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

Tue May 31 18:39:11 EDT 2016

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