Re: [R] Compiling R with --enable-R-shlib for rpy2 error
Thanks for the help! :)
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
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:lig...@statistik.tu-dortmund.de]
Sent: Monday, May 17, 2010 4:38 PM
To: Padma TAN
Cc: r-h...@r-project.org.
Subject: Re: [R] Compiling R with --enable-R-shlib for rpy2 error
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
> #02-01 Singapore 138672
> DID : 6478 8671
> Fax : 6478 9058
> email: ta...@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: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 Really, can't you use a recent version of R (2.9.2 is somewhat outdated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
>> [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)
>> Fi
Re: [R] 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: ta...@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: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
> [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" 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
>>
Re: [R] Compiling R with --enable-R-shlib for rpy2 error
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
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
[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" 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@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
[[alternative HTML version deleted]]
__
R-help@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.
[R] Compiling R with --enable-R-shlib for rpy2 error
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@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.
