attempt to apply non-function about ivis HOT 9 CLOSED

Hi there!

Before running ivis, if you're installing it for the first time you need to call install_ivis() in R:

devtools::install_github("beringresearch/ivis/R-package")
library(ivis)
install_ivis()

That will install all the python requirements - let us know if that helps

from ivis.

Thanks for your answer!
I have called install _ivis() in R in the first time, but there was an error --Error: one or more Python packages failed to install [error code 1]
And I tried to run "pip install ivis ”, but not succeed.
I don't know where is wrong, So how do I solve it?

from ivis.

Hi - Could you provide more details on that error pls - i.e. which python package is failing to install?

Probably has something to do with dependencies - are you installing under WSL?

from ivis.

Hi! This is the detail on that error, I never tried to install under WSL, and I don't how to run in WSL. Could you give me some suggestions?

install_ivis()
Creating a virtual environment (ivis)

• "C:/Users/Admin/AppData/Local/r-miniconda/condabin/conda.bat" "create" "--yes" "--name" "ivis" "python=3.8" "--quiet" "-c" "conda-forge"
  Collecting package metadata (current_repodata.json): ...working... done
  Solving environment: ...working... done

Package Plan

environment location: C:\Users\Admin\AppData\Local\R-MINI~1\envs\ivis

added / updated specs:
- python=3.8

The following NEW packages will be INSTALLED:

bzip2 conda-forge/win-64::bzip2-1.0.8-h8ffe710_4
ca-certificates conda-forge/win-64::ca-certificates-2022.6.15-h5b45459_0
libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5
libzlib conda-forge/win-64::libzlib-1.2.12-h8ffe710_2
openssl conda-forge/win-64::openssl-3.0.5-h8ffe710_0
pip conda-forge/noarch::pip-22.2.1-pyhd8ed1ab_0
python conda-forge/win-64::python-3.8.13-hcf16a7b_0_cpython
python_abi conda-forge/win-64::python_abi-3.8-2_cp38
setuptools conda-forge/win-64::setuptools-63.2.0-py38haa244fe_0
sqlite conda-forge/win-64::sqlite-3.39.2-h8ffe710_0
tk conda-forge/win-64::tk-8.6.12-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/win-64::xz-5.2.5-h62dcd97_1

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

• "C:/Users/Admin/AppData/Local/r-miniconda/condabin/conda.bat" "install" "--yes" "--name" "ivis" "-c" "conda-forge" "ivis[cpu]"
  Collecting package metadata (current_repodata.json): ...working... done
  Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
  Collecting package metadata (repodata.json): ...working... done
  Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

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

• ivis

Current channels:

• https://conda.anaconda.org/conda-forge/win-64
• https://conda.anaconda.org/conda-forge/noarch
• https://repo.anaconda.com/pkgs/main/win-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/win-64
• https://repo.anaconda.com/pkgs/r/noarch
• https://repo.anaconda.com/pkgs/msys2/win-64
• https://repo.anaconda.com/pkgs/msys2/noarch

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: one or more Python packages failed to install [error code 1]

from ivis.

Thanks for bringing this up, the R-package on Windows hasn't been something we use much and developed a few issues. I've pushed a series of commits to the master branch that should hopefully fix the issues you are having if you reinstall ivis.

from ivis.

Hi , thanks for your helping. I tried to reinstall ivis recently, but there was a new error when I run "install _ivis()". I can't understand this error, could you help me to solve this problem?

＞install _ivis()
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.
Error: Error installing package(s): ""ivis[cpu]""
In addition: Warning message:
In shell(fi, intern = intern) :
'C:\Users\Admin\AppData\Local\Temp\RtmpuOdl3b\filed484fb1424b.bat'The run failed with error code 2

from ivis.

This looks to me like an internet connection error. I can’t reproduce it unfortunately.

from ivis.

Thanks for your helping, I don't solve it successfully. I try to use other methods in Rstudio. Thanks for your answer., thank you!

from ivis.

Could you check to see if you can install from command line? I remember seeing that RStudio can have weird proxy settings preventing download from repo with a connection time out error.

from ivis.