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

[Padma TAN]

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?


Regards,
Padma Tan

Genome Institute of Singapore
60 Biopolis Street, Genome
#02-01 Singapore 138672
DID : 6478 8671
Fax : 6478 9058
email: tanwp at gis.a-star.edu.sg
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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Really, can't you use a recent version of R (2.9.2 is somewhat outdated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
>
>
>