The All of Us Researcher Workbench’s Jupyter Notebook server was updated on August 26, 2020 to include an upgrade of R from version 3.6 to 4.0 as well as some Python package and R library changes. Note that these updates are only the defaults; you may still choose to modify your runtime by installing new packages or changing package versions from within the notebooks housed in your workspaces. We do not anticipate that this update will have a major impact on standard Python or R notebook code, but it is possible that some existing code may need to be updated to account for the changes. Please contact support@researchallofus.org for help if you experience a notebook breakage and are unable to resolve it. See detailed changes below.
Timing Upgrade
Jupyter Notebook servers will be upgraded on a rolling basis from August 26th through September 9th (e.g. while using your notebook during this timeframe, the change may not yet be in effect). If you would like to receive the upgrade to your notebook immediately, you can navigate to the Workspace ‘About’ page, and click the “Reset notebook server” button.
To confirm you received the upgrade, you can check the R version, e.g. from an R notebook, run:
system("R --version", intern=TRUE)
Output:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Detailed changes:
python
Packages added:
astunparse
bagit
bgzip
CacheControl
cffi
cli-builder
click
cwltool
Cython
google-crc32c
gs-chunked-io
isodate
lockfile
mypy-extensions
networkx
opt-einsum
prov
psutil
pycparser
python-slugify
QtPy
rdflib
rdflib-jsonld
ruamel.yaml
scandir
schema-salad
shellescape
tensorboard
tensorboard-plugin-wit
tensorflow-estimator
terra-notebook-utils
terra-widgets
text-unidecode
typing-extensions
Packages removed:
Click
more-itertools
pluggy
py
pytest
pytest-pylint
whichcraft
Packages changed:
arrow: 0.15.5 -> 0.15.8
astroid: 2.3.3 -> 2.4.2
astropy: 4.0 -> 4.0.1.post1
backcall: 0.1.0 -> 0.2.0
bleach: 3.1.1 -> 3.1.5
cachetools: 4.0.0 -> 4.1.1
certifi: 2019.11.28 -> 2020.6.20
confuse: 1.0.0 -> 1.3.0
cookiecutter: 1.7.0 -> 1.7.2
decorator: 4.4.1 -> 4.4.2
google-api-core: 1.16.0 -> 1.22.0
google-auth: 1.11.2 -> 1.20.0
google-cloud-storage: 1.23.0 -> 1.30.0
google-pasta: 0.1.8 -> 0.2.0
google-resumable-media: 0.5.0 -> 0.7.0
googleapis-common-protos: 1.51.0 -> 1.52.0
grpcio: 1.27.2 -> 1.30.0
h5py: 2.7.1 -> 2.10.0
importlib-metadata: 1.5.0 -> 1.7.0
ipykernel: 5.1.4 -> 5.3.4
ipython: 7.12.0 -> 7.17.0
isort: 4.3.21 -> 5.2.2
jedi: 0.16.0 -> 0.17.2
Jinja2: 2.11.1 -> 2.11.2
joblib: 0.11 -> 0.16.0
jupyter-client: 6.0.0 -> 6.1.6
Keras-Preprocessing: 1.1.0 -> 1.1.2
kiwisolver: 1.1.0 -> 1.2.0
llvmlite: 0.31.0 -> 0.33.0
lxml: 4.5.0 -> 4.5.2
Mako: 1.1.1 -> 1.1.3
Markdown: 3.2.1 -> 3.2.2
matplotlib: 3.1.3 -> 3.3.1
nbformat: 5.0.4 -> 5.0.7
numba: 0.48.0 -> 0.50.1
numpy: 1.18.1 -> 1.19.0
packaging: 20.1 -> 20.4
parso: 0.6.1 -> 0.7.1
phik: 0.9.9 -> 0.10.0
Pillow: 7.0.0 -> 7.2.0
pip: 20.0.2 -> 20.2
prometheus-client: 0.7.1 -> 0.8.0
prompt-toolkit: 3.0.3 -> 3.0.5
protobuf: 3.7.1 -> 3.12.4
pydata-google-auth: 0.3.0 -> 1.1.0
Pygments: 2.5.2 -> 2.6.1
pylint: 2.4.4 -> 1.7.2
pyparsing: 2.4.6 -> 2.4.7
pyrsistent: 0.15.7 -> 0.16.0
pysam: 0.15.1 -> 0.15.4
python: 3.7.6 -> 3.7.8
python-apt: 1.6.5+ubuntu0.2 -> 1.6.5+ubuntu0.3
python-datauri: 0.2.8 -> 0.2.9
pytz: 2017.3 -> 2020.1
PyYAML: 5.3 -> 5.3.1
pyzmq: 19.0.0 -> 19.0.2
qtconsole: 4.6.0 -> 4.7.5
requests: 2.23.0 -> 2.24.0
rsa: 4.0 -> 4.6
scikit-learn: 0.20.0 -> 0.21.3
scipy: 1.2.0 -> 1.5.2
setuptools: 45.2.0 -> 49.2.1
tensorflow: 2.0.0a0 -> 2.3.0
urllib3: 1.25.8 -> 1.25.10
wcwidth: 0.1.8 -> 0.2.5
wrapt: 1.11.2 -> 1.12.1
zipp: 3.0.0 -> 3.1.0
r
Packages added:
blob
cpp11
isoband
rematch2
Packages removed:
clisymbols
fastmap
httpuv
plogr
plyr
reshape2
shiny
sourcetools
xtable
Packages changed:
backports: 1.1.5 -> 1.1.8
bigrquery: 1.2.0-1 -> 1.3.1-1
BiocVersion: 3.10.1 -> 3.11.1
bit: 1.1-15.2 -> 4.0.4
bit64: 0.9-7 -> 4.0.2
broom: 0.5.4 -> 0.7.0
callr: 3.4.2 -> 3.4.3
covr: 3.4.0 -> 3.5.0
crosstalk: 1.0.0 -> 1.1.0.1
dbplyr: 1.4.2 -> 1.4.4
devtools: 2.2.2 -> 2.3.1
dplyr: 0.8.4 -> 1.0.1
DT: 0.12 -> 0.14
ellipsis: 0.3.0 -> 0.3.1
forcats: 0.4.0 -> 0.5.0
fs: 1.3.1 -> 1.5.0
gargle: 0.4.0 -> 0.5.0
ggplot2: 3.2.1 -> 3.3.2
git2r: 0.26.1 -> 0.27.1
glue: 1.3.1 -> 1.4.1
googleAuthR: 1.1.1 -> 1.3.0
haven: 2.2.0 -> 2.3.1
htmltools: 0.4.0 -> 0.5.0
httr: 1.4.1 -> 1.4.2
IRkernel: 1.1 -> 1.1.1
jsonlite: 1.6.1 -> 1.7.0
knitr: 1.28 -> 1.29
later: 1.0.0 -> 1.1.0.1
lifecycle: 0.1.0 -> 0.2.0
lubridate: 1.7.4 -> 1.7.9
modelr: 0.1.6 -> 0.1.8
openssl: 1.4.1 -> 1.4.2
pillar: 1.4.3 -> 1.4.6
pkgbuild: 1.0.6 -> 1.1.0
pkgload: 1.0.2 -> 1.1.0
processx: 3.4.2 -> 3.4.3
promises: 1.1.0 -> 1.1.1
ps: 1.3.2 -> 1.3.3
purrr: 0.3.3 -> 0.3.4
r: 3.6.2 -> 4.0.2
rapidjsonr: 1.1 -> 1.2.0
Rcpp: 1.0.3 -> 1.0.5
remotes: 2.1.1 -> 2.2.0
reticulate: 1.14-9001 -> 1.16
rex: 1.1.2 -> 1.2.0
rlang: 0.4.5 -> 0.4.7
rmarkdown: 2.1 -> 2.3
roxygen2: 7.0.2 -> 7.1.1
rversions: 2.0.1 -> 2.0.2
rvest: 0.3.5 -> 0.3.6
scales: 1.1.0 -> 1.1.1
sys: 3.3 -> 3.4
testthat: 2.3.1 -> 2.3.2
tibble: 2.1.3 -> 3.0.3
tidyr: 1.0.2 -> 1.1.1
tidyselect: 1.0.0 -> 1.1.0
tinytex: 0.20 -> 0.25
usethis: 1.5.1 -> 1.6.1
uuid: 0.1-2 -> 0.1-4
vctrs: 0.2.3 -> 0.3.2
withr: 2.1.2 -> 2.2.0
xfun: 0.12 -> 0.16
xml2: 1.2.2 -> 1.3.2
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