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

Tue May 31 17:33:49 EDT 2016

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