static export from R not working
Adafede opened this issue · comments
Hi,
Looks like there is a little something not working but couldn't figure out what:
reticulate::install_miniconda(force = TRUE)
reticulate::conda_install('r-reticulate', 'python-kaleido')
reticulate::conda_install('r-reticulate', 'plotly', channel = 'plotly')
reticulate::use_miniconda('r-reticulate')
p <- plotly::plot_ly(x = 1:10)
plotly::save_image(p, "test.pdf")
sessionInfo()
gives
> reticulate::install_miniconda(force = TRUE)
* Installing Miniconda -- please wait a moment ...
* Downloading 'https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh' ...
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh'
Content type 'application/x-sh' length 57904526 bytes (55.2 MB)
==================================================
downloaded 55.2 MB
PREFIX=/Users/rutza/Library/r-miniconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/rutza/Library/r-miniconda
added / updated specs:
- brotlipy==0.7.0=py39h9ed2024_1003
- ca-certificates==2021.10.26=hecd8cb5_2
- certifi==2021.10.8=py39hecd8cb5_2
- cffi==1.15.0=py39hc55c11b_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.7.3=py39h9ed2024_1
- conda==4.11.0=py39hecd8cb5_0
- cryptography==36.0.0=py39hf6deb26_0
- idna==3.3=pyhd3eb1b0_0
- libcxx==12.0.0=h2f01273_0
- libffi==3.3=hb1e8313_2
- ncurses==6.3=hca72f7f_2
- openssl==1.1.1m=hca72f7f_0
- pip==21.2.4=py39hecd8cb5_0
- pycosat==0.6.3=py39h9ed2024_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==21.0.0=pyhd3eb1b0_1
- pysocks==1.7.1=py39hecd8cb5_0
- python.app==3=py39hca72f7f_0
- python==3.9.7=h88f2d9e_1
- readline==8.1.2=hca72f7f_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h9ed2024_0
- setuptools==58.0.4=py39hecd8cb5_0
- six==1.16.0=pyhd3eb1b0_0
- sqlite==3.37.0=h707629a_0
- tk==8.6.11=h7bc2e8c_0
- tqdm==4.62.3=pyhd3eb1b0_1
- tzdata==2021e=hda174b7_0
- urllib3==1.26.7=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h1de35cc_0
- yaml==0.2.5=haf1e3a3_0
- zlib==1.2.11=h4dc903c_4
The following NEW packages will be INSTALLED:
brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003
ca-certificates pkgs/main/osx-64::ca-certificates-2021.10.26-hecd8cb5_2
certifi pkgs/main/osx-64::certifi-2021.10.8-py39hecd8cb5_2
cffi pkgs/main/osx-64::cffi-1.15.0-py39hc55c11b_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
conda pkgs/main/osx-64::conda-4.11.0-py39hecd8cb5_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.7.3-py39h9ed2024_1
cryptography pkgs/main/osx-64::cryptography-36.0.0-py39hf6deb26_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
libcxx pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
ncurses pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
openssl pkgs/main/osx-64::openssl-1.1.1m-hca72f7f_0
pip pkgs/main/osx-64::pip-21.2.4-py39hecd8cb5_0
pycosat pkgs/main/osx-64::pycosat-0.6.3-py39h9ed2024_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-21.0.0-pyhd3eb1b0_1
pysocks pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0
python pkgs/main/osx-64::python-3.9.7-h88f2d9e_1
python.app pkgs/main/osx-64::python.app-3-py39hca72f7f_0
readline pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0
setuptools pkgs/main/osx-64::setuptools-58.0.4-py39hecd8cb5_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0
sqlite pkgs/main/osx-64::sqlite-3.37.0-h707629a_0
tk pkgs/main/osx-64::tk-8.6.11-h7bc2e8c_0
tqdm pkgs/main/noarch::tqdm-4.62.3-pyhd3eb1b0_1
tzdata pkgs/main/noarch::tzdata-2021e-hda174b7_0
urllib3 pkgs/main/noarch::urllib3-1.26.7-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
zlib pkgs/main/osx-64::zlib-1.2.11-h4dc903c_4
Preparing transaction: ...working... done
Executing transaction: ...working...
done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/rutza/Library/r-miniconda
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
brotlipy-0.7.0 |py39h89e85a6_1003 358 KB conda-forge
bzip2-1.0.8 | h0d85af4_4 155 KB conda-forge
ca-certificates-2021.10.8 | h033912b_0 139 KB conda-forge
certifi-2021.10.8 | py39h6e9494a_1 145 KB conda-forge
cffi-1.15.0 | py39he338e87_0 219 KB conda-forge
charset-normalizer-2.0.12 | pyhd8ed1ab_0 35 KB conda-forge
colorama-0.4.4 | pyh9f0ad1d_0 18 KB conda-forge
conda-4.11.0 | py39h6e9494a_0 16.9 MB conda-forge
conda-package-handling-1.7.3| py39h89e85a6_1 1.7 MB conda-forge
idna-3.3 | pyhd8ed1ab_0 55 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libzlib-1.2.11 | h9173be1_1013 58 KB conda-forge
ncurses-6.3 | he49afe7_0 926 KB conda-forge
openssl-3.0.0 | h0d85af4_2 2.5 MB conda-forge
pip-22.0.3 | pyhd8ed1ab_0 1.5 MB conda-forge
pycosat-0.6.3 |py39h89e85a6_1009 114 KB conda-forge
pycparser-2.21 | pyhd8ed1ab_0 100 KB conda-forge
pyopenssl-22.0.0 | pyhd8ed1ab_0 49 KB conda-forge
pysocks-1.7.1 | py39h6e9494a_4 28 KB conda-forge
python-3.9.10 |hea1dfa3_2_cpython 12.5 MB conda-forge
python_abi-3.9 | 2_cp39 4 KB conda-forge
readline-8.1 | h05e3726_0 266 KB conda-forge
requests-2.27.1 | pyhd8ed1ab_0 53 KB conda-forge
ruamel_yaml-0.15.80 |py39h89e85a6_1006 251 KB conda-forge
setuptools-60.9.1 | py39h6e9494a_0 1.2 MB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
sqlite-3.37.0 | h23a322b_0 1.8 MB conda-forge
tk-8.6.11 | h5dbffcc_1 3.3 MB conda-forge
tqdm-4.62.3 | pyhd8ed1ab_0 80 KB conda-forge
tzdata-2021e | he74cb21_0 121 KB conda-forge
urllib3-1.26.8 | pyhd8ed1ab_1 100 KB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
xz-5.2.5 | haf1e3a3_1 228 KB conda-forge
yaml-0.2.5 | h0d85af4_2 82 KB conda-forge
zlib-1.2.11 | h9173be1_1013 87 KB conda-forge
------------------------------------------------------------
Total: 44.9 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
colorama conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
python_abi conda-forge/osx-64::python_abi-3.9-2_cp39
The following packages will be REMOVED:
conda-content-trust-0.1.1-pyhd3eb1b0_0
libcxx-12.0.0-h2f01273_0
The following packages will be UPDATED:
charset-normalizer pkgs/main::charset-normalizer-2.0.4-p~ --> conda-forge::charset-normalizer-2.0.12-pyhd8ed1ab_0
libffi pkgs/main::libffi-3.3-hb1e8313_2 --> conda-forge::libffi-3.4.2-h0d85af4_5
openssl pkgs/main::openssl-1.1.1m-hca72f7f_0 --> conda-forge::openssl-3.0.0-h0d85af4_2
pip pkgs/main/osx-64::pip-21.2.4-py39hecd~ --> conda-forge/noarch::pip-22.0.3-pyhd8ed1ab_0
pycosat pkgs/main::pycosat-0.6.3-py39h9ed2024~ --> conda-forge::pycosat-0.6.3-py39h89e85a6_1009
pyopenssl pkgs/main::pyopenssl-21.0.0-pyhd3eb1b~ --> conda-forge::pyopenssl-22.0.0-pyhd8ed1ab_0
pysocks pkgs/main::pysocks-1.7.1-py39hecd8cb5~ --> conda-forge::pysocks-1.7.1-py39h6e9494a_4
python pkgs/main::python-3.9.7-h88f2d9e_1 --> conda-forge::python-3.9.10-hea1dfa3_2_cpython
setuptools pkgs/main::setuptools-58.0.4-py39hecd~ --> conda-forge::setuptools-60.9.1-py39h6e9494a_0
tk pkgs/main::tk-8.6.11-h7bc2e8c_0 --> conda-forge::tk-8.6.11-h5dbffcc_1
urllib3 pkgs/main::urllib3-1.26.7-pyhd3eb1b0_0 --> conda-forge::urllib3-1.26.8-pyhd8ed1ab_1
xz pkgs/main::xz-5.2.5-h1de35cc_0 --> conda-forge::xz-5.2.5-haf1e3a3_1
yaml pkgs/main::yaml-0.2.5-haf1e3a3_0 --> conda-forge::yaml-0.2.5-h0d85af4_2
zlib pkgs/main::zlib-1.2.11-h4dc903c_4 --> conda-forge::zlib-1.2.11-h9173be1_1013
The following packages will be SUPERSEDED by a higher-priority channel:
brotlipy pkgs/main::brotlipy-0.7.0-py39h9ed202~ --> conda-forge::brotlipy-0.7.0-py39h89e85a6_1003
ca-certificates pkgs/main::ca-certificates-2021.10.26~ --> conda-forge::ca-certificates-2021.10.8-h033912b_0
certifi pkgs/main::certifi-2021.10.8-py39hecd~ --> conda-forge::certifi-2021.10.8-py39h6e9494a_1
cffi pkgs/main::cffi-1.15.0-py39hc55c11b_1 --> conda-forge::cffi-1.15.0-py39he338e87_0
conda pkgs/main::conda-4.11.0-py39hecd8cb5_0 --> conda-forge::conda-4.11.0-py39h6e9494a_0
conda-package-han~ pkgs/main::conda-package-handling-1.7~ --> conda-forge::conda-package-handling-1.7.3-py39h89e85a6_1
idna pkgs/main::idna-3.3-pyhd3eb1b0_0 --> conda-forge::idna-3.3-pyhd8ed1ab_0
ncurses pkgs/main::ncurses-6.3-hca72f7f_2 --> conda-forge::ncurses-6.3-he49afe7_0
pycparser pkgs/main::pycparser-2.21-pyhd3eb1b0_0 --> conda-forge::pycparser-2.21-pyhd8ed1ab_0
readline pkgs/main::readline-8.1.2-hca72f7f_1 --> conda-forge::readline-8.1-h05e3726_0
requests pkgs/main::requests-2.27.1-pyhd3eb1b0~ --> conda-forge::requests-2.27.1-pyhd8ed1ab_0
ruamel_yaml pkgs/main::ruamel_yaml-0.15.100-py39h~ --> conda-forge::ruamel_yaml-0.15.80-py39h89e85a6_1006
six pkgs/main::six-1.16.0-pyhd3eb1b0_0 --> conda-forge::six-1.16.0-pyh6c4a22f_0
sqlite pkgs/main::sqlite-3.37.0-h707629a_0 --> conda-forge::sqlite-3.37.0-h23a322b_0
tqdm pkgs/main::tqdm-4.62.3-pyhd3eb1b0_1 --> conda-forge::tqdm-4.62.3-pyhd8ed1ab_0
tzdata pkgs/main::tzdata-2021e-hda174b7_0 --> conda-forge::tzdata-2021e-he74cb21_0
wheel pkgs/main::wheel-0.37.1-pyhd3eb1b0_0 --> conda-forge::wheel-0.37.1-pyhd8ed1ab_0
Downloading and Extracting Packages
bzip2-1.0.8 | 155 KB | ########## | 100%
yaml-0.2.5 | 82 KB | ########## | 100%
pyopenssl-22.0.0 | 49 KB | ########## | 100%
python_abi-3.9 | 4 KB | ########## | 100%
ruamel_yaml-0.15.80 | 251 KB | ########## | 100%
sqlite-3.37.0 | 1.8 MB | ########## | 100%
tk-8.6.11 | 3.3 MB | ########## | 100%
tzdata-2021e | 121 KB | ########## | 100%
wheel-0.37.1 | 31 KB | ########## | 100%
zlib-1.2.11 | 87 KB | ########## | 100%
libffi-3.4.2 | 50 KB | ########## | 100%
conda-4.11.0 | 16.9 MB | ########## | 100%
colorama-0.4.4 | 18 KB | ########## | 100%
cffi-1.15.0 | 219 KB | ########## | 100%
ca-certificates-2021 | 139 KB | ########## | 100%
brotlipy-0.7.0 | 358 KB | ########## | 100%
ncurses-6.3 | 926 KB | ########## | 100%
urllib3-1.26.8 | 100 KB | ########## | 100%
openssl-3.0.0 | 2.5 MB | ########## | 100%
idna-3.3 | 55 KB | ########## | 100%
six-1.16.0 | 14 KB | ########## | 100%
setuptools-60.9.1 | 1.2 MB | ########## | 100%
readline-8.1 | 266 KB | ########## | 100%
certifi-2021.10.8 | 145 KB | ########## | 100%
libzlib-1.2.11 | 58 KB | ########## | 100%
charset-normalizer-2 | 35 KB | ########## | 100%
pycparser-2.21 | 100 KB | ########## | 100%
pycosat-0.6.3 | 114 KB | ########## | 100%
conda-package-handli | 1.7 MB | ########## | 100%
tqdm-4.62.3 | 80 KB | ########## | 100%
pysocks-1.7.1 | 28 KB | ########## | 100%
python-3.9.10 | 12.5 MB | ########## | 100%
pip-22.0.3 | 1.5 MB | ########## | 100%
xz-5.2.5 | 228 KB | ########## | 100%
requests-2.27.1 | 53 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/rutza/Library/r-miniconda/envs/r-reticulate
added / updated specs:
- numpy
- python=3.8
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |13_osx64_openblas 12 KB conda-forge
libcblas-3.9.0 |13_osx64_openblas 12 KB conda-forge
libcxx-12.0.1 | habf9029_1 1.1 MB conda-forge
libgfortran-5.0.0 |9_3_0_h6c81a4c_23 19 KB conda-forge
libgfortran5-9.3.0 | h6c81a4c_23 1.7 MB conda-forge
liblapack-3.9.0 |13_osx64_openblas 12 KB conda-forge
libopenblas-0.3.18 |openmp_h3351f45_0 9.0 MB conda-forge
llvm-openmp-13.0.1 | hda6cdc1_0 305 KB conda-forge
numpy-1.22.2 | py38h9d72dae_0 6.3 MB conda-forge
python-3.8.12 |h43ca1e7_3_cpython 12.4 MB conda-forge
python_abi-3.8 | 2_cp38 4 KB conda-forge
setuptools-60.9.1 | py38h50d1736_0 1.2 MB conda-forge
------------------------------------------------------------
Total: 32.0 MB
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2021.10.8-h033912b_0
libblas conda-forge/osx-64::libblas-3.9.0-13_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-13_osx64_openblas
libcxx conda-forge/osx-64::libcxx-12.0.1-habf9029_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_23
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_23
liblapack conda-forge/osx-64::liblapack-3.9.0-13_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.18-openmp_h3351f45_0
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
llvm-openmp conda-forge/osx-64::llvm-openmp-13.0.1-hda6cdc1_0
ncurses conda-forge/osx-64::ncurses-6.3-he49afe7_0
numpy conda-forge/osx-64::numpy-1.22.2-py38h9d72dae_0
openssl conda-forge/osx-64::openssl-3.0.0-h0d85af4_2
pip conda-forge/noarch::pip-22.0.3-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.8.12-h43ca1e7_3_cpython
python_abi conda-forge/osx-64::python_abi-3.8-2_cp38
readline conda-forge/osx-64::readline-8.1-h05e3726_0
setuptools conda-forge/osx-64::setuptools-60.9.1-py38h50d1736_0
sqlite conda-forge/osx-64::sqlite-3.37.0-h23a322b_0
tk conda-forge/osx-64::tk-8.6.11-h5dbffcc_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h9173be1_1013
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
* Miniconda has been successfully installed at "~/Library/r-miniconda".
[1] "/Users/rutza/Library/r-miniconda"
> reticulate::conda_install('r-reticulate', 'python-kaleido')
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/rutza/Library/r-miniconda/envs/r-reticulate
added / updated specs:
- python-kaleido
The following packages will be downloaded:
package | build
---------------------------|-----------------
kaleido-core-0.2.1 | h0d85af4_0 71.9 MB conda-forge
mathjax-2.7.7 | 0 21.3 MB conda-forge
python-kaleido-0.2.1 | pyhd8ed1ab_0 18 KB conda-forge
------------------------------------------------------------
Total: 93.2 MB
The following NEW packages will be INSTALLED:
kaleido-core conda-forge/osx-64::kaleido-core-0.2.1-h0d85af4_0
mathjax conda-forge/osx-64::mathjax-2.7.7-0
python-kaleido conda-forge/noarch::python-kaleido-0.2.1-pyhd8ed1ab_0
Downloading and Extracting Packages
kaleido-core-0.2.1 | 71.9 MB | ########## | 100%
mathjax-2.7.7 | 21.3 MB | ########## | 100%
python-kaleido-0.2.1 | 18 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
> reticulate::conda_install('r-reticulate', 'plotly', channel = 'plotly')
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/rutza/Library/r-miniconda/envs/r-reticulate
added / updated specs:
- plotly
The following packages will be downloaded:
package | build
---------------------------|-----------------
plotly-5.6.0 | py_0 6.9 MB plotly
tenacity-8.0.1 | pyhd8ed1ab_0 21 KB conda-forge
------------------------------------------------------------
Total: 7.0 MB
The following NEW packages will be INSTALLED:
plotly plotly/noarch::plotly-5.6.0-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tenacity conda-forge/noarch::tenacity-8.0.1-pyhd8ed1ab_0
Downloading and Extracting Packages
plotly-5.6.0 | 6.9 MB | ########## | 100%
tenacity-8.0.1 | 21 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
> reticulate::use_miniconda('r-reticulate')
> p <- plotly::plot_ly(x = 1:10)
> plotly::save_image(p, "test.pdf")
No trace type specified:
Based on info supplied, a 'histogram' trace seems appropriate.
Read more about this trace type -> https://plotly.com/r/reference/#histogram
Error in py_run_string_impl(code, local, convert) :
ValueError: Failed to start Kaleido subprocess. Error stream:
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] fr_CH.UTF-8/fr_CH.UTF-8/fr_CH.UTF-8/C/fr_CH.UTF-8/fr_CH.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 pillar_1.7.0 compiler_4.1.2 tools_4.1.2 digest_0.6.29
[6] viridisLite_0.4.0 jsonlite_1.7.3 lifecycle_1.0.1 tibble_3.1.6 gtable_0.3.0
[11] lattice_0.20-45 pkgconfig_2.0.3 png_0.1-7 rlang_1.0.1 Matrix_1.4-0
[16] cli_3.2.0 DBI_1.1.2 crosstalk_1.2.0 fastmap_1.1.0 httr_1.4.2
[21] dplyr_1.0.8 htmlwidgets_1.5.4 generics_0.1.2 vctrs_0.3.8 rprojroot_2.0.2
[26] grid_4.1.2 tidyselect_1.1.1 here_1.0.1 reticulate_1.24 glue_1.6.1
[31] data.table_1.14.2 R6_2.5.1 fansi_1.0.2 plotly_4.10.0 tidyr_1.2.0
[36] ggplot2_3.3.5 purrr_0.3.4 magrittr_2.0.2 scales_1.1.1 ellipsis_0.3.2
[41] htmltools_0.5.2 assertthat_0.2.1 colorspace_2.0-2 utf8_1.2.2 lazyeval_0.2.2
[46] munsell_0.5.0 crayon_1.5.0
Coud not find any hints with
Error in py_run_string_impl(code, local, convert) :
ValueError: Failed to start Kaleido subprocess. Error stream:
Hope it is the right place to report 😄
While running more in-depth could reach the following, can maybe help:
Detailed traceback:
File "<string>", line 1, in <module>
File "/Users/rutza/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/kaleido/scopes/plotly.py", line 153, in transform
response = self._perform_transform(
File "/Users/rutza/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/kaleido/scopes/base.py", line 293, in _perform_transform
self._ensure_kaleido()
File "/Users/rutza/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/kaleido/scopes/base.py", line 198, in _ensure_kaleido
raise ValueError(message)
Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> py_run_string_impl
Execution halted
I believe I'm having the same issue- my R instance hangs when trying to save a static image.
Nothing I've tried seems to fix the issue. I've tried installing a separate instance of Anaconda in a location without spaces in the directory path, re-installing packages, etc.
I'm having the same issue. I get teh same error as in above code. If I use a path instead of just a file name save_image(p, tempfile(fileext = ".png")) I get:
Error in py_run_string_impl(code, local, convert) :
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 2-3: truncated \UXXXXXXXX escape (<string>, line 1)
I did discovere the issue after transfering to a new computer. Previously it worked fine.
> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=Finnish_Finland.utf8 LC_CTYPE=Finnish_Finland.utf8 LC_MONETARY=Finnish_Finland.utf8
[4] LC_NUMERIC=C LC_TIME=Finnish_Finland.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plotly_4.10.0 ggplot2_3.3.5 testthat_3.1.4 devtools_2.4.3 usethis_2.1.5
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.2 statfitools_0.3.7.9003 lubridate_1.8.0
[5] fontawesome_0.2.2 httr_1.4.2 rprojroot_2.0.3 googleAuthR_2.0.0
[9] tools_4.2.0 backports_1.4.1 utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 withr_2.5.0
[17] tidyselect_1.1.2 prettyunits_1.1.1 processx_3.5.3 curl_4.3.2
[21] compiler_4.2.0 cli_3.3.0 desc_1.4.1 scales_1.2.0
[25] callr_3.7.0 askpass_1.1 rappdirs_0.3.3 stringr_1.4.0
[29] digest_0.6.29 rmarkdown_2.14 pkgconfig_2.0.3 htmltools_0.5.2
[33] sessioninfo_1.2.2 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.2
[37] readxl_1.4.0 pttrobo_0.1.7 rstudioapi_0.13 generics_0.1.2
[41] zoo_1.8-10 jsonlite_1.8.0 crosstalk_1.2.0 dplyr_1.0.8
[45] zip_2.2.0 car_3.0-12 RCurl_1.98-1.6 magrittr_2.0.3
[49] Matrix_1.4-1 Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.3
[53] abind_1.4-5 reticulate_1.24 lifecycle_1.0.1 stringi_1.7.6
[57] yaml_2.3.5 carData_3.0-5 brio_1.1.3 pkgbuild_1.3.1
[61] grid_4.2.0 forcats_0.5.1 crayon_1.5.1 lattice_0.20-45
[65] knitr_1.39 ps_1.7.0 pillar_1.7.0 ggpubr_0.4.0
[69] ggsignif_0.6.3 pkgload_1.2.4 glue_1.6.2 evaluate_0.15
[73] data.table_1.14.2 remotes_2.4.2 png_0.1-7 vctrs_0.4.1
[77] cellranger_1.1.0 gtable_0.3.0 robonomistClient_2.2.4 openssl_2.0.0
[81] purrr_0.3.4 tidyr_1.2.0 assertthat_0.2.1 cachem_1.0.6
[85] xfun_0.30 googleCloudStorageR_0.7.0 broom_0.8.0 rstatix_0.7.0
[89] later_1.3.0 viridisLite_0.4.0 gargle_1.2.0 tibble_3.1.6
[93] websocket_1.4.1 memoise_2.0.1 ellipsis_0.3.2 here_1.0.1
I can't get this to run on my MacBook Pro M1 either.
p <- plot_ly(x = 1:10, y = 1:10, type = "scatter", mode = "marker")
save_image(p, "test.png")
Error in py_run_string_impl(code, local, convert) :
NameError: name 'sys' is not defined
I went through all the installation steps in ?plotly::save_image without issues.
install.packages('reticulate')
reticulate::install_miniconda()
reticulate::conda_install('r-reticulate', 'python-kaleido')
reticulate::conda_install('r-reticulate', 'plotly', channel = 'plotly')
reticulate::use_miniconda('r-reticulate')
I tried reticulate::import("sys") but that didn't work. Any help would be appreciated.
Error in py_run_string_impl(code, local, convert) :
NameError: name 'sys' is not defined
#not use：reticulate::import("sys")
reticulate::py_run_string("import sys")
it work!!!
Using Windows 10 and running this causes R to hang and does not render the test p:
library(reticulate)
use_miniconda('r-reticulate')
library(plotly)
p <- plot_ly(x = 1:10, y = 1:10, type = "scatter", mode = "marker")
save_image(p, "test.png")
Here is the traceback:
traceback(save_image(p, "test.png"))
Error in py_run_string_impl(code, local, convert) :
NameError: name 'sys' is not defined
Run `reticulate::py_last_error()` for details.
> reticulate::py_last_error()
-- Python Exception Message --------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 1, in <module>
NameError: name 'sys' is not defined
-- R Traceback ---------------------------------------------------------------------
x
1. +-base::traceback(save_image(p, "test.png"))
2. | \-base::.traceback(x, max.lines = max.lines)
3. | \-base (local) .is.positive.intlike(x)
4. \-plotly::save_image(p, "test.png")
5. \-kaleido()$transform(...)
6. \-reticulate::py_run_string(...)
7. \-reticulate:::py_run_string_impl(code, local, convert)
Current R version and sessionInfo:
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
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.
[Workspace loaded from ~/.RData]
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 mathjaxr_1.6-0 pillar_1.9.0
[4] compiler_4.1.2 tools_4.1.2 metadat_1.2-0
[7] nlme_3.1-153 jsonlite_1.8.7 lifecycle_1.0.3
[10] tibble_3.2.1 gtable_0.3.3 lattice_0.20-45
[13] pkgconfig_2.0.3 png_0.1-8 rlang_1.1.1
[16] Matrix_1.5-4 cli_3.6.1 rstudioapi_0.14
[19] gridExtra_2.3 metafor_4.2-0 dplyr_1.1.2
[22] generics_0.1.3 vctrs_0.6.3 grid_4.1.2
[25] tidyselect_1.2.0 reticulate_1.31 glue_1.6.2
[28] R6_2.5.1 fansi_1.0.4 distributional_0.3.2
[31] purrr_1.0.1 ggplot2_3.4.2 farver_2.1.1
[34] magrittr_2.0.3 scales_1.2.1 ggdist_3.2.1
[37] colorspace_2.1-0 numDeriv_2016.8-1.1 utf8_1.2.3
[40] munsell_0.5.0 crayon_1.5.2
rstudioapi::versionInfo()
$citation
To cite RStudio in publications use:
Posit team (2023). RStudio: Integrated Development Environment for R.
Posit Software, PBC, Boston, MA. URL http://www.posit.co/.
A BibTeX entry for LaTeX users is
@Manual{,
title = {RStudio: Integrated Development Environment for R},
author = {{Posit team}},
organization = {Posit Software, PBC},
address = {Boston, MA},
year = {2023},
url = {http://www.posit.co/},
}
$mode
[1] "desktop"
$version
[1] ‘2023.6.2.561’
$long_version
[1] "2023.06.2+561"
$release_name
[1] "Mountain Hydrangea"
Thanks for all the digging!
Did you try the extra step I mentioned in the help for export_plotly?
You need to include reticulate::py_run_string("import sys") to avoid that error. I had the same problem on my Mac.
Altogether the commands are:
install.packages('reticulate')
reticulate::install_miniconda()
reticulate::conda_install('r-reticulate', 'python-kaleido')
reticulate::conda_install('r-reticulate', 'plotly', channel = 'plotly')
reticulate::use_miniconda('r-reticulate')
reticulate::py_run_string("import sys") #this is the extra step neglected in help for save_plotly.
My export_plotly() should run whichever of these is needed, but perhaps that part failed. I check to see if kaleido, reticulate, and minconda are installed, but maybe if there was a partial install the check failed and the installation wasn't completed.
Thansk @mnneely.
It seems like my issue might have had to do with this:
https://stackoverflow.com/questions/72197496/r-plotlysave-image-kaleido-static-export-from-r-not-working
After failing to get tmp.png with the default kalido install I backed up to an older version:
reticulate::conda_install('r-reticulate', 'python-kaleido') # not working
reticulate::conda_install('r-reticulate', 'python-kaleido==0.1.*') # works
I don't know what the issue is or why it kept on hanging though...
Good find, but frustrating I agree. I have python-kaleido 0.2.1 running on my Mac (M1) and it works. I used reticulate::py_list_packages() as an easy way to list all the Python packages installed via reticulate::conda_install().
Thanks Michael,
I am running as follows:
reticulate::py_list_packages()
package version requirement channel
1 bzip2 1.0.8 bzip2=1.0.8 conda-forge
2 ca-certificates 2023.7.22 ca-certificates=2023.7.22 conda-forge
3 intel-openmp 2023.2.0 intel-openmp=2023.2.0 conda-forge
4 kaleido-core 0.1.0 kaleido-core=0.1.0 conda-forge
5 libblas 3.9.0 libblas=3.9.0 conda-forge
6 libcblas 3.9.0 libcblas=3.9.0 conda-forge
7 libffi 3.4.2 libffi=3.4.2 conda-forge
8 libhwloc 2.9.2 libhwloc=2.9.2 conda-forge
9 libiconv 1.17 libiconv=1.17 conda-forge
10 liblapack 3.9.0 liblapack=3.9.0 conda-forge
11 libsqlite 3.43.0 libsqlite=3.43.0 conda-forge
12 libxml2 2.11.5 libxml2=2.11.5 conda-forge
13 libzlib 1.2.13 libzlib=1.2.13 conda-forge
14 mathjax 2.7.7 mathjax=2.7.7 conda-forge
15 mkl 2022.1.0 mkl=2022.1.0 conda-forge
16 numpy 1.25.2 numpy=1.25.2 conda-forge
17 openssl 3.1.2 openssl=3.1.2 conda-forge
18 pip 23.2.1 pip=23.2.1 conda-forge
19 plotly 5.16.1 plotly=5.16.1 plotly
20 pthreads-win32 2.9.1 pthreads-win32=2.9.1 conda-forge
21 python 3.9.17 python=3.9.17 conda-forge
22 python-kaleido 0.1.0 python-kaleido=0.1.0 conda-forge
23 python_abi 3.9 python_abi=3.9 conda-forge
24 setuptools 68.1.2 setuptools=68.1.2 conda-forge
25 tbb 2021.10.0 tbb=2021.10.0 conda-forge
26 tenacity 8.2.2 tenacity=8.2.2 pkgs/main
27 tk 8.6.12 tk=8.6.12 conda-forge
28 tzdata 2023c tzdata=2023c conda-forge
29 ucrt 10.0.22621.0 ucrt=10.0.22621.0 conda-forge
30 vc 14.3 vc=14.3 conda-forge
31 vc14_runtime 14.36.32532 vc14_runtime=14.36.32532 conda-forge
32 vs2015_runtime 14.36.32532 vs2015_runtime=14.36.32532 conda-forge
33 wheel 0.41.2 wheel=0.41.2 conda-forge
34 xz 5.2.6 xz=5.2.6 conda-forge
Working so far!
From: Michael Neely ***@***.***>
Sent: Tuesday, August 29, 2023 1:32 PM
To: plotly/Kaleido ***@***.***>
Cc: Rhodes, Nathaniel ***@***.***>; Comment ***@***.***>
Subject: Re: [plotly/Kaleido] static export from R not working (Issue #129)
[External email: Use caution with links and attachments]
Good find, but frustrating I agree. I have python-kaleido 0.2.1 running on my Mac (M1) and it works. I used reticulate::py_list_packages() as an easy way to list all the Python packages installed via reticulate::conda_install().
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