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

Uwe Ligges Mon, 17 May 2010 01:40:22 -0700


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 packagesunder the old R version, then update.packages(checkBuilt=TRUE) shouldupdate 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
#02-01 Singapore 138672
DID : 6478 8671
Fax : 6478 9058
email: ta...@gis.a-star.edu.sg
  
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-----Original Message-----
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Friday, May 14, 2010 3:09 PM
To: Padma TAN
Cc: r-h...@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Really, can't you use a recent version of R (2.9.2 is somewhat outdated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"

[r...@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"<lig...@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

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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


______________________________________________
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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.


______________________________________________
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and provide commented, minimal, self-contained, reproducible code.

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

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