[R] Compiling R with --enable-R-shlib for rpy2 error

[Uwe Ligges]

On 17.05.2010 05:22, Padma TAN wrote:
> Hi,
>
> Thanks! :)
>
> I'll install the newer version of R. However do I have to recompile all the modules that I did for my previous version of R?



If you use the same library (or a copy of it) you used for packages 
under the old R version, then update.packages(checkBuilt=TRUE) should 
update all packages that need recompilation for you.

For details, please see the R Installation and Administration manual.

Best wishes,
Uwe Ligges




>
> Regards,
> Padma Tan
>
> Genome Institute of Singapore
> 60 Biopolis Street, Genome
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>
> -----Original Message-----
> From: Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de]
> Sent: Friday, May 14, 2010 3:09 PM
> To: Padma TAN
> Cc: r-help at R-project.org.
> Subject: Re: [R] Compiling R with --enable-R-shlib for rpy2 error
>
>
>
> On 14.05.2010 05:07, Padma TAN wrote:
>> Hi,
>>
>> Thanks for the reply!
>>
>> I am not sure if I did correctly. Now I configure with the following.
>>
>> ./configure --prefix=/usr/local/R/R-2.9.2 --with-gnu-ld --with-cairo --with-x --enable-R-fPIC
>
>
> Then you forgot --enable-R-shlib if you need it and I cannot find (in
> recent R) a hint that "--enable-R-fPIC" is a supported feature.
> Really, can't you use a recent version of R (2.9.2 is somewhat outdated
> now)?
>
>
> Uwe Ligges
>
>
>> Make and make install with no errors. However when I install rpy2, it states that "R was not built as a library"
>>
>> [root at plap03 rpy2-2.1.1]# python setup.py install
>> running install
>> running build
>> running build_py
>> running build_ext
>> R was not built as a library
>> Traceback (most recent call last):
>>     File "setup.py", line 302, in<module>
>>       [os.path.join('doc', 'source', 'rpy2_logo.png')])]
>>     File "/usr/local/python2.6/lib/python2.6/distutils/core.py", line 152, in setup
>>       dist.run_commands()
>>     File "/usr/local/python2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands
>>       self.run_command(cmd)
>>     File "/usr/local/python2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
>>       cmd_obj.run()
>>     File "/usr/local/python2.6/lib/python2.6/distutils/command/install.py", line 577, in run
>>       self.run_command('build')
>>     File "/usr/local/python2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
>>       self.distribution.run_command(command)
>>     File "/usr/local/python2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
>>       cmd_obj.run()
>>     File "/usr/local/python2.6/lib/python2.6/distutils/command/build.py", line 134, in run
>>       self.run_command(cmd_name)
>>     File "/usr/local/python2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
>>       self.distribution.run_command(command)
>>     File "/usr/local/python2.6/lib/python2.6/distutils/dist.py", line 994, in run_command
>>       cmd_obj.ensure_finalized()
>>     File "/usr/local/python2.6/lib/python2.6/distutils/cmd.py", line 117, in ensure_finalized
>>       self.finalize_options()
>>     File "setup.py", line 121, in finalize_options
>>       include_dirs = get_rconfig(r_home, '--cppflags')[0].split()
>>     File "setup.py", line 196, in get_rconfig
>>       raise Exception(cmd + '\nreturned\n' + rconfig)
>> Exception: "/usr/local/R/R-2.9.2/lib64/R/bin/R" CMD config --cppflags
>> returned
>>
>>
>> Thanks again :)
>>
>>
>>
>>
>> Regards,
>> Padma
>>
>> On 5/13/10 11:30 PM, "Uwe Ligges"<ligges at statistik.tu-dortmund.de>   wrote:
>>
>>
>>
>>
>> On 13.05.2010 11:45, Padma TAN wrote:
>>> Hi,
>>>
>>> I am trying to compile R with the command below in order to install rpy2.
>>>
>>> ./configure --prefix=/usr/local/R/R-2.9.2 --with-gnu-ld --with-cairo
>>> --with-x --enable-R-shlib
>>>
>>>
>>> However, error the I have gotten was:
>>> /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can
>>> not be used when making a shared object; recompile with -fPIC
>>> CConverters.o: could not read symbols: Bad value
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [libR.so] Error 1
>>>
>>> I don't really understand the error message. Is there anything I can change
>>> to compile properly so that I can install rpy2?
>>>
>>> Please help. Thanks in advance! :)
>>>
>>>
>>> Regards,
>>> Padma
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>> Note the last sentence above and try again, i.e. use a recent version of
>> R and report the version number as well as the OS and the compilers in use.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.