I haven't tested this, but it should be something like:
r_exec = os.path.join(r_home, 'bin', 'R')
# Changed ---------------------------------------
import subprocess
rp = subprocess.check_output([r_exec, '--version'],
stderr=subprocess.STDOUT).splitlines()
rversion = rp[0]
#Twist if 'R RHOME' spits out a warning
if rversion.startswith("WARNING"):
rversion = rp[1]
# End of changed section -------------------
m = re.match('^R ([^ ]+) ([^ ]+) .+$', rversion)
...
Thomas
On 26 March 2012 07:57, Yuanda Zhu <jianjian.i...@gmail.com> wrote:
> Hi Thomas,
>
> Please excuse my limited knowledge. I do not quite know how to replace it.
> Could you please write the full syntax for me? By the way, is this a
> compatibility problem between Python 3.2.2 and rpy2?
>
> Many thanks,
>
> Y.Z.
> On Mon, Mar 26, 2012 at 5:02 AM, Thomas Kluyver <tak...@gmail.com> wrote:
>>
>> Hi Yuanda,
>>
>> You should edit setup.py to use subprocess.check_output() instead of
>> os.popen3(). Note that it's not a direct replacement - popen3 returns
>> a file-like object with a readline method; check_output() returns a
>> string (use s.splitlines() to make a list of lines).
>>
>> For reference, you can see the current code here:
>> https://bitbucket.org/lgautier/rpy2/src/f075a4291e9c/setup.py#cl-185
>>
>> Thomas
>>
>> On 25 March 2012 21:54, Yuanda Zhu <jianjian.i...@gmail.com> wrote:
>> > Hi Thomas,
>> >
>> > Here is the traceback:
>> >
>> > Traceback (most recent call last):
>> > File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 462,
>> > in
>> > <module>
>> > [os.path.join('doc', 'source', 'rpy2_logo.png')])],
>> > File "F:\Python32\lib\distutils\core.py", line 148, in setup
>> > dist.run_commands()
>> > File "F:\Python32\lib\distutils\dist.py", line 917, in run_commands
>> > self.run_command(cmd)
>> > File "F:\Python32\lib\distutils\dist.py", line 936, in run_command
>> > cmd_obj.run()
>> > File "F:\Python32\lib\distutils\command\install.py", line 569, in run
>> > self.run_command('build')
>> > File "F:\Python32\lib\distutils\cmd.py", line 313, in run_command
>> > self.distribution.run_command(command)
>> > File "F:\Python32\lib\distutils\dist.py", line 936, in run_command
>> > cmd_obj.run()
>> > File "F:\Python32\lib\distutils\command\build.py", line 126, in run
>> > self.run_command(cmd_name)
>> > File "F:\Python32\lib\distutils\cmd.py", line 313, in run_command
>> > self.distribution.run_command(command)
>> > File "F:\Python32\lib\distutils\dist.py", line 935, in run_command
>> > cmd_obj.ensure_finalized()
>> > File "F:\Python32\lib\distutils\cmd.py", line 107, in ensure_finalized
>> > self.finalize_options()
>> > File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 144,
>> > in
>> > finalize_options
>> > rversion = get_rversion(r_home)
>> > File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 180,
>> > in
>> > get_rversion
>> > rp = os.popen3('"'+r_exec+'" --version')[2]
>> > AttributeError: 'module' object has no attribute 'popen3'
>> >
>> > Please help me, thank you very much
>> >
>> > Y.Z.
>> >
>> > On Mon, Mar 26, 2012 at 4:24 AM, Yuanda Zhu <jianjian.i...@gmail.com>
>> > wrote:
>> >>
>> >> Hi Niek,
>> >>
>> >> Here is the Traceback
>> >>
>> >>
>> >> Traceback (most recent call last):
>> >> File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 462,
>> >> in
>> >> <module>
>> >> [os.path.join('doc', 'source', 'rpy2_logo.png')])],
>> >> File "F:\Python32\lib\distutils\core.py", line 148, in setup
>> >> dist.run_commands()
>> >> File "F:\Python32\lib\distutils\dist.py", line 917, in run_commands
>> >> self.run_command(cmd)
>> >> File "F:\Python32\lib\distutils\dist.py", line 936, in run_command
>> >> cmd_obj.run()
>> >> File "F:\Python32\lib\distutils\command\install.py", line 569, in run
>> >> self.run_command('build')
>> >> File "F:\Python32\lib\distutils\cmd.py", line 313, in run_command
>> >> self.distribution.run_command(command)
>> >> File "F:\Python32\lib\distutils\dist.py", line 936, in run_command
>> >> cmd_obj.run()
>> >> File "F:\Python32\lib\distutils\command\build.py", line 126, in run
>> >> self.run_command(cmd_name)
>> >> File "F:\Python32\lib\distutils\cmd.py", line 313, in run_command
>> >> self.distribution.run_command(command)
>> >> File "F:\Python32\lib\distutils\dist.py", line 935, in run_command
>> >> cmd_obj.ensure_finalized()
>> >> File "F:\Python32\lib\distutils\cmd.py", line 107, in
>> >> ensure_finalized
>> >> self.finalize_options()
>> >> File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 144,
>> >> in
>> >> finalize_options
>> >> rversion = get_rversion(r_home)
>> >> File "G:\Backup\Setup\Python\Packages\rpy2-2.2.5\setup.py", line 180,
>> >> in
>> >> get_rversion
>> >> rp = os.popen3('"'+r_exec+'" --version')[2]
>> >>
>> >> AttributeError: 'module' object has no attribute 'popen3'
>> >>
>> >>
>> >> Please help me fix this, many thanks.
>> >>
>> >> Y.Z.
>> >>
>> >>
>> >> On Mon, Mar 26, 2012 at 3:59 AM, Thomas Kluyver <tak...@gmail.com>
>> >> wrote:
>> >>>
>> >>> On 25 March 2012 20:17, Yuanda Zhu <jianjian.i...@gmail.com> wrote:
>> >>> > AttributeError:'module' object has no attribute 'popen3'
>> >>>
>> >>> Can you post the traceback that goes with this? It's most likely a bug
>> >>> somewhere, as popen3 calls should be replaced using the subprocess
>> >>> module (see
>> >>>
>> >>> http://docs.python.org/library/subprocess.html#replacing-os-popen-os-popen2-os-popen3).
>> >>>
>> >>> Thanks,
>> >>> Thomas
>> >>>
>> >>>
>> >>>
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>> >>
>> >
>> >
>> >
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