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IRkernel / repr

String and byte representations for all kinds of R objects
https://irkernel.github.io/docs/repr/
GNU General Public License v3.0
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DT::datatable(iris) is not displaying anything on Jupyter notebook #148

Closed yilong-serum closed 2 years ago

yilong-serum commented 2 years ago

The following simple lines are not showing anything on Jupyter notebook. The cell output is simply empty/nothing.

library(DT)
datatable(iris)

Everything seems file in the debug messages on the terminal (running jupyter notebook --debug).

[D 10:55:46.551 NotebookApp] activity on c0a00a96-bdbf-4ade-9cd3-3a8b68025809: status (busy)
[D 10:55:46.552 NotebookApp] activity on c0a00a96-bdbf-4ade-9cd3-3a8b68025809: execute_input
[D 10:55:46.623 NotebookApp] activity on c0a00a96-bdbf-4ade-9cd3-3a8b68025809: display_data
[D 10:55:46.625 NotebookApp] activity on c0a00a96-bdbf-4ade-9cd3-3a8b68025809: status (idle)

I am using Conda and below are my packages. However, I did follow the instructions of the first tick box and install IRkernel through R as well.

Not sure if relevant, but if I use repr_html(), I just get a string as the cell output.

repr_html(datatable(iris))
'<!doctype html>\n<html>\n\t<head>\n\t\t<meta charset="utf-8">\n\t\t<script title="htmlwidgets" src="data:application/javascript;base64,KGZ1bmN0aW9u...
...

What else could I be checking to debug this?

``` # Name Version Build Channel _r-mutex 1.0.1 anacondar_1 conda-forge aioeasywebdav 2.4.0 py39h6e9494a_1001 conda-forge aiohttp 3.7.4.post0 py39h89e85a6_1 conda-forge amply 0.1.4 py_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge appnope 0.1.2 py39h6e9494a_2 conda-forge argon2-cffi 21.1.0 py39h89e85a6_2 conda-forge async-timeout 3.0.1 py_1000 conda-forge async_generator 1.10 py_0 conda-forge atk-1.0 2.36.0 he69c4ee_4 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 21.2.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bcrypt 3.2.0 py39h89e85a6_2 conda-forge biopython 1.79 py39h89e85a6_1 conda-forge black 21.10b0 pyhd8ed1ab_0 conda-forge bleach 4.1.0 pyhd8ed1ab_0 conda-forge boto3 1.19.12 pyhd8ed1ab_0 conda-forge botocore 1.22.12 pyhd8ed1ab_0 conda-forge brotlipy 0.7.0 py39h89e85a6_1003 conda-forge bwidget 1.9.14 h694c41f_1 conda-forge bzip2 1.0.8 h0d85af4_4 conda-forge c-ares 1.18.1 h0d85af4_0 conda-forge ca-certificates 2021.10.8 h033912b_0 conda-forge cachetools 4.2.4 pyhd8ed1ab_0 conda-forge cairo 1.16.0 he43a7df_1008 conda-forge cctools_osx-64 973.0.1 h3e07e27_2 conda-forge certifi 2021.10.8 py39h6e9494a_1 conda-forge cffi 1.15.0 py39he338e87_0 conda-forge chardet 4.0.0 py39h6e9494a_2 conda-forge charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge clang 12.0.1 h694c41f_4 conda-forge clang-12 12.0.1 default_he082bbe_4 conda-forge clang_osx-64 12.0.1 hb91bd55_2 conda-forge clangxx 12.0.1 default_he082bbe_4 conda-forge clangxx_osx-64 12.0.1 h7e1b574_2 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge coincbc 2.10.5 h35dd71c_1 conda-forge compiler-rt 12.0.1 he01351e_0 conda-forge compiler-rt_osx-64 12.0.1 hd3f61c9_0 conda-forge configargparse 1.5.3 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 35.0.0 py39h209aa08_2 conda-forge curl 7.79.1 hf45b732_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge datrie 0.8.2 py39h89e85a6_2 conda-forge debugpy 1.5.1 py39h9fcab8e_0 conda-forge decorator 5.1.0 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.18 py39h6e9494a_1 conda-forge dropbox 11.23.0 pyhd8ed1ab_0 conda-forge entrypoints 0.3 py39hde42818_1002 conda-forge expat 2.4.1 he49afe7_0 conda-forge fancycompleter 0.9.1 py39h6e9494a_1002 conda-forge fftw 3.3.10 nompi_h4024a70_101 conda-forge filechunkio 1.8 py_2 conda-forge filelock 3.3.2 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 h10f422b_1005 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 h4cff582_1 conda-forge fribidi 1.0.10 hbcb3906_0 conda-forge ftputil 5.0.1 pyhd8ed1ab_0 conda-forge gdk-pixbuf 2.42.6 h2e6141f_0 conda-forge gettext 0.19.8.1 hd1a6beb_1008 conda-forge gfortran_impl_osx-64 9.3.0 h9cc0e5e_23 conda-forge gfortran_osx-64 9.3.0 h18f7dce_14 conda-forge ghostscript 9.54.0 he49afe7_1 conda-forge giflib 5.2.1 hbcb3906_2 conda-forge gitdb 4.0.9 pyhd8ed1ab_0 conda-forge gitpython 3.1.24 pyhd8ed1ab_0 conda-forge gmp 6.2.1 h2e338ed_0 conda-forge google-api-core 2.2.1 pyhd8ed1ab_0 conda-forge google-api-python-client 2.28.0 pyhd8ed1ab_0 conda-forge google-auth 2.3.3 pyh6c4a22f_0 conda-forge google-auth-httplib2 0.1.0 pyhd8ed1ab_0 conda-forge google-cloud-core 2.1.0 pyh6c4a22f_0 conda-forge google-cloud-storage 1.42.3 pyh6c4a22f_0 conda-forge google-crc32c 1.1.2 py39ha7afe54_2 conda-forge google-resumable-media 2.1.0 pyh6c4a22f_0 conda-forge googleapis-common-protos 1.53.0 py39h6e9494a_1 conda-forge graphite2 1.3.13 h2e338ed_1001 conda-forge graphviz 2.49.3 h77de9ca_0 conda-forge grpcio 1.41.1 py39h757451a_1 conda-forge gsl 2.7 h93259b0_0 conda-forge gtk2 2.24.33 h675d97a_1 conda-forge gts 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conda-forge terminado 0.12.1 py39h6e9494a_1 conda-forge testpath 0.5.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.0.0 pyh8a188c0_0 conda-forge tk 8.6.11 h5dbffcc_1 conda-forge tktable 2.10 h49f0cf7_3 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 1.2.2 pyhd8ed1ab_0 conda-forge toposort 1.7 pyhd8ed1ab_0 conda-forge tornado 6.1 py39h89e85a6_2 conda-forge traitlets 5.1.1 pyhd8ed1ab_0 conda-forge typed-ast 1.4.3 py39h89e85a6_1 conda-forge typing-extensions 3.10.0.2 hd8ed1ab_0 conda-forge typing_extensions 3.10.0.2 pyha770c72_0 conda-forge tzdata 2021e he74cb21_0 conda-forge ubiquerg 0.6.1 pyh9f0ad1d_0 conda-forge uritemplate 3.0.1 py_0 conda-forge urllib3 1.26.7 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.37.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 3.5.2 py39h6e9494a_1 conda-forge wmctrl 0.4 pyhd8ed1ab_0 conda-forge wrapt 1.13.3 py39h89e85a6_1 conda-forge xmlrunner 1.7.7 py_0 conda-forge xorg-kbproto 1.0.7 h35c211d_1002 conda-forge xorg-libice 1.0.10 h0d85af4_0 conda-forge xorg-libsm 1.2.3 h0d85af4_1000 conda-forge xorg-libx11 1.7.2 h0d85af4_0 conda-forge xorg-libxau 1.0.9 h35c211d_0 conda-forge xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge xorg-libxext 1.3.4 h0d85af4_1 conda-forge xorg-libxrender 0.9.10 h0d85af4_1003 conda-forge xorg-libxt 1.2.1 h0d85af4_2 conda-forge xorg-renderproto 0.11.1 h0d85af4_1002 conda-forge xorg-xextproto 7.3.0 h35c211d_1002 conda-forge xorg-xproto 7.0.31 h35c211d_1007 conda-forge xz 5.2.5 haf1e3a3_1 conda-forge yaml 0.2.5 haf1e3a3_0 conda-forge yarl 1.5.1 py39hb5aae12_0 conda-forge zeromq 4.3.4 he49afe7_1 conda-forge zipp 3.6.0 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h9173be1_1013 conda-forge zstd 1.5.0 h582d3a0_0 conda-forge ```
flying-sheep commented 2 years ago

The following simple lines are not showing anything on Jupyter notebook. The cell output is simply empty/nothing.

Jupyter notebook is deprecated, use Jupyter Lab.

I assume there’s a bug with isolated cell output in jupyter notebook:

image

Works fine in Jupyter Lab (except for the DataTable CSS not being dark mode sensitive, but that’s its fault):

image

if I use repr_html(), I just get a string as the cell output.

that’s how repr works, it creates the raw representation (binary or string) of the requested type.

Benfeitas commented 2 years ago

Hi @flying-sheep , coming to this issue as I followed your suggestions above and it is working. Unfortunately, jlab only shows 1 or 2 rows of the output. Is it possible to enlarge the output window size?