Hi Jessica,
There's no denying that linux is a steep learning curve, although I expect
that I would face similar problems were I to start working in earnest on
windows.
The problem here, I would expect, is that in a new shell your environment
variables are not set. You should add the lines
export RDBASE=opt/RDKit_2014_03_1/
export
LD_LIBRARY_PATH=opt/RDKit_2014_03_1/build/lib/:usr/local/src/boost_1_55_0/libs/
export PYTHONPATH=opt/RDKit_2014_03_1/
that you typed as part of the installation system, into your .bashrc so
that every time you start a new shell/terminal or login again they are set
afresh. Incidentally, I am surprised that these aren't
export RDBASE=/opt/RDKit_2014_03_1/
export
LD_LIBRARY_PATH=/opt/RDKit_2014_03_1/build/lib/:usr/local/src/boost_1_55_0/libs/
export PYTHONPATH=/opt/RDKit_2014_03_1/
i.e. with a '=/opt' rather than '=opt' since I assume you installed RDKit
into /opt.
You might at some point want to install the 'environment-modules' package
http://modules.sourceforge.net/ which makes this sort of thing much easier,
and allows convenient switching between different versions of the same
project. This is not a standard package on ubuntu, apparently.
Regards,
Dave
On Wed, Jul 30, 2014 at 4:02 PM, Jessica Krause <jessica.kra...@tu-bs.de>
wrote:
> Dear all,
>
> after succeeding some minutes before with installing RDKit I have now
> trouble again.
>
> I have a situation where I need to reinstall RdKit (build from source
> http://www.blopig.com/blog/2013/02/how-to-install-rdkit-on-ubuntu-12-04/)
> in order to work with the python module.
>
> I get following errors when I start with python in a new terminal.
>
> >>> from rdkit import Chem
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ImportError: No module named rdkit
>
> Note:
>
> the error doesn't occur when I build from source again and work in the
> same terminal. Does it mean that I have to build from source and ctest
> everytime when I start a terminal or the PC?
>
> Thanks in advance.
>
> Best Regards,
>
> Jessica Krause.
>
>
>
>
>
>
>
>
>
>
>
> Dear Jean-Paul,
>
> I would like to thank you for your help. Now I have installed the
> RDKit_2014_03_1 on Ubuntu 14.04 with the link you mentioned above. Thanks a
> lot! It saved me time with working more hours on installing RDKit on
> Ubuntu. I have to mention that I reinstalled Ubuntu again to avoid the
> errors I got all the time before. I am new to working with Ubuntu and RDKit.
> Thanks again!
>
> Jessica
>
>
> On 26.07.2014 17:44, JP wrote:
>
> Not a direct solution to your problem, but have you tried the Ubuntu
> specific instructions at:
> http://www.blopig.com/blog/2013/02/how-to-install-rdkit-on-ubuntu-12-04/
>
> I have installed it successfully on 14.04.
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 24 July 2014 15:40, Jessica Krause <jessica.kra...@tu-bs.de> wrote:
>
>> Dear all,
>>
>> I tried to install RDKit 2014 on Ubuntu 14.04 but I did
>> not succeed!
>>
>>
>> While executing the make command in the RDKit_2014_03_1/build directory,
>> I recieved the following error:
>>
>> [ 0%] Built target inchi_support
>> [ 1%] Built target RDGeneral
>> [ 3%] Built target RDGeneral_static
>> [ 3%] Built target testDict
>> Linking CXX shared library ../../lib/libRDBoost.so
>> /usr/bin/ld: /usr/local/lib/libpython2.7.a(exceptions.o): relocation
>> R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared
>> object; recompile with -fPIC
>> /usr/local/lib/libpython2.7.a: error adding symbols: Bad value
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [lib/libRDBoost.so.1.2014.03.1] Error 1
>> make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>>
>>
>> the environmental variables that I have used are:
>>
>> export RDBASE=opt/RDKit_2014_03_1/
>> export
>> LD_LIBRARY_PATH=opt/RDKit_2014_03_1/build/lib/:usr/local/src/boost_1_55_0/libs/
>> export PYTHONPATH=opt/RDKit_2014_03_1/
>>
>>
>> Please help me with this problem.
>>
>> Thanks in advance.
>>
>> Regards,
>> Jessica Krause
>>
>>
>>
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