Issue in Windows 10 with pykdtree

[philw6]

danhamill, this is the Windows issue. I have started another issue so the Linux and Windows install issues dont get confused. You can see from the error output below that install of pyresample fails at: "pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory
error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2". On Googling this issue it seems a problem with the C++ compiler not fully supporting the C99 standard and having stdint.h. I have just installed the VS 2017 C++ tools in the hope this would work (apparently the stdint.h code was added back in 2013?). No luck as the below shows.

Output from the Anaconda2 Prompt:

(C:\Users\Phillip\Anaconda2) C:\Users\Phillip>pip install pyhum
Requirement already satisfied: pyhum in c:\users\phillip\appdata\roaming\python\python27\site-packages

(C:\Users\Phillip\Anaconda2) C:\Users\Phillip>python -c "import PyHum; PyHum.test.dotest()"
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_init_.py", line 67, in
from PyHum._pyhum_map import map
File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_pyhum_map.py", line 79, in
import pyresample
ImportError: No module named pyresample

(C:\Users\Phillip\Anaconda2) C:\Users\Phillip>pip install pyresample
Collecting pyresample
Requirement already satisfied: numpy in c:\users\phillip\anaconda2\lib\site-packages (from pyresample)
Collecting pykdtree>=1.1.1 (from pyresample)
Using cached pykdtree-1.2.1.tar.gz
In the tar file c:\users\phillip\appdata\local\temp\pip-mvyhtq-unpack\pykdtree-1.2.1.tar.gz the member pykdtree-1.2.1/README is invalid: unable to resolve link inside archive
Requirement already satisfied: setuptools>=3.2 in c:\users\phillip\anaconda2\lib\site-packages (from pyresample)
Requirement already satisfied: configobj in c:\users\phillip\anaconda2\lib\site-packages (from pyresample)
Requirement already satisfied: pyproj in c:\users\phillip\anaconda2\lib\site-packages (from pyresample)
Requirement already satisfied: pyyaml in c:\users\phillip\anaconda2\lib\site-packages (from pyresample)
Requirement already satisfied: six>=1.6.0 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample)
Requirement already satisfied: packaging>=16.8 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample)
Requirement already satisfied: appdirs>=1.4.0 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample)
Requirement already satisfied: pyparsing in c:\users\phillip\anaconda2\lib\site-packages (from packaging>=16.8->setuptools>=3.2->pyresample)
Building wheels for collected packages: pykdtree
Running setup.py bdist_wheel for pykdtree ... error
Complete output from command C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d c:\users\phillip\appdata\local\temp\tmpqfgpxzpip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win32-2.7
creating build\lib.win32-2.7\pykdtree
copying pykdtree\test_tree.py -> build\lib.win32-2.7\pykdtree
copying pykdtree_init_.py -> build\lib.win32-2.7\pykdtree
running build_ext
building 'pykdtree.kdtree' extension
creating build\temp.win32-2.7
creating build\temp.win32-2.7\Release
creating build\temp.win32-2.7\Release\pykdtree
C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Users\Phillip\Anaconda2\include -IC:\Users\Phillip\Anaconda2\PC -IC:\Users\Phillip\Anaconda2\lib\site-packages\numpy\core\include /Tcpykdtree/kdtree.c /Fobuild\temp.win32-2.7\Release\pykdtree/kdtree.obj /Ox /openmp
kdtree.c
c:\users\phillip\anaconda2\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
pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory
error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2

---

Failed building wheel for pykdtree
Running setup.py clean for pykdtree
Failed to build pykdtree
Installing collected packages: pykdtree, pyresample
Running setup.py install for pykdtree ... error
Complete output from command C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record c:\users\phillip\appdata\local\temp\pip-a4bahi-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win32-2.7
creating build\lib.win32-2.7\pykdtree
copying pykdtree\test_tree.py -> build\lib.win32-2.7\pykdtree
copying pykdtree_init_.py -> build\lib.win32-2.7\pykdtree
running build_ext
building 'pykdtree.kdtree' extension
creating build\temp.win32-2.7
creating build\temp.win32-2.7\Release
creating build\temp.win32-2.7\Release\pykdtree
C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Users\Phillip\Anaconda2\include -IC:\Users\Phillip\Anaconda2\PC -IC:\Users\Phillip\Anaconda2\lib\site-packages\numpy\core\include /Tcpykdtree/kdtree.c /Fobuild\temp.win32-2.7\Release\pykdtree/kdtree.obj /Ox /openmp
kdtree.c
c:\users\phillip\anaconda2\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
pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory
error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2

----------------------------------------

Command "C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record c:\users\phillip\appdata\local\temp\pip-a4bahi-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\

(C:\Users\Phillip\Anaconda2) C:\Users\Phillip>

[danhamill]

Which version of scipy do you have?

…

On May 22, 2017, at 10:35 PM, philw6 ***@***.***> wrote: danhamill, this is the Windows issue. I have started another issue so the Linux and Windows install issues dont get confused. You can see from the error output below that install of pyresample fails at: "pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2". On Googling this issue it seems a problem with the C++ compiler not fully supporting the C99 standard and having stdint.h. I have just installed the VS 2017 C++ tools in the hope this would work (apparently the stdint.h code was added back in 2013?). No luck as the below shows. Output from the Anaconda2 Prompt: (C:\Users\Phillip\Anaconda2) C:\Users\Phillip>pip install pyhum Requirement already satisfied: pyhum in c:\users\phillip\appdata\roaming\python\python27\site-packages (C:\Users\Phillip\Anaconda2) C:\Users\Phillip>python -c "import PyHum; PyHum.test.dotest()" Traceback (most recent call last): File "", line 1, in File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_init_.py", line 67, in from PyHum._pyhum_map import map File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_pyhum_map.py", line 79, in import pyresample ImportError: No module named pyresample (C:\Users\Phillip\Anaconda2) C:\Users\Phillip>pip install pyresample Collecting pyresample Requirement already satisfied: numpy in c:\users\phillip\anaconda2\lib\site-packages (from pyresample) Collecting pykdtree>=1.1.1 (from pyresample) Using cached pykdtree-1.2.1.tar.gz In the tar file c:\users\phillip\appdata\local\temp\pip-mvyhtq-unpack\pykdtree-1.2.1.tar.gz the member pykdtree-1.2.1/README is invalid: unable to resolve link inside archive Requirement already satisfied: setuptools>=3.2 in c:\users\phillip\anaconda2\lib\site-packages (from pyresample) Requirement already satisfied: configobj in c:\users\phillip\anaconda2\lib\site-packages (from pyresample) Requirement already satisfied: pyproj in c:\users\phillip\anaconda2\lib\site-packages (from pyresample) Requirement already satisfied: pyyaml in c:\users\phillip\anaconda2\lib\site-packages (from pyresample) Requirement already satisfied: six>=1.6.0 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample) Requirement already satisfied: packaging>=16.8 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample) Requirement already satisfied: appdirs>=1.4.0 in c:\users\phillip\anaconda2\lib\site-packages (from setuptools>=3.2->pyresample) Requirement already satisfied: pyparsing in c:\users\phillip\anaconda2\lib\site-packages (from packaging>=16.8->setuptools>=3.2->pyresample) Building wheels for collected packages: pykdtree Running setup.py bdist_wheel for pykdtree ... error Complete output from command C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d c:\users\phillip\appdata\local\temp\tmpqfgpxzpip-wheel- --python-tag cp27: running bdist_wheel running build running build_py creating build creating build\lib.win32-2.7 creating build\lib.win32-2.7\pykdtree copying pykdtree\test_tree.py -> build\lib.win32-2.7\pykdtree copying pykdtree_init_.py -> build\lib.win32-2.7\pykdtree running build_ext building 'pykdtree.kdtree' extension creating build\temp.win32-2.7 creating build\temp.win32-2.7\Release creating build\temp.win32-2.7\Release\pykdtree C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Users\Phillip\Anaconda2\include -IC:\Users\Phillip\Anaconda2\PC -IC:\Users\Phillip\Anaconda2\lib\site-packages\numpy\core\include /Tcpykdtree/kdtree.c /Fobuild\temp.win32-2.7\Release\pykdtree/kdtree.obj /Ox /openmp kdtree.c c:\users\phillip\anaconda2\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 pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2 Failed building wheel for pykdtree Running setup.py clean for pykdtree Failed to build pykdtree Installing collected packages: pykdtree, pyresample Running setup.py install for pykdtree ... error Complete output from command C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record c:\users\phillip\appdata\local\temp\pip-a4bahi-record\install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build\lib.win32-2.7 creating build\lib.win32-2.7\pykdtree copying pykdtree\test_tree.py -> build\lib.win32-2.7\pykdtree copying pykdtree_init_.py -> build\lib.win32-2.7\pykdtree running build_ext building 'pykdtree.kdtree' extension creating build\temp.win32-2.7 creating build\temp.win32-2.7\Release creating build\temp.win32-2.7\Release\pykdtree C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Users\Phillip\Anaconda2\include -IC:\Users\Phillip\Anaconda2\PC -IC:\Users\Phillip\Anaconda2\lib\site-packages\numpy\core\include /Tcpykdtree/kdtree.c /Fobuild\temp.win32-2.7\Release\pykdtree/kdtree.obj /Ox /openmp kdtree.c c:\users\phillip\anaconda2\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 pykdtree/kdtree.c(354) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory error: command 'C:\Users\Phillip\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe' failed with exit status 2 ---------------------------------------- Command "C:\Users\Phillip\Anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record c:\users\phillip\appdata\local\temp\pip-a4bahi-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\phillip\appdata\local\temp\pip-build-b3ewnc\pykdtree\ (C:\Users\Phillip\Anaconda2) C:\Users\Phillip> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[danhamill]

After a more detailed review of my notes, I found the latest version of pyresample (1.1.6) does is not compatible with scipy. The workaround I found was to install pyresample version 1.1.4. F.Y.I I am using scipy version 0.18.1.

pip install pyresample==1.1.4`

If that workaround is not to your liking, I also did a little research and It appears that you can install pykdtree using appveyor. I don't have visual studio, but it looks like there is a way to add the missing header file.

Good luck.

[philw6]

Thanks Dan, installing the older pyresample version (1.1.4) worked. It is now installed and working. Unfortunately doing the test failed for a different reason though with TypeError: ufunc 'isfinite' not supported for the input types... I'll keep searching but it looks like it might be an issue with matplotlib

[danhamill]

Do you have a full traceback? You could try a different backend. Maybe: matplotlib.use('Qt4Agg')

…

On May 23, 2017, at 6:12 PM, philw6 ***@***.***> wrote: Thanks Dan, installing the older pyresample version (1.1.4) worked. It is now installed and working. Unfortunately doing the test failed for a different reason though with TypeError: ufunc 'isfinite' not supported for the input types... I'll keep searching but it looks like it might be an issue with matplotlib — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[philw6]

The full traceback is below:

(C:\Users\Phillip\Anaconda2) C:\Users\Phillip>python -c "import PyHum; PyHum.test.dotest()"
Input file is C:\Users\Phillip\pyhum_test\test.DAT
Son files are in C:\Users\Phillip\pyhum_test
cs2cs arguments are epsg:26949
Draft: 0.3
Celerity of sound: 1450.0 m/s
Port and starboard will be flipped
Transducer length is 0.108 m
Bed picking is auto
Chunks based on distance of 100 m
Data is from the 998 series
Bearing will be calculated from coordinates
Bearing will be filtered
Checking the epsg code you have chosen for compatibility with Basemap ...
... epsg code compatible
WARNING: Because files have to be read in byte by byte,
this could take a very long time ...
port sonar data will be parsed into 3.0, 99 m chunks
starboard sonar data will be parsed into 3.0, 99 m chunks
memory-mapping failed in sliding window - trying memory intensive version
low-freq. sonar data will be parsed into 3.0, 99 m chunks
high-freq. sonar data will be parsed into 3.0, 99 m chunks
memory-mapping failed in sliding window - trying memory intensive version
Processing took 49.4254002521 seconds to analyse
Done!
Input file is C:\Users\Phillip\pyhum_test\test.DAT
Sonar file path is C:\Users\Phillip\pyhum_test
Max. transducer power is 1000.0 W
pH is 7.0
Temperature is 10.0
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum\test.py", line 134, in dotest
PyHum.correct(humfile, sonpath, maxW, doplot, dofilt, correct_withwater, ph, temp, salinity)
File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_pyhum_correct.py", line 528, in correct
plot_dwnlow_scans(low_fp[p], dist_m, shape_low, ft, sonpath, p)
File "C:\Users\Phillip\AppData\Roaming\Python\Python27\site-packages\PyHum_pyhum_correct.py", line 848, in plot_dwnlow_scans
plt.axis('normal'); plt.axis('tight')
File "C:\Users\Phillip\Anaconda2\lib\site-packages\matplotlib\pyplot.py", line 1537, in axis
return gca().axis(*v, **kwargs)
File "C:\Users\Phillip\Anaconda2\lib\site-packages\matplotlib\axes_base.py", line 1583, in axis
self.autoscale_view(tight=False)
File "C:\Users\Phillip\Anaconda2\lib\site-packages\matplotlib\axes_base.py", line 2322, in autoscale_view
'minposy', self.yaxis, self._ymargin, y_stickies, self.set_ybound)
File "C:\Users\Phillip\Anaconda2\lib\site-packages\matplotlib\axes_base.py", line 2301, in handle_single_axis
do_lower_margin = not np.any(np.isclose(x0, stickies))
File "C:\Users\Phillip\Anaconda2\lib\site-packages\numpy\core\numeric.py", line 2451, in isclose
yfin = isfinite(y)
TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

[dbuscombe-usgs]

Unless I'm mistaken, pykdtree is sort of useless on Windows because it relies on openMP for speed. You could install without dependencies using

pip install PyHum --no-deps

and manually install any missing libraries except pykdtree. PyHum will use scipy kdtree if pykdtree is not found. On Windows, you shouldn't notice any performance difference.

On the latest pyresample error, you could try installing the gcc binaries

https://github.com/develersrl/gccwinbinaries