In normalizePath(path.expand(path), winslash, mustWork)

[spsanderson]

I am running rstudio from Anaconda in an rstudio channel. I run the library(keras) and install_keras(method = "conda") commands and it errors out on a cannot find python.exe in the path

I also have R and RStudio installed outside of Anaconda and get nowhere there either.

sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages:
[1] keras_2.2.4.9001

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 lattice_0.20-38 zeallot_0.1.0 grid_3.5.3 R6_2.4.0 jsonlite_1.6
[7] magrittr_1.5 tfruns_1.4 whisker_0.3-2 Matrix_1.2-15 reticulate_1.11.1 generics_0.0.2
[13] tools_3.5.3 yaml_2.2.0 compiler_3.5.3 base64enc_0.1-3 tensorflow_1.13.1

library(keras)
install_keras(method = "conda")
Creating r-tensorflow conda environment for TensorFlow installation...
Collecting package metadata: ...working... done
Solving environment: ...working... done

Package Plan

environment location: C:\Users\Steve\ANACON~1\envs\r-tensorflow

added / updated specs:
- python=3.7

The following NEW packages will be INSTALLED:

ca-certificates pkgs/main/win-64::ca-certificates-2019.1.23-0
certifi pkgs/main/win-64::certifi-2019.3.9-py37_0
openssl pkgs/main/win-64::openssl-1.1.1b-he774522_1
pip pkgs/main/win-64::pip-19.0.3-py37_0
python pkgs/main/win-64::python-3.7.3-h8c8aaf0_0
setuptools pkgs/main/win-64::setuptools-40.8.0-py37_0
sqlite pkgs/main/win-64::sqlite-3.27.2-he774522_0
vc pkgs/main/win-64::vc-14.1-h0510ff6_4
vs2015_runtime pkgs/main/win-64::vs2015_runtime-14.15.26706-h3a45250_0
wheel pkgs/main/win-64::wheel-0.33.1-py37_0
wincertstore pkgs/main/win-64::wincertstore-0.2-py37_0

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

To activate this environment, use

 $ conda activate r-tensorflow

To deactivate an active environment, use

 $ conda deactivate

Collecting package metadata: ...working... done
Solving environment: ...working... done

Package Plan

environment location: C:\Users\Steve\ANACON~1\envs\r-tensorflow

added / updated specs:
- h5py
- keras
- pillow
- pyyaml
- requests
- scipy
- tensorflow-hub
- tensorflow-probability
- tensorflow==1.13.1

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
pillow-6.0.0               |   py36h9a613e6_0         674 KB  conda-forge
tensorflow-hub-0.4.0       |             py_0          52 KB  conda-forge
werkzeug-0.15.2            |             py_0         257 KB  conda-forge
------------------------------------------------------------
                                       Total:         983 KB

The following NEW packages will be INSTALLED:

_tflow_select pkgs/main/win-64::_tflow_select-2.3.0-mkl
absl-py conda-forge/win-64::absl-py-0.7.1-py36_0
asn1crypto conda-forge/win-64::asn1crypto-0.24.0-py36_1003
astor conda-forge/noarch::astor-0.7.1-py_0
blas pkgs/main/win-64::blas-1.0-mkl
cffi conda-forge/win-64::cffi-1.12.2-py36hb32ad35_1
chardet conda-forge/win-64::chardet-3.0.4-py36_1003
cryptography conda-forge/win-64::cryptography-2.6.1-py36hb32ad35_0
freetype conda-forge/win-64::freetype-2.10.0-h5db478b_0
gast conda-forge/noarch::gast-0.2.2-py_0
grpcio pkgs/main/win-64::grpcio-1.16.1-py36h351948d_1
h5py conda-forge/win-64::h5py-2.9.0-nompi_py36h3cb27cb_1102
hdf5 conda-forge/win-64::hdf5-1.10.4-nompi_hcc15c50_1106
icc_rt pkgs/main/win-64::icc_rt-2019.0.0-h0cc432a_1
idna conda-forge/win-64::idna-2.8-py36_1000
intel-openmp pkgs/main/win-64::intel-openmp-2019.3-203
jpeg conda-forge/win-64::jpeg-9c-hfa6e2cd_1001
keras conda-forge/win-64::keras-2.1.6-py36_0
keras-applications conda-forge/noarch::keras-applications-1.0.7-py_0
keras-preprocessi~ conda-forge/noarch::keras-preprocessing-1.0.9-py_0
libblas conda-forge/win-64::libblas-3.8.0-4_mkl
libcblas conda-forge/win-64::libcblas-3.8.0-4_mkl
libgpuarray conda-forge/win-64::libgpuarray-0.7.6-hfa6e2cd_1003
liblapack conda-forge/win-64::liblapack-3.8.0-4_mkl
libmklml pkgs/main/win-64::libmklml-2019.0.3-0
libpng conda-forge/win-64::libpng-1.6.36-h7602738_1000
libprotobuf conda-forge/win-64::libprotobuf-3.7.0-h1a1b453_2
libtiff conda-forge/win-64::libtiff-4.0.10-h36446d0_1001
mako conda-forge/noarch::mako-1.0.7-py_1
markdown conda-forge/noarch::markdown-2.6.11-py_0
markupsafe conda-forge/win-64::markupsafe-1.1.1-py36hfa6e2cd_0
mkl pkgs/main/win-64::mkl-2019.1-144
numpy conda-forge/win-64::numpy-1.16.2-py36h8078771_1
olefile conda-forge/noarch::olefile-0.46-py_0
pillow conda-forge/win-64::pillow-6.0.0-py36h9a613e6_0
protobuf conda-forge/win-64::protobuf-3.7.0-py36he025d50_0
pycparser conda-forge/win-64::pycparser-2.19-py36_1
pygpu conda-forge/win-64::pygpu-0.7.6-py36h452e1ab_1000
pyopenssl conda-forge/win-64::pyopenssl-19.0.0-py36_0
pyreadline conda-forge/win-64::pyreadline-2.1-py36_1000
pysocks conda-forge/win-64::pysocks-1.6.8-py36_1002
pyyaml conda-forge/win-64::pyyaml-5.1-py36hfa6e2cd_0
requests conda-forge/win-64::requests-2.21.0-py36_1000
scipy pkgs/main/win-64::scipy-1.2.1-py36h29ff71c_0
six conda-forge/win-64::six-1.12.0-py36_1000
tensorboard conda-forge/win-64::tensorboard-1.13.1-py36_0
tensorflow pkgs/main/win-64::tensorflow-1.13.1-mkl_py36hd212fbe_0
tensorflow-base pkgs/main/win-64::tensorflow-base-1.13.1-mkl_py36hcaf7020_0
tensorflow-estima~ conda-forge/win-64::tensorflow-estimator-1.13.0-py36h39e3cac_0
tensorflow-hub conda-forge/noarch::tensorflow-hub-0.4.0-py_0
tensorflow-probab~ conda-forge/noarch::tensorflow-probability-0.5.0-py_1
termcolor conda-forge/noarch::termcolor-1.1.0-py_2
theano conda-forge/win-64::theano-1.0.4-py36h6538335_1000
tk conda-forge/win-64::tk-8.6.9-hfa6e2cd_1001
urllib3 conda-forge/win-64::urllib3-1.24.1-py36_1000
vs2015_win-64 conda-forge/win-64::vs2015_win-64-14.0.25123-h17c34da_3
werkzeug conda-forge/noarch::werkzeug-0.15.2-py_0
win_inet_pton conda-forge/win-64::win_inet_pton-1.1.0-py36_0
yaml conda-forge/win-64::yaml-0.1.7-hfa6e2cd_1001
zlib conda-forge/win-64::zlib-1.2.11-h2fa13f4_1004

The following packages will be UPDATED:

ca-certificates pkgs/main::ca-certificates-2019.1.23-0 --> conda-forge::ca-certificates-2019.3.9-hecc5488_0
openssl pkgs/main::openssl-1.1.1b-he774522_1 --> conda-forge::openssl-1.1.1b-hfa6e2cd_2
wincertstore pkgs/main::wincertstore-0.2-py37_0 --> conda-forge::wincertstore-0.2-py36_1002

The following packages will be SUPERSEDED by a higher-priority channel:

certifi pkgs/main::certifi-2019.3.9-py37_0 --> conda-forge::certifi-2019.3.9-py36_0
pip pkgs/main::pip-19.0.3-py37_0 --> conda-forge::pip-19.0.3-py36_0
python pkgs/main::python-3.7.3-h8c8aaf0_0 --> conda-forge::python-3.6.7-he025d50_1004
setuptools pkgs/main::setuptools-40.8.0-py37_0 --> conda-forge::setuptools-40.8.0-py36_0
wheel pkgs/main::wheel-0.33.1-py37_0 --> conda-forge::wheel-0.33.1-py36_0

Downloading and Extracting Packages
werkzeug-0.15.2 | 257 KB | ########## | 100%
pillow-6.0.0 | 674 KB | ########## | 100%
tensorflow-hub-0.4.0 | 52 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

Installation complete.

Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
path[1]="C:\Users\Steve\ANACON~1\envs\rstudio/python.exe": The system cannot find the file specified

Restarting R session...

How could the installation complete if it could not even find python? A bit confused

[dfalbel]

Can you tell me the output of:

library(keras)
reticulate::py_config()

reticulate may be searching for python in different conda envs and this could be just a spurious message, since your rstudio conda env does not have python installed.

[spsanderson]

Sorry for late reply, took the family on a short getaway to visit parents. Here is the asked for output: python: C:\Users\Steve\Anaconda3\envs\r-tensorflow\python.exe libpython: C:/Users/Steve/Anaconda3/envs/r-tensorflow/python36.dll pythonhome: C:\Users\Steve\ANACON~1\envs\R-TENS~1 version: 3.6.7 (default, Feb 28 2019, 07:28:18) [MSC v.1900 64 bit (AMD64)] Architecture: 64bit numpy: C:\Users\Steve\ANACON~1\envs\R-TENS~1\lib\site-packages\numpy numpy_version: 1.16.2 tensorflow: C:\Users\Steve\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\__init__.p python versions found: C:\Users\Steve\Anaconda3\envs\r-tensorflow\python.exe C:\Users\Steve\AppData\Local\Programs\Python\Python37\python.exe C:\Users\Steve\AppData\Local\Programs\Python\Python37\\python.exe C:\Users\Steve\ANACON~1\python.exe C:\Users\Steve\Anaconda3\python.exe

…

On Thu, Apr 4, 2019 at 9:50 AM Daniel Falbel ***@***.***> wrote: Can you tell me the output of: library(keras) reticulate::py_config() reticulate may search python in different conda envs and this could be just a spurious message. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#728 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB4my6zzJ3dLzJMmiEM9Pa_t-oGG1Qo8ks5vdgMTgaJpZM4cazbH> .

-- Steven P Sanderson II, MPH Book on Lulu <http://goo.gl/lmrlFI>

[dfalbel]

No problems :)

It seems to me that your installation is fine and the error message was just spurious. I'll close the issue, feel free to reopen it if you have any more problems.