vtraag
error with "pip install leiden"
Hi, I am trying to use the leiden alg (algorithm=4) with FindClusters in Seurat in Rstudio. When I try to run this, it gives the error: "Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg)", even though I've done library(leiden). When I go to my terminal to try pip install leidenalg, I get the following process and I am not sure how to fix, thanks!
ANACON~1\envs\r-reticulate\Lib\site-packages>python -m pip install leiden
Collecting leiden
Using cached leiden-1.0.2.tar.gz (12 kB)
Preparing metadata (setup.py) ... done
Collecting nose
Using cached nose-1.3.7-py3-none-any.whl (154 kB)
Collecting hgvs
Using cached hgvs-1.5.2-py2.py3-none-any.whl (99 kB)
Collecting pygr
Using cached pygr-0.8.2.tar.gz (1.6 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [7 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "C:\Users\annda\AppData\Local\Temp\pip-install-4k34nfc4\pygr_a4d9c1e205a448a5be0f47150fe1116e\setup.py", line 19
print 'Setuptools not imported, falling back to distutils'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Please note that the package is called leidenalg, not leiden. You should hence use pip install leidenalg. Hopefully that solves your problem?
Please note that the package is called
leidenalg, notleiden. You should hence usepip install leidenalg. Hopefully that solves your problem?
This doesn't solve it either sadly. It says install successfully but when I try to use Leidenalg in R, it says "Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg)"
OK, let's see what goes wrong where then. What packages have you installed, in which language (R, Python) and in what environments (base environments, virtual environments, Anaconda environments) and in what OS?
OK, let's see what goes wrong where then. What packages have you installed, in which language (R, Python) and in what environments (base environments, virtual environments, Anaconda environments) and in what OS?
Ok! I'm using RStudio for this, are you asking what all packages I have installed or what packages I'm trying to use in conjunction with leiden? I am using my base environment in RStudio, OS is Windows 11.
OK, it seems you are using Anaconda to run Python, is that correct? If so, leidenalg is probably correctly installed in the Anaconda environment, but that environment is probably not active when you launch R. As a result, the R leiden package is unable to find the Python leidenalg package.
You could try to install the package from within R using this:
library("reticulate")
py_install("leidenalg")
That way, reticulate hopefully installs the R package in an appropriate environment.
OK, it seems you are using Anaconda to run Python, is that correct? If so,
leidenalgis probably correctly installed in the Anaconda environment, but that environment is probably not active when you launch R. As a result, the Rleidenpackage is unable to find the Pythonleidenalgpackage.You could try to install the package from within
Rusing this:library("reticulate") py_install("leidenalg")That way,
reticulatehopefully installs the R package in an appropriate environment.
I did the py_install but I am still getting the same error message
OK, sorry to hear. Perhaps you should check with the people from Seurat? They should probably have some idea as to how best solve this.
OK, sorry to hear. Perhaps you should check with the people from Seurat? They should probably have some idea as to how best solve this.
I checked with them originally and they told me to ask here because they were not sure.
I'm not entirely sure about your setup. When I try to install a new conda environment that contains both the leiden R package and leidenalg, it all seems to work correctly.
That is, I create a new environment called r-leiden using conda create -n r-leiden -c conda-forge r-leiden leidenalg numpy. After activating the environment using conda activate r-leidenI can runR(which should now run the R installed fromconda-forge). When importing leideninRusinglibrary(leiden)` you are asked to create a conda environment, which you should not, in this case, since this is already a conda environment. I then get the following output.
> library(leiden)
create conda environment (yes/no)?no
no
using environment: NA
Unable to set up conda environment r-reticulate
run in terminal:
conda init
conda create -n r-reticulate
conda environment r-reticulate installed
python modules igraph and leidenalg installed
> library(igraph)
> G <- igraph::graph.famous('Zachary')
> part <- leiden::leiden(G)
> part
[1] 2 2 2 2 4 4 4 2 1 1 4 2 2 2 1 1 4 2 1 2 1 2 1 3 3 3 1 3 3 1 1 3 1 1
Hopefully this setup works for you!
I'm not entirely sure about your setup. When I try to install a new conda environment that contains both the
leidenR package andleidenalg, it all seems to work correctly.That is, I create a new environment called
r-leidenusingconda create -n r-leiden -c conda-forge r-leiden leidenalg numpy. After activating the environment usingconda activater-leidenI can runR(which should now run the R installed fromconda-forge). When importingleideninRusinglibrary(leiden)` you are asked to create a conda environment, which you should not, in this case, since this is already a conda environment. I then get the following output.> library(leiden) create conda environment (yes/no)?no no using environment: NA Unable to set up conda environment r-reticulate run in terminal: conda init conda create -n r-reticulate conda environment r-reticulate installed python modules igraph and leidenalg installed > library(igraph) > G <- igraph::graph.famous('Zachary') > part <- leiden::leiden(G) > part [1] 2 2 2 2 4 4 4 2 1 1 4 2 2 2 1 1 4 2 1 2 1 2 1 3 3 3 1 3 3 1 1 3 1 1Hopefully this setup works for you!
This helps! I did the first part in the terminal and that worked, I am just confused on how to open RStudio from there.
I'm not sure if RStudio works nicely from an Anaconda environment: https://community.rstudio.com/t/using-rstudio-within-a-conda-environment/128780.
However, if you just use your system R (i.e. not installed via conda), I'm also able to get it working. When I install leiden using install.packages('leiden') and then do library(leiden) I then select "yes" to create a separate conda environment, giving the following result on my computer:
Log
create conda environment (yes/no)?yes
yes
sh: 1: /home/vtraag/.local/share/r-miniconda/bin/conda: not found
+ '/home/vtraag/mambaforge/bin/conda' 'create' '--yes' '--name' 'r-reticulate' 'python=3.8' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/vtraag/mambaforge/envs/r-reticulate
added / updated specs:
- python=3.8
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.8.15 |h4a9ceb5_0_cpython 19.9 MB conda-forge
------------------------------------------------------------
Total: 19.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
ca-certificates conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.39-hcc3a1bd_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libsqlite conda-forge/linux-64::libsqlite-3.40.0-h753d276_0
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-3.0.7-h0b41bf4_1
pip conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.8.15-h4a9ceb5_0_cpython
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
setuptools conda-forge/noarch::setuptools-65.5.1-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Retrieving notices: ...working... done
+ '/home/vtraag/mambaforge/bin/conda' 'install' '--yes' '--name' 'r-reticulate' '-c' 'conda-forge' 'conda'
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.14.0
latest version: 22.11.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/vtraag/mambaforge/envs/r-reticulate
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
brotlipy-0.7.0 |py38h0a891b7_1005 342 KB conda-forge
cffi-1.15.1 | py38h4a40e3a_3 230 KB conda-forge
conda-22.11.1 | py38h578d9bd_1 905 KB conda-forge
conda-package-handling-2.0.2| pyh38be061_0 247 KB conda-forge
conda-package-streaming-0.7.0| pyhd8ed1ab_1 17 KB conda-forge
cryptography-38.0.4 | py38h80a4ca7_0 1.3 MB conda-forge
pycosat-0.6.4 | py38h0a891b7_1 108 KB conda-forge
python_abi-3.8 | 3_cp38 6 KB conda-forge
ruamel.yaml-0.17.21 | py38h0a891b7_2 172 KB conda-forge
ruamel.yaml.clib-0.2.7 | py38h1de0b5d_1 143 KB conda-forge
zstandard-0.19.0 | py38h5945529_1 374 KB conda-forge
------------------------------------------------------------
Total: 3.8 MB
The following NEW packages will be INSTALLED:
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py38h0a891b7_1005
certifi conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-1.15.1-py38h4a40e3a_3
charset-normalizer conda-forge/noarch::charset-normalizer-2.1.1-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
conda conda-forge/linux-64::conda-22.11.1-py38h578d9bd_1
conda-package-han~ conda-forge/noarch::conda-package-handling-2.0.2-pyh38be061_0
conda-package-str~ conda-forge/noarch::conda-package-streaming-0.7.0-pyhd8ed1ab_1
cryptography conda-forge/linux-64::cryptography-38.0.4-py38h80a4ca7_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
pluggy conda-forge/noarch::pluggy-1.0.0-pyhd8ed1ab_5
pycosat conda-forge/linux-64::pycosat-0.6.4-py38h0a891b7_1
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-22.1.0-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python_abi conda-forge/linux-64::python_abi-3.8-3_cp38
requests conda-forge/noarch::requests-2.28.1-pyhd8ed1ab_1
ruamel.yaml conda-forge/linux-64::ruamel.yaml-0.17.21-py38h0a891b7_2
ruamel.yaml.clib conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py38h1de0b5d_1
toolz conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
tqdm conda-forge/noarch::tqdm-4.64.1-pyhd8ed1ab_0
urllib3 conda-forge/noarch::urllib3-1.26.13-pyhd8ed1ab_0
zstandard conda-forge/linux-64::zstandard-0.19.0-py38h5945529_1
zstd conda-forge/linux-64::zstd-1.5.2-h6239696_4
Downloading and Extracting Packages
python_abi-3.8 | 6 KB | ########################################################## | 100%
conda-package-stream | 17 KB | ########################################################## | 100%
conda-package-handli | 247 KB | ########################################################## | 100%
brotlipy-0.7.0 | 342 KB | ########################################################## | 100%
conda-22.11.1 | 905 KB | ########################################################## | 100%
pycosat-0.6.4 | 108 KB | ########################################################## | 100%
cffi-1.15.1 | 230 KB | ########################################################## | 100%
ruamel.yaml.clib-0.2 | 143 KB | ########################################################## | 100%
zstandard-0.19.0 | 374 KB | ########################################################## | 100%
cryptography-38.0.4 | 1.3 MB | ########################################################## | 100%
ruamel.yaml-0.17.21 | 172 KB | ########################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Retrieving notices: ...working... done
using environment: r-reticulate
conda environment r-reticulate installed
install dependencies (yes/no)?
Unable to install python modules igraph and leidenalg
run in terminal:
conda install -n r-reticulate -c conda-forge vtraag python-igraph pandas umap learn
python modules igraph and leidenalg installed
Warning message:
In system2(conda, c("update", "--yes", "--name", "base", "conda")) :
error in running command
This has now setup a new conda environment r-reticulate. The only thing then left to do is install leidenalg (and numpy) using
conda install -n r-reticulate -c conda-forge leidenalg numpy
after which I can again run
> G <- igraph::graph.famous('Zachary')
> leiden(G)
[1] 2 2 2 2 4 4 4 2 1 1 4 2 2 2 1 1 4 2 1 2 1 2 1 3 3 3 1 3 3 1 1 3 1 1
but now from my system R, and hence this should also work from RStudio.