"Wrapper passed wrong version number" error (Seurat v2)

[asmariyaz23]

Hello,

I tried to install and run fast_tsne in bin folder, but it fails saying the following everytime:
=============== t-SNE v1.1.0 ===============
Wrapper passed wrong version number: --version
Could you help me understand why this could be happening? I am using a MacOS and compiled FFTW from source without any errors.

Thank you
Asma

[linqiaozhi]

Hi Asma, thanks for the interest in FIt-SNE!

How exactly are you running it? Which of the wrappers are you using?

[asmariyaz23]

Actually I am using Seurat which in turn runs your package, here is how I do it:

source('/Users/asma/FIt-SNE/fast_tsne.R', chdir=T)
mtg.matrix <- RunTSNE(object = mtg.matrix, reduction.use = "pca", dims.use = 1:75, tsne.method = "FIt-SNE", nthreads = 4, reduction.name = "FItSNE", reduction.key = "FItSNE_", fast_tsne_path = "/Users/asma/FIt-SNE/bin/fast_tsne",max_iter = 2000)
=============== t-SNE v1.1.0 ===============
Wrapper passed wrong version number: /var/folders/hy/cnv0qv797s95l6p5jw46k0x00000gn/T//RtmpphcF34/fftRtsne_data_d59876214d65.dat
Error in fftRtsne(X = as.matrix(x = data.use), dims = dim.embed, rand_seed = seed.use,  : 
  tsne call failed

Any pointers for me?

Thank you again!
Asma

[jlmelville]

It looks like Seurat have embedded a version of the R wrapper script into their code (see here). It doesn't seem to work with version 1.1.0 of FIt-SNE. You might have more luck with version 1.0, although that didn't work for me, either (but it did get further).

But you will probably have more luck reporting the issue to Seurat: https://github.com/satijalab/seurat/issues

[linqiaozhi]

Thanks @jlmelville, yes, the problem is with the Seurat wrapper. As of this PR, Seurat 3.0 is compatible with FIt-SNE 1.1.0. However, Seurat v2.X does not appear to be. I'm not sure if they are actively developing Seurat v2.0, but since many people are still using it, it is probably worth fixing it.

In the interim, the commit 9ff367a should work.