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py_install("louvain") error #232

Open Lucyyang1991 opened 5 years ago

Lucyyang1991 commented 5 years ago

Thanks so much for the monocle3. When I'm trying install the monocle3 py_install("louvain"), the error is

Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Error: Error 1 occurred installing packages into conda environment r-reticulate

sonali-bioc commented 5 years ago

Use this instead : py_install("r-reticulate", "louvain")

cjpark85 commented 5 years ago

I'm having exactly same problem. 'py_install("r-reticulate", "louvain")' doesn't work. How can I install louvain?

py_install('umap-learn', pip = T, pip_ignore_installed = T) # Ensure the latest version of UMAP is installed Collecting umap-learn Collecting scipy>=0.19 (from umap-learn) Using cached https://files.pythonhosted.org/packages/58/f0/d00c0e01e077da883f030af3ff5ce653a0e9e4786f83faa89a6e18c98612/scipy-1.2.1-cp37-cp37m-win_amd64.whl Collecting scikit-learn>=0.16 (from umap-learn) Using cached https://files.pythonhosted.org/packages/47/a6/5cfab2684c3da61dece651796aefb2542a1970a8ba9b9efee4f730ccd90b/scikit_learn-0.20.3-cp37-cp37m-win_amd64.whl Collecting numpy>=1.13 (from umap-learn) Using cached https://files.pythonhosted.org/packages/4e/9d/c129d78e6b942303b762ccfdf1f8339de80c5e6021b14ef0c99ec5bdc6aa/numpy-1.16.3-cp37-cp37m-win_amd64.whl Collecting numba>=0.37 (from umap-learn) Using cached https://files.pythonhosted.org/packages/97/67/cd0da34fb0a78f3e290d540f1ad223300856da2f1db2d77ec9945671ec04/numba-0.43.1-cp37-cp37m-win_amd64.whl Collecting llvmlite>=0.28.0dev0 (from numba>=0.37->umap-learn) Using cached https://files.pythonhosted.org/packages/a4/af/437bb1822e86002e59cf552f74c5963edb8b1edcfba902a7868b16558bef/llvmlite-0.28.0-cp37-cp37m-win_amd64.whl Installing collected packages: numpy, scipy, scikit-learn, llvmlite, numba, umap-learn Successfully installed llvmlite-0.28.0 numba-0.43.1 numpy-1.16.3 scikit-learn-0.20.3 scipy-1.2.1 umap-learn-0.3.8

Installation complete.

py_install("louvain") Collecting package metadata: ...working... done Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Error: Error 1 occurred installing packages into conda environment r-reticulate

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.949 LC_CTYPE=Korean_Korea.949 LC_MONETARY=Korean_Korea.949 [4] LC_NUMERIC=C LC_TIME=Korean_Korea.949

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] reticulate_1.12 usethis_1.5.0 devtools_2.0.2 BiocInstaller_1.32.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 rstudioapi_0.10 magrittr_1.5 pkgload_1.0.2 lattice_0.20-38 R6_2.4.0
[7] rlang_0.3.4 tools_3.5.2 grid_3.5.2 pkgbuild_1.0.3 sessioninfo_1.1.1 cli_1.1.0
[13] withr_2.1.2 remotes_2.0.4 assertthat_0.2.1 digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4
[19] Matrix_1.2-17 processx_3.3.1 callr_3.2.0 fs_1.3.1 ps_1.3.0 curl_3.3
[25] memoise_1.1.0 glue_1.3.1 compiler_3.5.2 desc_1.2.0 backports_1.1.4 prettyunits_1.0.2 [31] jsonlite_1.6

zhouchenhao commented 5 years ago

Try py_install("python-louvain")

zezhuo commented 5 years ago

Try py_install("python-louvain")

Hi @zhouchenhao , I install python-louvain package, and successfully import community.

> library(reticulate)
> import("community")
Module(community)
> L07_cds <-  cluster_cells(L07_cds, resolution=c(10^seq(-6,-1)))
Error in system("which python", intern = TRUE) : 'which' not found

Louvain Community Detection Installing To build and install run from source: python setup.py install You can also install from pip with: pip install python-louvain The package name on pip is python-louvain but it is imported as community in python. You will find documentation about this module at http://python-louvain.readthedocs.io/

However, louvian and python-louvian are different package. It seems that Monocle3 calls louvian only?

Any suggestions about my inssue? Thanks!

Regards, Nelson