[Rpy] Errors in installing rpy2
Hi all,
I have been trying to install rpy2-2.5.2 on a high performance computer and
run into the following errors:
Traceback (most recent call last):
File "setup.py", line 275, in
ri_ext = getRinterface_ext()
File "setup.py", line 189, in getRinterface_ext
ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
File "setup.py", line 135, in cmd_config
output = output.strip()
AttributeError: 'list' object has no attribute 'strip'
The python version is python2.7. And the R version is R3.1.1.
Any suggestion is welcome.
Thanks a lot.
Best,
Xinxin
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Re: [Rpy] Errors in installing rpy2
Hi Laurent,
The newly released package still doesn't seem to work for me.
This time I ran into different errors.
Traceback (most recent call last):
File "setup.py", line 280, in
ri_ext = getRinterface_ext()
File "setup.py", line 190, in getRinterface_ext
ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
File "setup.py", line 134, in cmd_config
warnings.warning("R emitting a warning: %s" % output[0])
AttributeError: 'module' object has no attribute 'warning'
Thanks a lot.
Xinxin
On Sat, Dec 13, 2014 at 2:07 AM, Laurent Gautier wrote:
>
> rpy2-2.5.3 is now on Pypi. Try:
> pip install rpy2 --upgrade
>
> 2014-12-12 12:48 GMT-05:00 Ian York :
>
>> For what it's worth, I noted the same bug a couple weeks ago. In case
>> it didn't go through, I said:
>>
>> I have installed rpy2 on this machine in the past and had no problems,
>> but now I am unable to get rpy2 properly installed either using pip or
>> source. I'm running OSX 10.9.5 (Mavericks), and R version 3.1.1
>> (2014-07-10) -- "Sock it to Me" (Platform: x86_64-apple-darwin13.1.0
>> (64-bit)).
>>
>> Both source and pip show similar errors. For example, when I try
>>
>> pip install https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>
>> I get the following traceback:
>>
>> -
>>
>> Traceback (most recent call last):
>> File "", line 17, in
>> File
>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>> line 275, in
>> ri_ext = getRinterface_ext()
>> File
>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>> line 189, in getRinterface_ext
>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>> File
>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>> line 135, in cmd_config
>> output = output.strip()
>> AttributeError: 'list' object has no attribute 'strip'
>> -
>>
>> (I used https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>> because I was seeing a separate error before this, and while trying to
>> find a solution to that one I saw the suggestion to use
>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz. That
>> eliminated the previous error but brought in the "strip" error.)
>>
>> On trying to install from source (rpy2 2.5.1)
>>
>> I get a similar error:
>> -
>>
>> ~/Downloads/rpy2-2.5.1 > python setup.py build install
>> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
>> /Library/Frameworks/R.framework/Resources/bin/R CMD config --ldflags
>> Traceback (most recent call last):
>> File "setup.py", line 278, in
>> ri_ext = getRinterface_ext()
>> File "setup.py", line 192, in getRinterface_ext
>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>> File "setup.py", line 135, in cmd_config
>> output = output.strip()
>> AttributeError: 'list' object has no attribute 'strip'
>>
>> -
>>
>> I made a guess that the offending line should be output[0].strip() but
>> then I got the following error:
>>
>> -
>>
>> Traceback (most recent call last):
>> File "setup.py", line 280, in
>> ri_ext = getRinterface_ext()
>> File "setup.py", line 206, in getRinterface_ext
>> include_dirs.extend(args.I)
>> TypeError: 'NoneType' object is not iterable
>>
>> -
>>
>> Suggestions welcome.
>>
>> On Fri, Dec 12, 2014 at 12:33 PM, Laurent Gautier
>> wrote:
>> > This might be a genuine bug.
>> >
>> > I opened an issue:
>> >
>> https://bitbucket.org/lgautier/rpy2/issue/247/error-when-getting-the-r-configuration-and
>> >
>> > 2014-12-12 7:21 GMT-05:00 Laurent Gautier :
>> >>
>> >> Hi,
>> >>
>> >> This might be a bug in the install script. Consider opening an issue on
>> >> bitbucket.
>> >>
>> >> Thanks,
>> >>
>> >> Laurent
>> &g
Re: [Rpy] Errors in installing rpy2
Hi Lanrent,
Error report still exists.
Traceback (most recent call last):
File "setup.py", line 280, in
ri_ext = getRinterface_ext()
File "setup.py", line 202, in getRinterface_ext
include_dirs.extend(args.I)
TypeError: 'NoneType' object is not iterable
Thanks a lot.
Xinxin
On Sat, Dec 13, 2014 at 10:49 AM, Laurent Gautier
wrote:
>
> Typo in the fix.
>
> Try a snapshot from bitbucket:
>
> pip install https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>
>
> 2014-12-12 21:08 GMT-05:00 Xinxin Peng :
>
>> Hi Laurent,
>>
>> The newly released package still doesn't seem to work for me.
>> This time I ran into different errors.
>>
>> Traceback (most recent call last):
>> File "setup.py", line 280, in
>> ri_ext = getRinterface_ext()
>> File "setup.py", line 190, in getRinterface_ext
>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>> File "setup.py", line 134, in cmd_config
>> warnings.warning("R emitting a warning: %s" % output[0])
>> AttributeError: 'module' object has no attribute 'warning'
>>
>> Thanks a lot.
>> Xinxin
>>
>>
>> On Sat, Dec 13, 2014 at 2:07 AM, Laurent Gautier
>> wrote:
>>>
>>> rpy2-2.5.3 is now on Pypi. Try:
>>> pip install rpy2 --upgrade
>>>
>>> 2014-12-12 12:48 GMT-05:00 Ian York :
>>>
>>>> For what it's worth, I noted the same bug a couple weeks ago. In case
>>>> it didn't go through, I said:
>>>>
>>>> I have installed rpy2 on this machine in the past and had no problems,
>>>> but now I am unable to get rpy2 properly installed either using pip or
>>>> source. I'm running OSX 10.9.5 (Mavericks), and R version 3.1.1
>>>> (2014-07-10) -- "Sock it to Me" (Platform: x86_64-apple-darwin13.1.0
>>>> (64-bit)).
>>>>
>>>> Both source and pip show similar errors. For example, when I try
>>>>
>>>> pip install
>>>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>>
>>>> I get the following traceback:
>>>>
>>>> -
>>>>
>>>> Traceback (most recent call last):
>>>> File "", line 17, in
>>>> File
>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>> line 275, in
>>>> ri_ext = getRinterface_ext()
>>>> File
>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>> line 189, in getRinterface_ext
>>>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>>>> File
>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>> line 135, in cmd_config
>>>> output = output.strip()
>>>> AttributeError: 'list' object has no attribute 'strip'
>>>> -
>>>>
>>>> (I used https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>> because I was seeing a separate error before this, and while trying to
>>>> find a solution to that one I saw the suggestion to use
>>>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz. That
>>>> eliminated the previous error but brought in the "strip" error.)
>>>>
>>>> On trying to install from source (rpy2 2.5.1)
>>>>
>>>> I get a similar error:
>>>> -
>>>>
>>>> ~/Downloads/rpy2-2.5.1 > python setup.py build install
>>>> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
>>>> /Library/Frameworks/R.framework/Resources/bin/R CMD config --ldflags
>>>> Traceback (most recent call last):
>>>> File "setup.py", line 278, in
>>>> ri_ext = getRinterface_ext()
>>>> File "setup.py", line 192, in getRinterface_ext
>>>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>>>> File "setup.py", line 135, in cmd_config
>>>> output = output.strip()
>>>> AttributeError: 'list' object has no attribute 'strip'
>>>>
>>>> ---
Re: [Rpy] Errors in installing rpy2
Hi Laurent,
There are still errors in other place.
Traceback (most recent call last):
File "setup.py", line 283, in
ri_ext = getRinterface_ext()
File "setup.py", line 203, in getRinterface_ext
warnigs.warn('No include specified')
NameError: global name 'warnigs' is not defined
Thanks,
Xinxin
On Sat, Dec 13, 2014 at 11:54 AM, Laurent Gautier
wrote:
>
> That's an error in a different place. We are progressing
>
> Try again:
> pip install https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>
> 2014-12-12 22:15 GMT-05:00 Xinxin Peng :
>
>> Hi Lanrent,
>>
>> Error report still exists.
>>
>> Traceback (most recent call last):
>> File "setup.py", line 280, in
>> ri_ext = getRinterface_ext()
>> File "setup.py", line 202, in getRinterface_ext
>> include_dirs.extend(args.I)
>> TypeError: 'NoneType' object is not iterable
>>
>>
>> Thanks a lot.
>> Xinxin
>>
>> On Sat, Dec 13, 2014 at 10:49 AM, Laurent Gautier
>> wrote:
>>>
>>> Typo in the fix.
>>>
>>> Try a snapshot from bitbucket:
>>>
>>> pip install https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>
>>>
>>> 2014-12-12 21:08 GMT-05:00 Xinxin Peng :
>>>
>>>> Hi Laurent,
>>>>
>>>> The newly released package still doesn't seem to work for me.
>>>> This time I ran into different errors.
>>>>
>>>> Traceback (most recent call last):
>>>> File "setup.py", line 280, in
>>>> ri_ext = getRinterface_ext()
>>>> File "setup.py", line 190, in getRinterface_ext
>>>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>>>> File "setup.py", line 134, in cmd_config
>>>> warnings.warning("R emitting a warning: %s" % output[0])
>>>> AttributeError: 'module' object has no attribute 'warning'
>>>>
>>>> Thanks a lot.
>>>> Xinxin
>>>>
>>>>
>>>> On Sat, Dec 13, 2014 at 2:07 AM, Laurent Gautier
>>>> wrote:
>>>>>
>>>>> rpy2-2.5.3 is now on Pypi. Try:
>>>>> pip install rpy2 --upgrade
>>>>>
>>>>> 2014-12-12 12:48 GMT-05:00 Ian York :
>>>>>
>>>>>> For what it's worth, I noted the same bug a couple weeks ago. In case
>>>>>> it didn't go through, I said:
>>>>>>
>>>>>> I have installed rpy2 on this machine in the past and had no problems,
>>>>>> but now I am unable to get rpy2 properly installed either using pip or
>>>>>> source. I'm running OSX 10.9.5 (Mavericks), and R version 3.1.1
>>>>>> (2014-07-10) -- "Sock it to Me" (Platform: x86_64-apple-darwin13.1.0
>>>>>> (64-bit)).
>>>>>>
>>>>>> Both source and pip show similar errors. For example, when I try
>>>>>>
>>>>>> pip install
>>>>>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>>>>
>>>>>> I get the following traceback:
>>>>>>
>>>>>> -
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>> File "", line 17, in
>>>>>> File
>>>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>>>> line 275, in
>>>>>> ri_ext = getRinterface_ext()
>>>>>> File
>>>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>>>> line 189, in getRinterface_ext
>>>>>> ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
>>>>>> File
>>>>>> "/var/folders/7h/kxq84vrx6cq4mh8ycssjhzc4y2bpx0/T/pip-M_AK2m-build/setup.py",
>>>>>> line 135, in cmd_config
>>>>>> output = output.strip()
>>>>>> AttributeError: 'list' object has no attribute 'strip'
>>>>>> -
>>>>>>
>>>>>> (I used https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>>&
Re: [Rpy] Errors in installing rpy2
Hi Laurent,
I am using gcc rather than clang.
I have corrected the typo in setup.py. This time I can run more installing
steps.
However, the installation was interrupted at the gcc compiling stage.
It seems that the problem is due to the unsuitable string after the
paramter -I.
=
gcc ... - I / b i n / R / l i b 6 4 / R / i n c l u d e
gcc: I: No such file or directory
gcc: b: No such file or directory
gcc: i: No such file or directory
gcc: n: No such file or directory
gcc: R: No such file or directory
gcc: l: No such file or directory
gcc: i: No such file or directory
gcc: b: No such file or directory
gcc: 6: No such file or directory
gcc: 4: No such file or directory
gcc: R: No such file or directory
gcc: i: No such file or directory
gcc: n: No such file or directory
gcc: c: No such file or directory
gcc: l: No such file or directory
gcc: u: No such file or directory
gcc: d: No such file or directory
gcc: e: No such file or directory
gcc: cannot specify -o with -c or -S with multiple files
error: command 'gcc' failed with exit status 1
=
Thanks,
Xinxin
On Sun, Dec 14, 2014 at 9:38 AM, Xinxin Peng wrote:
>
> Hi Laurent,
>
> I am using gcc rather than clang.
>
> I have corrected the typo in setup.py. This time I can run more installing
> steps.
> However, the installation was interrupted at the gcc compiling stage.
>
> It seems that the problem is due to the unsuitable string after the
> paramter -I.
>
> =
> gcc ... - I / b i n / R / l i b 6 4 / R / i n c l u d e
>
> gcc: I: No such file or directory
> gcc: b: No such file or directory
> gcc: i: No such file or directory
> gcc: n: No such file or directory
> gcc: R: No such file or directory
> gcc: l: No such file or directory
> gcc: i: No such file or directory
> gcc: b: No such file or directory
> gcc: 6: No such file or directory
> gcc: 4: No such file or directory
> gcc: R: No such file or directory
> gcc: i: No such file or directory
> gcc: n: No such file or directory
> gcc: c: No such file or directory
> gcc: l: No such file or directory
> gcc: u: No such file or directory
> gcc: d: No such file or directory
> gcc: e: No such file or directory
> gcc: cannot specify -o with -c or -S with multiple files
> error: command 'gcc' failed with exit status 1
> =
>
> Thanks,
> Xinxin
>
>
> On Sun, Dec 14, 2014 at 2:59 AM, Laurent Gautier
> wrote:
>>
>> Typo: warnigs -> warnings
>> Try again.
>>
>> Are you using clang rather than gcc by the way ?
>>
>> 2014-12-13 0:19 GMT-05:00 Xinxin Peng :
>>
>>> Hi Laurent,
>>>
>>> There are still errors in other place.
>>>
>>>
>>> Traceback (most recent call last):
>>> File "setup.py", line 283, in
>>> ri_ext = getRinterface_ext()
>>> File "setup.py", line 203, in getRinterface_ext
>>> warnigs.warn('No include specified')
>>> NameError: global name 'warnigs' is not defined
>>>
>>>
>>> Thanks,
>>> Xinxin
>>>
>>> On Sat, Dec 13, 2014 at 11:54 AM, Laurent Gautier
>>> wrote:
>>>>
>>>> That's an error in a different place. We are progressing
>>>>
>>>> Try again:
>>>> pip install
>>>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>>
>>>> 2014-12-12 22:15 GMT-05:00 Xinxin Peng :
>>>>
>>>>> Hi Lanrent,
>>>>>
>>>>> Error report still exists.
>>>>>
>>>>> Traceback (most recent call last):
>>>>> File "setup.py", line 280, in
>>>>> ri_ext = getRinterface_ext()
>>>>> File "setup.py", line 202, in getRinterface_ext
>>>>> include_dirs.extend(args.I)
>>>>> TypeError: 'NoneType' object is not iterable
>>>>>
>>>>>
>>>>> Thanks a lot.
>>>>> Xinxin
>>>>>
>>>>> On Sat, Dec 13, 2014 at 10:49 AM, Laurent Gautier
>>>>> wrote:
>>>>>>
>>>>>> Typo in the fix.
>>>>>>
>>>>>> Try a snapshot from bitbucket:
>>>>>>
>>>>>> pip install
>>>>>> https://bitbucket.org/lgautier/rpy2/get/version_2.5.x.tar.gz
>>>>>>
>>>>>>
>>>>>> 2014-12-12 21:08 GMT-05:00 Xinxin Peng :
>>>>>>
>>>>>>> Hi Laurent,
>>>>>>>
>>>>>&g
Re: [Rpy] Errors in installing rpy2
Hi Laurent, I have created a issue on this problem on bitbucket. Thanks a lot, Xinxin On Sun, Dec 14, 2014 at 10:25 AM, Laurent Gautier wrote: > > Hi Xinxin, > > It might be better to follow up on the bitbucket issue page ( > https://bitbucket.org/lgautier/rpy2/issue/246/typeerror-nonetype-object-is-not-iterable) > rather than on the list. The issue page can be associated easily with > revisions in the code, and allow you to share the full logs from the build > step without the concern of making an email too long. > > Here `args.I` appear to be an string rather than a sequence (which should > never be the case). > > Best, > > > Laurent > > > On 12/13/2014 08:41 PM, Xinxin Peng wrote: > > Hi Laurent, > > I am using gcc rather than clang. > > I have corrected the typo in setup.py. This time I can run more installing > steps. > However, the installation was interrupted at the gcc compiling stage. > > It seems that the problem is due to the unsuitable string after the > paramter -I. > > = > gcc ... - I / b i n / R / l i b 6 4 / R / i n c l u d e > > gcc: I: No such file or directory > gcc: b: No such file or directory > gcc: i: No such file or directory > gcc: n: No such file or directory > gcc: R: No such file or directory > gcc: l: No such file or directory > gcc: i: No such file or directory > gcc: b: No such file or directory > gcc: 6: No such file or directory > gcc: 4: No such file or directory > gcc: R: No such file or directory > gcc: i: No such file or directory > gcc: n: No such file or directory > gcc: c: No such file or directory > gcc: l: No such file or directory > gcc: u: No such file or directory > gcc: d: No such file or directory > gcc: e: No such file or directory > gcc: cannot specify -o with -c or -S with multiple files > error: command 'gcc' failed with exit status 1 > = > > Thanks, > Xinxin > > On Sun, Dec 14, 2014 at 9:38 AM, Xinxin Peng wrote: >> >> Hi Laurent, >> >> I am using gcc rather than clang. >> >> I have corrected the typo in setup.py. This time I can run more >> installing steps. >> However, the installation was interrupted at the gcc compiling stage. >> >> It seems that the problem is due to the unsuitable string after the >> paramter -I. >> >> = >> gcc ... - I / b i n / R / l i b 6 4 / R / i n c l u d e >> >> gcc: I: No such file or directory >> gcc: b: No such file or directory >> gcc: i: No such file or directory >> gcc: n: No such file or directory >> gcc: R: No such file or directory >> gcc: l: No such file or directory >> gcc: i: No such file or directory >> gcc: b: No such file or directory >> gcc: 6: No such file or directory >> gcc: 4: No such file or directory >> gcc: R: No such file or directory >> gcc: i: No such file or directory >> gcc: n: No such file or directory >> gcc: c: No such file or directory >> gcc: l: No such file or directory >> gcc: u: No such file or directory >> gcc: d: No such file or directory >> gcc: e: No such file or directory >> gcc: cannot specify -o with -c or -S with multiple files >> error: command 'gcc' failed with exit status 1 >> = >> >> Thanks, >> Xinxin >> >> >> > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
