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KrishnaswamyLab / phateR

PHATE dimensionality reduction method implemented in R
GNU General Public License v2.0
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reticulate issue #43

Closed moldach closed 11 months ago

moldach commented 4 years ago

I had phateR working on my computer for about a day and now all of a sudden it's stopped working.

Trying to follow trouble shooting from Issue #22:

image

Then I enter the python terminal:

library(reticulate)
repl_python()
>>> import phate

ImportError: attempted relative import with no known parent package

conda_create("r-reticulate")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/tsundoku/.local/share/r-miniconda/envs/r-reticulate

  added / updated specs:
    - python

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.11.27-0
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  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py38_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate r-reticulate
#
# To deactivate an active environment, use
#
#     $ conda deactivate

[1] "/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/bin/python"

Then I need to reinstall some stuff:

py_install("numpy", pip = T)
py_install("phate", pip = T)

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Collecting phate
  Using cached https://files.pythonhosted.org/packages/4a/0c/2f2850b6afd5ba9b58020b15c0fb0daf903fc9c8dc7653eab16ad2683bd5/phate-1.0.2-py3-none-any.whl
Collecting future
  Using cached https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz
Requirement already satisfied, skipping upgrade: numpy>=1.16.0 in /home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages (from phate) (1.18.1)
Collecting tasklogger>=1.0
  Using cached https://files.pythonhosted.org/packages/5d/6b/cb2a724eff19829a0ada0217f403f54fca1e48c7de6fc3383e0a8b8fa121/tasklogger-1.0.0-py3-none-any.whl
Collecting scikit-learn>=0.20.0
  Using cached https://files.pythonhosted.org/packages/db/5d/dddb8b82ee573df2ccaacb210e1df56daec33dd62aa637005dbc7b889eea/scikit_learn-0.22.1-cp38-cp38-manylinux1_x86_64.whl
Collecting matplotlib>=3.0
  Using cached https://files.pythonhosted.org/packages/53/6c/7b400d45f0ecd6703b2779a7dfda6578579a353748e1b43d8353cb7f5b7f/matplotlib-3.1.2-cp38-cp38-manylinux1_x86_64.whl
Collecting sgdpy>=1.4.1
  Using cached https://files.pythonhosted.org/packages/85/d5/5e0f97ec65cf3cbe16f681da8f22aa3404343781a91fde73a77df9cdebb5/sgdpy-1.4.1.tar.gz
Collecting graphtools>=1.3.1
  Using cached https://files.pythonhosted.org/packages/1a/44/15f4920625c87b92a62900575c84c41cd9900b9abf5f41b7cacb9f767f2f/graphtools-1.4.1-py3-none-any.whl
Collecting scprep>=0.11.1
  Using cached https://files.pythonhosted.org/packages/c6/b3/e039c5181e50aa0cc9057639f100ab50483f6dfb67b602bcffe1093c1ae4/scprep-1.0.3-py3-none-any.whl
Collecting scipy>=1.1.0
  Using cached https://files.pythonhosted.org/packages/f3/08/8bdcdcd149ea41b655956feb7c19ebf7e1f561738bd5570b6ae015daf411/scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl
Collecting Deprecated
  Using cached https://files.pythonhosted.org/packages/f6/89/62912e01f3cede11edcc0abf81298e3439d9c06c8dce644369380ed13f6d/Deprecated-1.2.7-py2.py3-none-any.whl
Collecting joblib>=0.11
  Using cached https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached https://files.pythonhosted.org/packages/5d/bc/1e58593167fade7b544bfe9502a26dc860940a79ab306e651e7f13be68c2/pyparsing-2.4.6-py2.py3-none-any.whl
Collecting python-dateutil>=2.1
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting cycler>=0.10
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1
  Using cached https://files.pythonhosted.org/packages/64/8b/a70681c9a471f8187fed80d0aa9c9bb55ec3bf9daa50bd1cdc0c73d4910c/kiwisolver-1.1.0-cp38-cp38-manylinux1_x86_64.whl
Collecting pygsp>=0.5.1
  Using cached https://files.pythonhosted.org/packages/d4/89/2f4aa73cccf12bec5179ac5d52a68b508120c838b7e5d456f5ea0c8beade/PyGSP-0.5.1-py2.py3-none-any.whl
Collecting decorator>=4.3.0
  Using cached https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting pandas>=0.25
  Using cached https://files.pythonhosted.org/packages/7b/fd/41698f20fd297cef2dc43a72a8ca42d149eaf7d954f1fb2bd3fc366a658d/pandas-0.25.3-cp38-cp38-manylinux1_x86_64.whl
Collecting wrapt<2,>=1.10
  Using cached https://files.pythonhosted.org/packages/23/84/323c2415280bc4fc880ac5050dddfb3c8062c2552b34c2e512eb4aa68f79/wrapt-1.11.2.tar.gz
Collecting six>=1.5
  Downloading https://files.pythonhosted.org/packages/65/eb/1f97cb97bfc2390a276969c6fae16075da282f5058082d4cb10c6c5c1dba/six-1.14.0-py2.py3-none-any.whl
Requirement already satisfied, skipping upgrade: setuptools in /home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages (from kiwisolver>=1.0.1->matplotlib>=3.0->phate) (44.0.0.post20200106)
Collecting pytz>=2017.2
  Using cached https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl
Building wheels for collected packages: future, sgdpy, wrapt
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-cp38-none-any.whl size=491057 sha256=2607e3d07b808538a05ce34e8ca9eb03bec28d4edadedb84a74f382d01206ced
  Stored in directory: /home/tsundoku/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e
  Building wheel for sgdpy (setup.py): started
  Building wheel for sgdpy (setup.py): finished with status 'done'
  Created wheel for sgdpy: filename=sgdpy-1.4.1-cp38-cp38-linux_x86_64.whl size=469607 sha256=536790449d0cf068d72844dd623565e8468cdb4694dfa6d8f9443a390bcf522e
  Stored in directory: /home/tsundoku/.cache/pip/wheels/97/1e/cd/b54cbaa0a2c161bbfd2381229422c5b5373a9c668c96185180
  Building wheel for wrapt (setup.py): started
  Building wheel for wrapt (setup.py): finished with status 'done'
  Created wheel for wrapt: filename=wrapt-1.11.2-cp38-cp38-linux_x86_64.whl size=77846 sha256=c381205fa56437fd5a17cb54384728b7ff53239d0e23a220e52b6f25c58bc2c3
  Stored in directory: /home/tsundoku/.cache/pip/wheels/d7/de/2e/efa132238792efb6459a96e85916ef8597fcb3d2ae51590dfd
Successfully built future sgdpy wrapt
Installing collected packages: future, tasklogger, joblib, scipy, scikit-learn, pyparsing, six, python-dateutil, cycler, kiwisolver, matplotlib, sgdpy, pygsp, graphtools, decorator, pytz, pandas, scprep, wrapt, Deprecated, phate
Successfully installed Deprecated-1.2.7 cycler-0.10.0 decorator-4.4.1 future-0.18.2 graphtools-1.4.1 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 pandas-0.25.3 phate-1.0.2 pygsp-0.5.1 pyparsing-2.4.6 python-dateutil-2.8.1 pytz-2019.3 scikit-learn-0.22.1 scipy-1.4.1 scprep-1.0.3 sgdpy-1.4.1 six-1.14.0 tasklogger-1.0.0 wrapt-1.11.2

I restart Rstudio and then try to import phate in python:

>>> import phate

ImportError: attempted relative import with no known parent package

scottgigante commented 4 years ago

Can you show the full python traceback? You may have to do this in repl_python or in python itself.

Also, can you print the contents of your working directory? I suspect there may be a folder in your working directory called phate which may be being imported instead of the installed package.

moldach commented 4 years ago

Hi @scottgigante

Things had become so hopeless that I had to result to 💣R/Python/Anaconda and start from a clean-slate. This should make things easier to trouble shoot now though as I've followed THE RStudio directions for setting up Python/reticulate with R after having installed Python with anaconda.

In the terminal:

which python
/home/tsundoku/anaconda3/bin/python

which pip
/home/tsundoku/anaconda3/bin/pip

Create a virtualenv:

/home/tsundoku/anaconda3/bin/virtualenv .venv
Using base prefix '/home/tsundoku/anaconda3'
New python executable in /home/tsundoku/RProjects/phate-test/.venv/bin/python
Installing setuptools, pip, wheel...
done.

Now source the environment and print which python again:

source .venv/bin/activate
(.venv) tsundoku@tsundoku-OptiPlex-7070:~/RProjects/phate-test$ which python
/home/tsundoku/RProjects/phate-test/.venv/bin/python

Try to install PHATE as recommended with --user param (it doesn't like it):

pip install --user phate

ERROR: Can not perform a '--user' install. User site-packages are not visible in this virtualenv.

Remove --user param:

pip install phate
Collecting phate
  Using cached phate-1.0.2-py3-none-any.whl (22 kB)
Collecting Deprecated
  Using cached Deprecated-1.2.7-py2.py3-none-any.whl (8.3 kB)
Collecting scprep>=0.11.1
  Using cached scprep-1.0.3-py3-none-any.whl (95 kB)
Collecting matplotlib>=3.0
  Using cached matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl (13.1 MB)
Collecting scipy>=1.1.0
  Using cached scipy-1.4.1-cp37-cp37m-manylinux1_x86_64.whl (26.1 MB)
Collecting scikit-learn>=0.20.0
  Using cached scikit_learn-0.22.1-cp37-cp37m-manylinux1_x86_64.whl (7.0 MB)
Collecting numpy>=1.16.0
  Using cached numpy-1.18.1-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB)
Collecting graphtools>=1.3.1
  Using cached graphtools-1.4.1-py3-none-any.whl (39 kB)
Processing /home/tsundoku/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0/future-0.18.2-py3-none-any.whl
Collecting tasklogger>=1.0
  Using cached tasklogger-1.0.0-py3-none-any.whl (14 kB)
Collecting sgdpy>=1.4.1
  Using cached sgdpy-1.4.1-cp37-cp37m-manylinux2010_x86_64.whl (480 kB)
Processing /home/tsundoku/.cache/pip/wheels/23/5f/62/304b411f20be41821465a82bc98baabc5e68c3cdd1eb99db71/wrapt-1.11.2-cp37-cp37m-linux_x86_64.whl
Collecting decorator>=4.3.0
  Using cached decorator-4.4.1-py2.py3-none-any.whl (9.2 kB)
Collecting pandas>=0.25
  Using cached pandas-0.25.3-cp37-cp37m-manylinux1_x86_64.whl (10.4 MB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached pyparsing-2.4.6-py2.py3-none-any.whl (67 kB)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.1.0-cp37-cp37m-manylinux1_x86_64.whl (90 kB)
Collecting joblib>=0.11
  Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting pygsp>=0.5.1
  Using cached PyGSP-0.5.1-py2.py3-none-any.whl (1.8 MB)
Collecting pytz>=2017.2
  Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting six>=1.5
  Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
Requirement already satisfied: setuptools in ./.venv/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=3.0->phate) (45.1.0)
Installing collected packages: wrapt, Deprecated, numpy, scipy, decorator, joblib, scikit-learn, six, python-dateutil, pytz, pandas, scprep, pyparsing, cycler, kiwisolver, matplotlib,pygsp, future, tasklogger, graphtools, sgdpy, phate
Successfully installed Deprecated-1.2.7 cycler-0.10.0 decorator-4.4.1 future-0.18.2 graphtools-1.4.1 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 numpy-1.18.1 pandas-0.25.3 phate-1.0.2 pygsp-0.5.1 pyparsing-2.4.6 python-dateutil-2.8.1 pytz-2019.3 scikit-learn-0.22.1 scipy-1.4.1 scprep-1.0.3 sgdpy-1.4.1 six-1.14.0

Now within .Rprofile set:

Sys.setenv(RETICULATE_PYTHON = ".venv/bin/python")

Restart RStudio and try to install phateR:

install.packages("phateR")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/phateR_1.0.0.tar.gz'
Content type 'application/x-gzip' length 3971691 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

* installing *source* package ‘phateR’ ...
** package ‘phateR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘phateR’:
 .onLoad failed in loadNamespace() for 'phateR', details:
  call: reticulate::py_discover_config(required_module = "phate")
  error: Python specified in RETICULATE_PYTHON (.venv/bin/python) does not exist
Error: loading failed
** testing if installed package can be loaded from final location
Error: package or namespace load failed for ‘phateR’:
 .onLoad failed in loadNamespace() for 'phateR', details:
  call: reticulate::py_discover_config(required_module = "phate")
  error: Python specified in RETICULATE_PYTHON (.venv/bin/python) does not exist
Error: loading failed
Error: .onLoad failed in loadNamespace() for 'phateR', details:
  call: reticulate::py_discover_config(required_module = "phate")
  error: Python specified in RETICULATE_PYTHON (.venv/bin/python) does not exist
** testing if installed package keeps a record of temporary installation path
* DONE (phateR)

The downloaded source packages are in
    ‘/tmp/RtmpRS9la9/downloaded_packages’

Here is my sessionInfo():

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] reticulate_1.14 BRRR_1.2       

loaded via a namespace (and not attached):
[1] compiler_3.6.2 magrittr_1.5   tools_3.6.2    rappdirs_0.3.1 Rcpp_1.0.3     audio_0.1-6    stringi_1.4.5  jsonlite_1.6  
[9] stringr_1.4.0

From the terminal again if I try and import phate it doesn't work (I guess that makes sense since I'm doing the install in a virtualenv - it shouldn't be available globally)

python
Python 3.7.4 (default, Aug 13 2019, 20:35:49)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import phate
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'phate'

Hopefully these details can help solve the issue. Please note that the RStudio method of using a virtualenv worked for numerous other python packages for me: umap-learn, fast_tsne, fastcluster, scipy, sklearn, etc.

akgold commented 4 years ago

Hi @moldach,

This is a bit beyond my expertise...one thing I might try. In the line where you declare the ‘RETICULATE_PYTHON’ variable, try using the full path to the venv. Let me know if that doesn’t work and I’ll consult with some more knowledgeable folks.

scottgigante commented 4 years ago

Some further troubleshooting:

moldach commented 4 years ago

Hi @moldach,

This is a bit beyond my expertise...one thing I might try. In the line where you declare the ‘RETICULATE_PYTHON’ variable, try using the full path to the venv. Let me know if that doesn’t work and I’ll consult with some more knowledgeable folks.

So originally I had set RETICULATE_PYTHON as suggested in the RStudio tutorial: Sys.setenv(RETICULATE_PYTHON = ".venv/bin/python")

Changing this to the full path of the venv works!: Sys.setenv(RETICULATE_PYTHON = "/home/tsundoku/RProjects/phate-test/.venv/bin/python").

This is problematic though when working on different projects/venv's....

I suppose @scottgigante suggestion works also but wondering if this can be improved for users so they won't have to (remember) to place Sys.setenv(RETICULATE_PYTHON = ".venv/bin/python") after calling library(reticulate) in every project/script 🤔

R -e 'Sys.setenv(RETICULATE_PYTHON = ".venv/bin/python"); reticulate::py_discover_config("phate")'
python:         /home/tsundoku/RProjects/phate-test/.venv/bin/python
libpython:      /home/tsundoku/anaconda3/lib/libpython3.7m.so
pythonhome:     /home/tsundoku/anaconda3:/home/tsundoku/anaconda3
virtualenv:     /home/tsundoku/RProjects/phate-test/.venv/bin/activate_this.py
version:        3.7.4 (default, Aug 13 2019, 20:35:49)  [GCC 7.3.0]
numpy:          /home/tsundoku/RProjects/phate-test/.venv/lib/python3.7/site-packages/numpy
numpy_version:  1.18.1
phate:          /home/tsundoku/RProjects/phate-test/.venv/lib/python3.7/site-packages/phate

NOTE: Python version was forced by RETICULATE_PYTHON

Thank you for your help and prompt response - I appreciate it.

scottgigante commented 4 years ago

Hi @moldach ,

You can set RETICULATE_PYTHON in your .Renviron file, either in the local directory to have this set for any projects run in that directory, or in your home directory to have this set for all R sessions. See more: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html

That aside, in theory py_discover_config should find PHATE automatically. Could you try running R -e 'reticulate::py_discover_config("phate")'?

moldach commented 4 years ago

Thanks for sharing that, I'll have to take a look later.

(.venv) tsundoku@tsundoku-OptiPlex-7070:~/RProjects/UMAP-examples-mammoth-$ R -e 'reticulate::py_discover_config("phate")'

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> reticulate::py_discover_config("phate")
python:         /home/tsundoku/RProjects/phate-test/.venv/bin/python
libpython:      /home/tsundoku/anaconda3/lib/libpython3.7m.so
pythonhome:     /home/tsundoku/anaconda3:/home/tsundoku/anaconda3
virtualenv:     /home/tsundoku/RProjects/phate-test/.venv/bin/activate_this.py
version:        3.7.4 (default, Aug 13 2019, 20:35:49)  [GCC 7.3.0]
numpy:          /home/tsundoku/RProjects/phate-test/.venv/lib/python3.7/site-packages/numpy
numpy_version:  1.18.1
phate:          /home/tsundoku/RProjects/phate-test/.venv/lib/python3.7/site-packages/phate

NOTE: Python version was forced by RETICULATE_PYTHON

After running this I'm able to import phate

scottgigante commented 4 years ago

Excellent, glad to hear it. Feel free to close this issue if you're successfully up and running.