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Anaconda Distribution (formerly Anaconda Individual Edition)
Miniconda
Anaconda.org
What happened?
Trying to run R with jupyter notebook in a conda env.
Installed r, r essentials, jupyter and IRkernel
The kernel dies every time I execute a code (even a simple code).
I have seen similar issues with previous versions being reported. (https://groups.google.com/g/jupyter/c/aRWI9bnhWbY?pli=1)
My current version is R version 4.3.1 (2023-06-16) -- "Beagle Scouts" (this is in Linux)
In windows OS the version R version 4.1.3 (2022-03-10) -- "One Push-Up" works just fine with jupyter but I was having issues with downloading the package dependencies so I switched to Linux. Is this a bug in the R version ? Please let me know how to solve this issue. Thanks!
Expected behavior or outcome
Expected: The kernel should work and not die.
Conda info
active environment : base
active env location : /home/name/anaconda3
shell level : 1
user config file : /home/name/.condarc
populated config files : /home/name/.condarc
conda version : 24.5.0
conda-build version : 24.1.2
python version : 3.11.7.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
__conda=24.5.0=0
__glibc=2.35=0
__linux=5.10.16.3=0
__unix=0=0
base environment : /home/name/anaconda3 (writable)
conda av data dir : /home/name/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/name/anaconda3/pkgs
/home/name/.conda/pkgs
envs directories : /home/name/anaconda3/envs
/home/name/.conda/envs
platform : linux-64
user-agent : conda/24.5.0 requests/2.31.0 CPython/3.11.7 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/22.04.3 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.6 aau/0.4.3 c/2XXUzg_YxO-yJp39sfnkEw s/DIdJQR_w5f6vqo-EoKiRoQ e/0rg0qUJQD6_ktjZMm1jjHg
UID:GID : 1000:1000
netrc file : None
offline mode : False
Checklist
Impacted product
What happened?
Trying to run R with jupyter notebook in a conda env.
Installed r, r essentials, jupyter and IRkernel
The kernel dies every time I execute a code (even a simple code).
I have seen similar issues with previous versions being reported. (https://groups.google.com/g/jupyter/c/aRWI9bnhWbY?pli=1)
My current version is R version 4.3.1 (2023-06-16) -- "Beagle Scouts" (this is in Linux)
In windows OS the version R version 4.1.3 (2022-03-10) -- "One Push-Up" works just fine with jupyter but I was having issues with downloading the package dependencies so I switched to Linux. Is this a bug in the R version ? Please let me know how to solve this issue. Thanks!
Expected behavior or outcome
Expected: The kernel should work and not die.
Conda info
Conda config
Conda list
# Name Version Build Channel _libgcc_mutex 0.1 main defaults _openmp_mutex 5.1 1_gnu defaults _r-mutex 1.0.0 anacondar_1 defaults _sysroot_linux-64_curr_repodata_hack 3 haa98f57_10 defaults anyio 4.2.0 py312h06a4308_0 defaults argon2-cffi 21.3.0 pyhd3eb1b0_0 defaults argon2-cffi-bindings 21.2.0 py312h5eee18b_0 defaults asttokens 2.0.5 pyhd3eb1b0_0 defaults async-lru 2.0.4 py312h06a4308_0 defaults attrs 23.1.0 py312h06a4308_0 defaults babel 2.11.0 py312h06a4308_0 defaults beautifulsoup4 4.12.2 py312h06a4308_0 defaults binutils_impl_linux-64 2.38 h2a08ee3_1 defaults binutils_linux-64 2.38.0 hc2dff05_0 defaults blas 1.0 openblas defaults bleach 4.1.0 pyhd3eb1b0_0 defaults brotli-python 1.0.9 py312h6a678d5_8 defaults bwidget 1.9.16 h9eba36c_0 defaults bzip2 1.0.8 h5eee18b_6 defaults c-ares 1.19.1 h5eee18b_0 defaults ca-certificates 2024.3.11 h06a4308_0 defaults cairo 1.16.0 hb05425b_5 defaults certifi 2024.2.2 py312h06a4308_0 defaults cffi 1.16.0 py312h5eee18b_1 defaults charset-normalizer 2.0.4 pyhd3eb1b0_0 defaults comm 0.2.1 py312h06a4308_0 defaults curl 8.7.1 hdbd6064_0 defaults cyrus-sasl 2.1.28 h52b45da_1 defaults dbus 1.13.18 hb2f20db_0 defaults debugpy 1.6.7 py312h6a678d5_0 defaults decorator 5.1.1 pyhd3eb1b0_0 defaults defusedxml 0.7.1 pyhd3eb1b0_0 defaults executing 0.8.3 pyhd3eb1b0_0 defaults expat 2.6.2 h6a678d5_0 defaults fontconfig 2.14.1 h4c34cd2_2 defaults freetype 2.12.1 h4a9f257_0 defaults fribidi 1.0.10 h7b6447c_0 defaults gcc_impl_linux-64 11.2.0 h1234567_1 defaults gcc_linux-64 11.2.0 h5c386dc_0 defaults gfortran_impl_linux-64 11.2.0 h1234567_1 defaults gfortran_linux-64 11.2.0 hc2dff05_0 defaults glib 2.78.4 h6a678d5_0 defaults glib-tools 2.78.4 h6a678d5_0 defaults graphite2 1.3.14 h295c915_1 defaults gst-plugins-base 1.14.1 h6a678d5_1 defaults gstreamer 1.14.1 h5eee18b_1 defaults gxx_impl_linux-64 11.2.0 h1234567_1 defaults gxx_linux-64 11.2.0 hc2dff05_0 defaults harfbuzz 4.3.0 hf52aaf7_2 defaults icu 73.1 h6a678d5_0 defaults idna 3.7 py312h06a4308_0 defaults ipykernel 6.28.0 py312h06a4308_0 defaults ipython 8.20.0 py312h06a4308_0 defaults ipywidgets 8.1.2 py312h06a4308_0 defaults jedi 0.18.1 py312h06a4308_1 defaults jinja2 3.1.3 py312h06a4308_0 defaults jpeg 9e h5eee18b_1 defaults json5 0.9.6 pyhd3eb1b0_0 defaults jsonschema 4.19.2 py312h06a4308_0 defaults jsonschema-specifications 2023.7.1 py312h06a4308_0 defaults jupyter-lsp 2.2.0 py312h06a4308_0 defaults jupyter_client 8.6.0 py312h06a4308_0 defaults jupyter_console 6.6.3 py312h06a4308_1 defaults jupyter_core 5.5.0 py312h06a4308_0 defaults jupyter_events 0.8.0 py312h06a4308_0 defaults jupyter_server 2.10.0 py312h06a4308_0 defaults jupyter_server_terminals 0.4.4 py312h06a4308_1 defaults jupyterlab 4.0.11 py312h06a4308_0 defaults jupyterlab_pygments 0.1.2 py_0 defaults jupyterlab_server 2.25.1 py312h06a4308_0 defaults jupyterlab_widgets 3.0.10 py312h06a4308_0 defaults kernel-headers_linux-64 3.10.0 h57e8cba_10 defaults krb5 1.20.1 h143b758_1 defaults ld_impl_linux-64 2.38 h1181459_1 defaults lerc 3.0 h295c915_0 defaults libclang 14.0.6 default_hc6dbbc7_1 defaults libclang13 14.0.6 default_he11475f_1 defaults libcups 2.4.2 h2d74bed_1 defaults libcurl 8.7.1 h251f7ec_0 defaults libdeflate 1.17 h5eee18b_1 defaults libedit 3.1.20230828 h5eee18b_0 defaults libev 4.33 h7f8727e_1 defaults libffi 3.4.4 h6a678d5_1 defaults libgcc-devel_linux-64 11.2.0 h1234567_1 defaults libgcc-ng 11.2.0 h1234567_1 defaults libgfortran-ng 11.2.0 h00389a5_1 defaults libgfortran5 11.2.0 h1234567_1 defaults libglib 2.78.4 hdc74915_0 defaults libgomp 11.2.0 h1234567_1 defaults libiconv 1.16 h5eee18b_3 defaults libllvm14 14.0.6 hdb19cb5_3 defaults libnghttp2 1.57.0 h2d74bed_0 defaults libopenblas 0.3.21 h043d6bf_0 defaults libpng 1.6.39 h5eee18b_0 defaults libpq 12.17 hdbd6064_0 defaults libsodium 1.0.18 h7b6447c_0 defaults libssh2 1.11.0 h251f7ec_0 defaults libstdcxx-devel_linux-64 11.2.0 h1234567_1 defaults libstdcxx-ng 11.2.0 h1234567_1 defaults libtiff 4.5.1 h6a678d5_0 defaults libuuid 1.41.5 h5eee18b_0 defaults libwebp-base 1.3.2 h5eee18b_0 defaults libxcb 1.15 h7f8727e_0 defaults libxkbcommon 1.0.1 h5eee18b_1 defaults libxml2 2.10.4 hfdd30dd_2 defaults lz4-c 1.9.4 h6a678d5_1 defaults make 4.2.1 h1bed415_1 defaults markupsafe 2.1.3 py312h5eee18b_0 defaults matplotlib-inline 0.1.6 py312h06a4308_0 defaults mistune 3.0.2 pypi_0 pypi mysql 5.7.24 h721c034_2 defaults nbclient 0.8.0 py312h06a4308_0 defaults nbconvert 7.16.4 pypi_0 pypi nbformat 5.9.2 py312h06a4308_0 defaults ncurses 6.4 h6a678d5_0 defaults nest-asyncio 1.6.0 py312h06a4308_0 defaults notebook 7.0.8 py312h06a4308_0 defaults notebook-shim 0.2.3 py312h06a4308_0 defaults openssl 3.0.13 h7f8727e_2 defaults overrides 7.4.0 py312h06a4308_0 defaults packaging 23.2 py312h06a4308_0 defaults pandoc 2.12 h06a4308_3 defaults pandocfilters 1.5.0 pyhd3eb1b0_0 defaults pango 1.50.7 h05da053_0 defaults parso 0.8.3 pyhd3eb1b0_0 defaults pcre2 10.42 hebb0a14_1 defaults pexpect 4.8.0 pyhd3eb1b0_3 defaults pip 24.0 py312h06a4308_0 defaults pixman 0.40.0 h7f8727e_1 defaults platformdirs 3.10.0 py312h06a4308_0 defaults ply 3.11 py312h06a4308_1 defaults prometheus_client 0.14.1 py312h06a4308_0 defaults prompt-toolkit 3.0.43 py312h06a4308_0 defaults prompt_toolkit 3.0.43 hd3eb1b0_0 defaults psutil 5.9.0 py312h5eee18b_0 defaults ptyprocess 0.7.0 pyhd3eb1b0_2 defaults pure_eval 0.2.2 pyhd3eb1b0_0 defaults pycparser 2.21 pyhd3eb1b0_0 defaults pygments 2.15.1 py312h06a4308_1 defaults pyqt 5.15.10 py312h6a678d5_0 defaults pyqt5-sip 12.13.0 py312h5eee18b_0 defaults pysocks 1.7.1 py312h06a4308_0 defaults python 3.12.3 h996f2a0_1 defaults python-dateutil 2.9.0post0 py312h06a4308_2 defaults python-fastjsonschema 2.16.2 py312h06a4308_0 defaults python-json-logger 2.0.7 py312h06a4308_0 defaults pytz 2024.1 py312h06a4308_0 defaults pyyaml 6.0.1 py312h5eee18b_0 defaults pyzmq 25.1.2 py312h6a678d5_0 defaults qt-main 5.15.2 h53bd1ea_10 defaults qtconsole 5.5.1 py312h06a4308_0 defaults qtpy 2.4.1 py312h06a4308_0 defaults r 4.3.1 r43_0 defaults r-askpass 1.2.0 r43h76d94ec_0 defaults r-backports 1.4.1 r43h76d94ec_0 defaults r-base 4.3.1 h1ae530e_0 defaults r-base64enc 0.1_3 r43h76d94ec_4 defaults r-bit 4.0.5 r43h76d94ec_0 defaults r-bit64 4.0.5 r43h76d94ec_0 defaults r-blob 1.2.4 r43h6115d3f_0 defaults r-boot 1.3_28.1 r43h6115d3f_0 defaults r-broom 1.0.5 r43h6115d3f_0 defaults r-bslib 0.5.1 r43h6115d3f_0 defaults r-cachem 1.0.8 r43h76d94ec_0 defaults r-callr 3.7.3 r43h6115d3f_0 defaults r-caret 6.0_94 r43h76d94ec_0 defaults r-cellranger 1.1.0 r43h6115d3f_0 defaults r-class 7.3_22 r43h76d94ec_0 defaults r-cli 3.6.1 r43h884c59f_0 defaults r-clipr 0.8.0 r43h6115d3f_0 defaults r-clock 0.7.0 r43h884c59f_0 defaults r-cluster 2.1.4 r43h640688f_0 defaults r-codetools 0.2_19 r43h6115d3f_0 defaults r-colorspace 2.1_0 r43h76d94ec_0 defaults r-commonmark 1.9.0 r43h76d94ec_0 defaults r-conflicted 1.2.0 r43h142f84f_0 defaults r-cpp11 0.4.6 r43h6115d3f_0 defaults r-crayon 1.5.2 r43h6115d3f_0 defaults r-curl 5.1.0 r43h76d94ec_0 defaults r-data.table 1.14.8 r43h76d94ec_0 defaults r-dbi 1.1.3 r43h6115d3f_0 defaults r-dbplyr 2.3.4 r43h6115d3f_0 defaults r-diagram 1.6.5 r43h6115d3f_0 defaults r-digest 0.6.33 r43h884c59f_0 defaults r-dplyr 1.1.3 r43h884c59f_0 defaults r-dtplyr 1.3.1 r43h6115d3f_0 defaults r-e1071 1.7_13 r43h884c59f_0 defaults r-ellipsis 0.3.2 r43h76d94ec_0 defaults r-essentials 4.3.1 r43_0 defaults r-evaluate 0.22 r43h6115d3f_0 defaults r-fansi 1.0.5 r43h76d94ec_0 defaults r-farver 2.1.1 r43h884c59f_0 defaults r-fastmap 1.1.1 r43h884c59f_0 defaults r-fontawesome 0.5.2 r43h6115d3f_0 defaults r-forcats 1.0.0 r43h6115d3f_0 defaults r-foreach 1.5.2 r43h6115d3f_0 defaults r-foreign 0.8_85 r43h76d94ec_0 defaults r-formatr 1.14 r43h6115d3f_0 defaults r-fs 1.6.3 r43h884c59f_0 defaults r-future 1.33.0 r43h6115d3f_0 defaults r-future.apply 1.11.0 r43h6115d3f_0 defaults r-gargle 1.5.2 r43h142f84f_0 defaults r-generics 0.1.3 r43h142f84f_0 defaults r-ggplot2 3.4.4 r43h6115d3f_0 defaults r-glmnet 4.1_8 r43hb5eb8f6_0 defaults r-globals 0.16.2 r43h142f84f_0 defaults r-glue 1.6.2 r43h76d94ec_0 defaults r-googledrive 2.1.1 r43h6115d3f_0 defaults r-googlesheets4 1.1.1 r43h6115d3f_0 defaults r-gower 1.0.1 r43h76d94ec_0 defaults r-gtable 0.3.4 r43h6115d3f_0 defaults r-hardhat 1.3.0 r43h6115d3f_0 defaults r-haven 2.5.3 r43h884c59f_0 defaults r-highr 0.10 r43h6115d3f_0 defaults r-hms 1.1.3 r43h6115d3f_0 defaults r-htmltools 0.5.6.1 r43h76d94ec_0 defaults r-httpuv 1.6.11 r43h884c59f_0 defaults r-httr 1.4.7 r43h6115d3f_0 defaults r-ids 1.0.1 r43h142f84f_0 defaults r-ipred 0.9_14 r43h76d94ec_0 defaults r-irdisplay 1.1 r43h6115d3f_0 defaults r-irkernel 1.3.2 r43_0 defaults r-isoband 0.2.7 r43h884c59f_0 defaults r-iterators 1.0.14 r43h6115d3f_0 defaults r-jquerylib 0.1.4 r43h6115d3f_0 defaults r-jsonlite 1.8.7 r43h76d94ec_0 defaults r-kernsmooth 2.23_22 r43h640688f_0 defaults r-knitr 1.44 r43h6115d3f_0 defaults r-labeling 0.4.3 r43h6115d3f_0 defaults r-later 1.3.1 r43h884c59f_0 defaults r-lattice 0.22_5 r43h76d94ec_0 defaults r-lava 1.7.2.1 r43h6115d3f_0 defaults r-lifecycle 1.0.3 r43h142f84f_0 defaults r-listenv 0.9.0 r43h142f84f_0 defaults r-lubridate 1.9.3 r43h76d94ec_0 defaults r-magrittr 2.0.3 r43h76d94ec_0 defaults r-mass 7.3_60 r43h76d94ec_0 defaults r-matrix 1.6_1.1 r43h76d94ec_0 defaults r-memoise 2.0.1 r43h6115d3f_0 defaults r-mgcv 1.9_0 r43h76d94ec_0 defaults r-mime 0.12 r43h76d94ec_0 defaults r-modelmetrics 1.2.2.2 r43h884c59f_0 defaults r-modelr 0.1.11 r43h6115d3f_0 defaults r-munsell 0.5.0 r43h6115d3f_0 defaults r-nlme 3.1_163 r43h640688f_0 defaults r-nnet 7.3_19 r43h76d94ec_0 defaults r-numderiv 2016.8_1.1 r43h6115d3f_0 defaults r-openssl 2.1.1 r43h76d94ec_0 defaults r-parallelly 1.36.0 r43h6115d3f_0 defaults r-pbdzmq 0.3_10 r43h884c59f_0 defaults r-pillar 1.9.0 r43h6115d3f_0 defaults r-pkgconfig 2.0.3 r43h6115d3f_0 defaults r-plyr 1.8.9 r43h884c59f_0 defaults r-prettyunits 1.2.0 r43h142f84f_0 defaults r-proc 1.18.4 r43h884c59f_0 defaults r-processx 3.8.2 r43h76d94ec_0 defaults r-prodlim 2023.08.28 r43h884c59f_0 defaults r-progress 1.2.2 r43h142f84f_0 defaults r-progressr 0.14.0 r43h6115d3f_0 defaults r-promises 1.2.1 r43h884c59f_0 defaults r-proxy 0.4_27 r43h76d94ec_0 defaults r-ps 1.7.5 r43h76d94ec_0 defaults r-purrr 1.0.2 r43h76d94ec_0 defaults r-quantmod 0.4.25 r43h6115d3f_0 defaults r-r6 2.5.1 r43h6115d3f_0 defaults r-ragg 1.2.6 r43h884c59f_0 defaults r-randomforest 4.7_1.1 r43h640688f_0 defaults r-rappdirs 0.3.3 r43h76d94ec_0 defaults r-rcolorbrewer 1.1_3 r43h6115d3f_1 defaults r-rcpp 1.0.11 r43h884c59f_0 defaults r-rcppeigen 0.3.3.9.3 r43h884c59f_0 defaults r-readr 2.1.4 r43h884c59f_0 defaults r-readxl 1.4.3 r43h884c59f_0 defaults r-recipes 1.0.8 r43h6115d3f_0 defaults r-recommended 4.3.1 r43_0 defaults r-rematch 2.0.0 r43h6115d3f_0 defaults r-rematch2 2.1.2 r43h142f84f_0 defaults r-repr 1.1.6 r43h6115d3f_0 defaults r-reprex 2.0.2 r43h6115d3f_0 defaults r-reshape2 1.4.4 r43h884c59f_0 defaults r-rlang 1.1.1 r43h884c59f_0 defaults r-rmarkdown 2.25 r43h6115d3f_0 defaults r-rpart 4.1.21 r43h76d94ec_0 defaults r-rstudioapi 0.15.0 r43h6115d3f_0 defaults r-rvest 1.0.3 r43h6115d3f_0 defaults r-sass 0.4.7 r43h884c59f_0 defaults r-scales 1.2.1 r43h6115d3f_0 defaults r-selectr 0.4_2 r43h6115d3f_0 defaults r-shape 1.4.6 r43h142f84f_0 defaults r-shiny 1.7.5.1 r43h6115d3f_0 defaults r-sourcetools 0.1.7_1 r43h884c59f_0 defaults r-spatial 7.3_17 r43h76d94ec_0 defaults r-squarem 2021.1 r43h142f84f_0 defaults r-stringi 1.7.12 r43h884c59f_0 defaults r-stringr 1.5.0 r43h6115d3f_0 defaults r-survival 3.5_7 r43h76d94ec_0 defaults r-sys 3.4.2 r43h76d94ec_0 defaults r-systemfonts 1.0.5 r43h884c59f_0 defaults r-textshaping 0.3.7 r43h884c59f_0 defaults r-tibble 3.2.1 r43h76d94ec_0 defaults r-tidyr 1.3.0 r43h884c59f_0 defaults r-tidyselect 1.2.0 r43h6115d3f_0 defaults r-tidyverse 2.0.0 r43h6115d3f_0 defaults r-timechange 0.2.0 r43h884c59f_0 defaults r-timedate 4022.108 r43h6115d3f_0 defaults r-tinytex 0.48 r43h142f84f_0 defaults r-ttr 0.24.3 r43h76d94ec_0 defaults r-tzdb 0.4.0 r43h884c59f_0 defaults r-utf8 1.2.4 r43h76d94ec_0 defaults r-uuid 1.1_1 r43h76d94ec_0 defaults r-vctrs 0.6.4 r43h884c59f_0 defaults r-viridislite 0.4.2 r43h6115d3f_0 defaults r-vroom 1.6.4 r43h884c59f_0 defaults r-withr 2.5.1 r43h6115d3f_0 defaults r-xfun 0.40 r43h76d94ec_0 defaults r-xml2 1.3.5 r43h884c59f_0 defaults r-xtable 1.8_4 r43h6115d3f_0 defaults r-xts 0.13.1 r43h76d94ec_0 defaults r-yaml 2.3.7 r43h76d94ec_0 defaults r-zoo 1.8_12 r43h76d94ec_0 defaults readline 8.2 h5eee18b_0 defaults referencing 0.30.2 py312h06a4308_0 defaults requests 2.32.2 py312h06a4308_0 defaults rfc3339-validator 0.1.4 py312h06a4308_0 defaults rfc3986-validator 0.1.1 py312h06a4308_0 defaults rpds-py 0.10.6 py312hb02cf49_0 defaults send2trash 1.8.2 py312h06a4308_0 defaults setuptools 69.5.1 py312h06a4308_0 defaults sip 6.7.12 py312h6a678d5_0 defaults six 1.16.0 pyhd3eb1b0_1 defaults sniffio 1.3.0 py312h06a4308_0 defaults soupsieve 2.5 py312h06a4308_0 defaults sqlite 3.45.3 h5eee18b_0 defaults stack_data 0.2.0 pyhd3eb1b0_0 defaults sysroot_linux-64 2.17 h57e8cba_10 defaults terminado 0.17.1 py312h06a4308_0 defaults tinycss2 1.2.1 py312h06a4308_0 defaults tk 8.6.14 h39e8969_0 defaults tktable 2.10 h3d55465_1 defaults tornado 6.3.3 py312h5eee18b_0 defaults traitlets 5.7.1 py312h06a4308_0 defaults typing-extensions 4.11.0 py312h06a4308_0 defaults typing_extensions 4.11.0 py312h06a4308_0 defaults tzdata 2024a h04d1e81_0 defaults urllib3 2.2.1 py312h06a4308_0 defaults wcwidth 0.2.5 pyhd3eb1b0_0 defaults webencodings 0.5.1 py312h06a4308_2 defaults websocket-client 1.8.0 py312h06a4308_0 defaults wheel 0.43.0 py312h06a4308_0 defaults widgetsnbextension 4.0.10 py312h06a4308_0 defaults xz 5.4.6 h5eee18b_1 defaults yaml 0.2.5 h7b6447c_0 defaults zeromq 4.3.5 h6a678d5_0 defaults zlib 1.2.13 h5eee18b_1 defaults zstd 1.5.5 hc292b87_2 defaults
Additional information
No response
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