[Neuroimaging] Fwd: [dipy] Issues trying to install dipy

Wed Jun 1 12:56:25 EDT 2016

Dear Eleftherios,
thanks for the suggestion.

Uninstalling MinGW ports me back to the original error of the thread:
File: "C:\Anaconda3\lib\distutils\cygwinccompiler.py", line 126, __init__
if self.ld_version >= "2.10.90":
TypeError: unorderable types: NoneType() >= str()

I agree that no extra compiler should be necessary, but one of the links
Ariel suggested was pointing in that direction.

Anyway, yes, let's see if we can solve it through a hangout and come back
to the list with the solution.

Sincerely,
JON HAITZ

On 1 June 2016 at 00:39, Eleftherios Garyfallidis <garyfallidis at gmail.com>
wrote:

> Hi Jon,
>
> When I develop DIPY using Anaconda in Windows I don't think I need to
> install a compiler separately. Anaconda is coming with its own MinGW
> compiler. Could it be that you are adding an extra compiler when it is not
> necessary?
>
> Also I 'll be happy to hangout and help you with your installation
> problem. Send me an e-mail off the list please to arrange a meeting.
>
> Cheers,
> Eleftherios
>
>
>
> On Tue, May 31, 2016 at 5:34 PM Jon Haitz Legarreta <
> jhlegarreta at vicomtech.org> wrote:
>
>> Hi Greg,
>> using the virtual env I'm able to run the examples without major issues.
>> Indeed, for the virtual env I downloaded the conda-forge dipy package.
>>
>> But my intent is to build from the latest source.
>>
>> Thanks,
>> JON HAITZ
>>
>>
>>
>>
>>
>> On 31 May 2016 at 22:01, Gregory Lee <grlee77 at gmail.com> wrote:
>>
>>> Hi Jon,
>>>
>>> Do you need to build from the lastest source or are you just trying to
>>> install a working version to run examples?  If the later, it may be worth
>>> trying the pre-built conda packages Ariel recently created at conda-forge.
>>> To install:
>>>
>>> conda install -c conda-forge dipy
>>>
>>> - Greg
>>>
>>> On Tue, May 31, 2016 at 2:58 PM, Jon Haitz Legarreta <
>>> jhlegarreta at vicomtech.org> wrote:
>>>
>>>> Dear Eleftherios,
>>>> thanks for the follow-up.
>>>>
>>>> No, I did not contact the Anaconda developers, since I was a little bit
>>>> lost in the messages/source problem. But if your guess is that it is more
>>>> likely an Anaconda problem, I will contact them and let you know.
>>>>
>>>> On the other hand, you are right; I installed Anaconda, then tried to
>>>> set up dipy for development.
>>>>
>>>> Also I have a virtual environment where I downloaded the dipy
>>>> dependencies. I do not know if the latter step can be avoided or else,
>>>> whether one can be substituted by the other: i.e. and whether when one
>>>> installs dipy for development from sources, dipy scripts take care of
>>>> putting in place the necessary packages. I just thought that creating a
>>>> virtual env with just the dipy dependencies would be cleaner for
>>>> development (i.e. avoid clashes with other packages or repos, etc.)
>>>>
>>>> Since one of the links posted suggested it, I installed MinGW, but had
>>>> no other compiler installer on my machine.
>>>>
>>>> Sincerely,
>>>> JON HAITZ
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 31 May 2016 at 00:16, Eleftherios Garyfallidis <
>>>> garyfallidis at gmail.com> wrote:
>>>>
>>>>> Hi Jon,
>>>>>
>>>>> The error is not related to SSE or to OMP. Those are ommitted and then
>>>>> the compilation continues properly. The problem appears later. Here is the
>>>>> message
>>>>>
>>>>> C:\Anaconda3\libs/python35.lib: error adding symbols: File format not recognized
>>>>> collect2.exe: error: ld returned 1 exit status
>>>>>
>>>>> Have you contacted the Anaconda developers? This looks like a problem
>>>>> on their side.
>>>>>
>>>>> Let us know what they said to you. Otherwise I wonder if this is a
>>>>> specific problem with Python 3 or if it affects also Python 2. You may want
>>>>> to try that too. The problem does look more likely to be related to the
>>>>> compiler used.
>>>>>
>>>>> Am I correct to say that the only thing that you did was to install
>>>>> Anaconda and then pip install dipy? Did you have other compilers already
>>>>> installed in your system?
>>>>>
>>>>> Best regards,
>>>>> Eleftherios
>>>>>
>>>>> On Mon, May 30, 2016 at 5:51 PM Jon Haitz Legarreta <
>>>>> jhlegarreta at vicomtech.org> wrote:
>>>>>
>>>>>> Dear Ariel,
>>>>>> thanks for your suggestion.
>>>>>>
>>>>>> The patches in the link seem to help a little bit, but the process
>>>>>> seems still to be unsuccessful: the MinGW gcc complains with the message:
>>>>>> gcc: error: /arch:SSE2: No such file or directory
>>>>>>
>>>>>> Attached is the new log.
>>>>>>
>>>>>> Again, googling was not of much help. I got bits and parts of related
>>>>>> errors, but have no clear picture of the issue.
>>>>>>
>>>>>> Any suggestion is appreciated.
>>>>>>
>>>>>> JON HAITZ
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 24 May 2016 at 01:08, Ariel Rokem <arokem at gmail.com> wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, May 23, 2016 at 3:19 PM, Jon Haitz Legarreta <
>>>>>>> jhlegarreta at vicomtech.org> wrote:
>>>>>>>
>>>>>>>> Hi there,
>>>>>>>> thank you Matthew and Ariel.
>>>>>>>>
>>>>>>>> The link pointed by Ariel does not seem to be a solution; after
>>>>>>>> having installed MinGW, as suggested in the link and although I'm aware it
>>>>>>>> might be unnecessary, the Anaconda3 powershell still yields a similar
>>>>>>>> error, now pointing to MSVC (which I do not have on my system):
>>>>>>>>
>>>>>>>>   File "C:\Anaconda3\lib\distutils\cygwinccompiler.py", line 157,
>>>>>>>> in __init__
>>>>>>>>     self.dll_libraries = get_msvcr()
>>>>>>>>   File "C:\Anaconda3\lib\distutils\cygwinccompiler.py", line 86, in
>>>>>>>> get_msvcr
>>>>>>>>     raise ValueError("Unknown MS Compiler version %s " % msc_ver)
>>>>>>>> ValueError: Unknown MS Compiler version 1900
>>>>>>>>
>>>>>>>> Looks like maybe you ran into this corner case?
>>>>>>>
>>>>>>> http://stackoverflow.com/a/34427014/3532933
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> I'll try to investigate further, and will let you know.
>>>>>>>>
>>>>>>>> Kind regards,
>>>>>>>> JON HAITZ
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 21 May 2016 at 16:55, Ariel Rokem <arokem at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Jon and Matthew,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sat, May 21, 2016 at 7:30 AM, Matthew Brett <
>>>>>>>>> matthew.brett at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> On Sat, May 21, 2016 at 9:18 AM, Jon Haitz Legarreta
>>>>>>>>>> <jhlegarreta at vicomtech.org> wrote:
>>>>>>>>>> > Hi there,
>>>>>>>>>> > has anybody experienced the issue below?
>>>>>>>>>> >
>>>>>>>>>> > Thanks,
>>>>>>>>>> > JON HAITZ
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > ---------- Forwarded message ----------
>>>>>>>>>> > From: Jon Haitz Legarreta <jhlegarreta at vicomtech.org>
>>>>>>>>>> > Date: 18 May 2016 at 19:10
>>>>>>>>>> > Subject: [dipy] Issues trying to install dipy
>>>>>>>>>> > To: neuroimaging at python.org
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > Hi there,
>>>>>>>>>> > I'm a newbie to dipy.
>>>>>>>>>> >
>>>>>>>>>> > I was trying to follow the instructions in [1] to have dipy
>>>>>>>>>> installed from
>>>>>>>>>> > the source code, so that I could execute the dipy examples.
>>>>>>>>>> >
>>>>>>>>>> > I'm using Windows 10 and Anaconda 3.
>>>>>>>>>> >
>>>>>>>>>> > When trying to execute
>>>>>>>>>> > python setup.py develop
>>>>>>>>>> >
>>>>>>>>>> > the Anaconda prompt yields an error that says in the end:
>>>>>>>>>> > File: "C:\Anaconda3\lib\distutils\cygwinccompiler.py", line
>>>>>>>>>> 126, __init__
>>>>>>>>>> > if self.ld_version >= "2.10.90":
>>>>>>>>>> > TypeError: unorderable types: NoneType() >= str()
>>>>>>>>>> >
>>>>>>>>>> > I've been googling for a solution without success.
>>>>>>>>>> >
>>>>>>>>>> > I don't know whether this looks like Anaconda3 is trying to use
>>>>>>>>>> cygwin
>>>>>>>>>> > instead of mingw32, and whether that is the root cause.
>>>>>>>>>> >
>>>>>>>>>> > In either case, does anyone know how to solve the issue?
>>>>>>>>>> >
>>>>>>>>>> > Attached is the trace (it's short) of the error if this is of
>>>>>>>>>> any help.
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > Thank you,
>>>>>>>>>> > JON HAITZ
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > [1] http://nipy.org/dipy/installation.html#install-source-nix
>>>>>>>>>>
>>>>>>>>>> I'm sorry, I'm afraid I don't personally use Anaconda, so I have
>>>>>>>>>> no
>>>>>>>>>> experience of fixing compilation errors on Anaconda.   Ariel -
>>>>>>>>>> have
>>>>>>>>>> you come across this?
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> And I don't personally use Windows...
>>>>>>>>>
>>>>>>>>> Might this be helpful:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://stackoverflow.com/questions/24683305/python-cant-install-packages-typeerror-unorderable-types-nonetype-str
>>>>>>>>>
>>>>>>>>> It seems like it could be related, though it's all Greek to me.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>> Ariel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> You could also try on the anaconda support channels (issues,
>>>>>>>>>> mailing
>>>>>>>>>> list) - it may well be a general problem rather than one specific
>>>>>>>>>> to
>>>>>>>>>> dipy,
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> Matthew
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Neuroimaging mailing list
>>>>>>>>> Neuroimaging at python.org
>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>
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>>>>>>>
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>>>>>
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