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

Gregory Lee grlee77 at gmail.com
Tue May 31 16:01:52 EDT 2016 

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
>>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>
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>>>>>
>>>>
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>
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