[Neuroimaging] Fwd: [dipy] Issues trying to install dipy
Jon Haitz Legarreta
jhlegarreta at vicomtech.org
Mon May 30 17:50:33 EDT 2016
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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running develop
running egg_info
writing dipy.egg-info\PKG-INFO
writing requirements to dipy.egg-info\requires.txt
writing dependency_links to dipy.egg-info\dependency_links.txt
writing top-level names to dipy.egg-info\top_level.txt
C:\Anaconda3\lib\site-packages\setuptools-19.6.2-py3.5.egg\setuptools\dist.py:285: UserWarning: Normalizing '0.12.0dev' to '0.12.0.dev0'
package init file 'dipy\data\tests\__init__.py' not found (or not a regular file)
reading manifest file 'dipy.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'Changelog'
warning: no files found matching 'TODO'
writing manifest file 'dipy.egg-info\SOURCES.txt'
running build_ext
C:\MinGW\bin\gcc.exe -mdll -O -Wall -IC:\Anaconda3\include -IC:\Anaconda3\include -c test.c -o test.o /arch:SSE2
gcc: error: /arch:SSE2: No such file or directory
Flags ['/arch:SSE2'] omitted because of compile or link error
C:\MinGW\bin\gcc.exe -mdll -O -Wall -IC:\Anaconda3\include -IC:\Anaconda3\include -c test.c -o test.o -msse2 -mfpmath=sse
C:\MinGW\bin\gcc.exe -shared -s test.o -LC:\Anaconda3\libs -LC:\Anaconda3\PCbuild\amd64 -lvcruntime140 -o testlib.dll
c:/mingw/bin/../lib/gcc/mingw32/4.9.3/../../../../mingw32/bin/ld.exe: cannot find -lvcruntime140
collect2.exe: error: ld returned 1 exit status
Flags ['-msse2', '-mfpmath=sse'] omitted because of compile or link error
C:\MinGW\bin\gcc.exe -mdll -O -Wall -IC:\Anaconda3\include -IC:\Anaconda3\include -c test.c -o test.o -fopenmp
test.c:1:17: fatal error: omp.h: No such file or directory
#include <omp.h>
^
compilation terminated.
Flags ['-fopenmp', '-fopenmp'] omitted because of compile or link error
skipping 'dipy\reconst\peak_direction_getter.c' Cython extension (up-to-date)
building 'dipy.reconst.peak_direction_getter' extension
C:\MinGW\bin\gcc.exe -mdll -O -Wall -Isrc -IC:\Anaconda3\lib\site-packages\numpy\core\include -Ibuild -IC:\Anaconda3\include -IC:\Anaconda3\include -c dipy\reconst\peak_direction_getter.c -o build\temp.win-amd64-3.5\Release\dipy\reconst\peak_direction_getter.o
In file included from C:\Anaconda3\include/Python.h:65:0,
from dipy\reconst\peak_direction_getter.c:4:
C:\Anaconda3\include/pytime.h:113:5: warning: 'struct timeval' declared inside parameter list
_PyTime_round_t round);
^
C:\Anaconda3\include/pytime.h:113:5: warning: its scope is only this definition or declaration, which is probably not what you want
C:\Anaconda3\include/pytime.h:118:5: warning: 'struct timeval' declared inside parameter list
_PyTime_round_t round);
^
In file included from C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1781:0,
from C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
from C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
from dipy\reconst\peak_direction_getter.c:242:
C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:12:9: note: #pragma message: C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#pragma message(_WARN___LOC__"Using deprecated NumPy API, disable it by " \
^
In file included from C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:27:0,
from C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
from dipy\reconst\peak_direction_getter.c:242:
C:\Anaconda3\lib\site-packages\numpy\core\include/numpy/__multiarray_api.h:1634:1: warning: '_import_array' defined but not used [-Wunused-function]
_import_array(void)
^
dipy\reconst\peak_direction_getter.c: In function '__pyx_pw_4dipy_7reconst_21peak_direction_getter_30PeaksAndMetricsDirectionGetter_5initial_direction':
dipy\reconst\peak_direction_getter.c:21688:13: warning: '__pyx_v_numpeaks' may be used uninitialized in this function [-Wmaybe-uninitialized]
return PyInt_FromLong((long) value);
^
dipy\reconst\peak_direction_getter.c:2565:12: note: '__pyx_v_numpeaks' was declared here
npy_intp __pyx_v_numpeaks;
^
writing build\temp.win-amd64-3.5\Release\dipy\reconst\peak_direction_getter.cp35-win_amd64.def
C:\MinGW\bin\gcc.exe -shared -s build\temp.win-amd64-3.5\Release\dipy\reconst\peak_direction_getter.o build\temp.win-amd64-3.5\Release\dipy\reconst\peak_direction_getter.cp35-win_amd64.def -LC:\Anaconda3\libs -LC:\Anaconda3\PCbuild\amd64 -lpython35 -lvcruntime140 -o C:\SDKs\dipy\dipy-head\dipy\dipy\reconst\peak_direction_getter.cp35-win_amd64.pyd
c:/mingw/bin/../lib/gcc/mingw32/4.9.3/../../../../mingw32/bin/ld.exe: C:\Anaconda3\libs/python35.lib(python35.dll): Recognised but unhandled machine type (0x8664) in Import Library Format archive
C:\Anaconda3\libs/python35.lib: error adding symbols: File format not recognized
collect2.exe: error: ld returned 1 exit status
error: command 'C:\\MinGW\\bin\\gcc.exe' failed with exit status 1
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