pip install error about pyfit-sne HOT 17 CLOSED

Got the same error (both on a linux and on a windows machine).
Would that be due to this ? :

Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s) 

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Same error here. @florian-huber @ccshao did either of you figure out how to install?

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@whitews : no, I wasn't able to install. Started looking at other t-sne implementations but that's going slow... I will give an update if I find something that works for me.

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I built the fit-tsne instead, see https://github.com/KlugerLab/FIt-SNE.
If everything works, there should be a binary exec file, which should be put into a folder contained by PATH. Then seurat is able to find and use it. Good luck.

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same issue here on Ubuntu

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@whitews : no, I wasn't able to install. Started looking at other t-sne implementations but that's going slow... I will give an update if I find something that works for me.

did you manage to fix this issue? it have been trying for a couple of day and no luck so far :(

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@farouktif Nope, we moved on to tsne-cuda:

https://github.com/CannyLab/tsne-cuda

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I will look into this in further detail as soon as I can--sorry for the delays.

Until then, please consider using the Python wrapper here:
https://github.com/KlugerLab/FIt-SNE

It's not a package (i.e. not installed by pip), but works very well.

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I got the same errors with Flt-SNE install in Ubuntu. Thanks in advance for looking into this.

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@JBreunig Just take a quick look and see if this commit fixed your problem. @dkobak also reported problems with a new install on Ubuntu, looks like he resolved it.

KlugerLab/FIt-SNE#81

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@linqiaozhi The errors shown in the first message in this thread look rather unrelated to what I fixed there...

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@JBreunig Just take a quick look and see if this commit fixed your problem. @dkobak also reported problems with a new install on Ubuntu, looks like he resolved it.

KlugerLab/FIt-SNE#81

I was able to compile and use the new commit. Thanks!!

(Had no luck again with fitsne before that though I had previously used it on another Ubuntu workstation and Windows. But no need for it anyway since your installation instructions worked fine.)

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@JBreunig Just to clarify: do you mean that you managed to run FIt-SNE with a Python wrapper, or did you somehow integrate that commit 81 into the pyFIt-SNE and managed to run pyFIt-SNE?

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Sorry for the typo above (fixed), I compiled it and it ran fine from Python. I had tried before that to install fitsne again with no luck.

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I updated pyFIt-SNE to the latest version of FIt-SNE which implements Dmitry's fix.

Please re-open if you are still having this problem.

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I still get this error if I try to install from pypi. If I try to compile it with g++, I get the following:

In file included from src/tsne.cpp:40:
src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
    7 | #include <fftw3.h>
      |          ^~~~~~~~~
compilation terminated.
In file included from src/nbodyfft.cpp:5:
src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
    7 | #include <fftw3.h>
      |          ^~~~~~~~~
compilation terminated.

This question as asked 9 months ago on stackoverflow, showing the same behaviour, but no one could answer. Thank you in advance for looking into this.

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That because you did not have fftw3. Try to install it and add -I/path/to/include/ -L/path/to/lib/ to FIt-SNE install command.

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