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

Tue May 31 14:58:08 EDT 2016

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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