Following the thread, Pip in nightly build not working , I got pip working as demonstrated. But this fails: >>> pipmain([‘install’, ‘Rpy2’]) Collecting Rpy2 Using cached https://files.pythonhosted.org/packages/f1/98/c7652cc9d7fc0afce74d2c30a52b9c9ac391713a63d037e4ab8feb56c530/rpy2-2.9.4.tar.gz C…

Note that you only need to use Slicer’s built-in Python interpreter to directly access GUI and scene data. You can run Python scripts in any external environment with any Python packages installed as described here .

I think this is the same issue as this: [image] Slicer-Python Packages Use and Install Support Why I cant install this package pipmain([‘install’,‘scikit-fuzzy’]) Collecting scikit-fuzzy Using cached https://files.pythonhosted.org/packages/fb/79/71a79d2663ed662d30461aca…

Yes, from briefly looking at the Rpy2 documentation there are some precompiled binaries. If you’re using Windows, you’re not going to be able to use this package in Slicer’s environment at this time. I recommend using pure python packages when using Slicer on Windows. From the other thread that you…

@lassoan @jamesobutler I am trying to get Rpy2 working within Slicer so that we can do some computations in R and visualize the results in Slicer using the extension we are building. So, if this is the use case, should I try to get it working with the internal python or use the external environment…

If you’re needing Rpy2, use the external environment method as suggested by @lassoan . Can you describe the computation that you are doing in R? There could be another way of doing this without using R.

Thanks @jamesobutler . There are many different types of analyses that one can use landmark based shape analyses to investigate different biological questions (phylogenetics, ecology, evolutionary trajectories etc). Most of these are already implemented in R as different packages (and surprisingly a…

[image] muratmaga: Most of these are already implemented in R as different packages We do landmark-based shape analysis using VTK and also experimenting with SlicerSALT and they work quite well. What analysis do you plan to do? What R packages would you like to use? I’ve done a quick search …

Try geomorph as well. It provides the basic procrustes superimposition and its typical outputs (consensus shape, procrustes residuals, riemann distances, centroid sizes, etc). From there you can do eigen decomposition on your resultant coordinates and take your data to do phylogenetic analysis (phy…

If pyRserve works and is fast enough for your needs, then that sounds like a good option; network-based, de-coupled solutions are generally easier to maintain. If it turns out not to be fast enough, you may be able to build Rpy2 from source as part of your extension. This would assume it only links …

[image] muratmaga: Try geomorph as well. Thanks, yes, indeed geomorph seems to have a few features that are not available in VTK. Also, if your community uses geomorph as reference implementation then you may have little choice. I’m surprised that geomorph uses GPL license. It is too bad, be…

I can’t generalize, but I think there a lot of packages that are out there with GPL. You need to understand that people behind these packages are not team, but academicians that are spending a lot of time on very specific topic. Though, I am not sure I understand your reluctance. GPL has only impli…

Rpy2 pip installation fails

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muratmaga (Murat Maga) November 27, 2018, 6:11am 2

I think this is the same issue as this:

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Rpy2 pip installation fails

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