin Ivanov
Eberhard-Karls-Universität Tübingen
Mathematisch-Naturwissenschaftliche Fakultät
Fachbereich Geowissenschaften
Water & Earth System Science (WESS)
Keplerstraße 17, 72074 Tübingen, Deutschland
Tel. +4970712975023</pre>
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