Compiling R with --enable-R-shlib for rpy2 error
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 -------------------------------------------------------------------------------------------------------------------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ---------------------------------------------------------------------------------------------------------------------------------------------------------- -----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 Really, can't you use a recent version of R (2.9.2 is somewhat outdated now)?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