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run.RCTD entered a frozen state using max_cores>1 #253

@lexuziandyu

Description

@lexuziandyu

When I run RCTD in multicore mode, my Jupyter Notebook shows that it's running continuously, and the command line interface is in the same state. However, there are no processes in the background, and it has entered a frozen state. How can I resolve this issue?
Here's my conda env info:

packages in environment at /User/miniconda3/envs/R441:

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
_r-mutex 1.0.1 anacondar_1 conda-forge
adwaita-icon-theme 48.0 h06a4308_0
anyio 4.10.0 py310h06a4308_0
aom 3.9.1 hac33072_0 conda-forge
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py310h5eee18b_1
asttokens 3.0.0 py310h06a4308_0
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attrs 24.3.0 py310h06a4308_0
beautifulsoup4 4.13.5 py310h06a4308_0
binutils_impl_linux-64 2.40 h5293946_0
bleach 6.2.0 py310h06a4308_0
blosc 1.21.6 hef167b5_0 conda-forge
bwidget 1.10.1 ha770c72_1 conda-forge
bzip2 1.0.8 h5eee18b_6
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.11.4 h06a4308_0
cairo 1.18.4 h3394656_0 conda-forge
cffi 1.17.1 py310h1fdaa30_1
comm 0.2.1 py310h06a4308_0
curl 8.14.1 h332b0f4_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.16.2 h5bd4931_0
debugpy 1.8.11 py310h6a678d5_0
decorator 5.2.1 py310h06a4308_0
defusedxml 0.7.1 pyhd3eb1b0_0
epoxy 1.5.10 hb03c661_2 conda-forge
exceptiongroup 1.2.0 py310h06a4308_0
executing 2.2.1 py310h06a4308_0
expat 2.7.1 h6a678d5_0
fftw 3.3.10 nompi_hf1063bd_110 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 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
freexl 2.0.0 h9dce30a_2 conda-forge
fribidi 1.0.16 hb03c661_0 conda-forge
gcc_impl_linux-64 15.2.0 hcacfade_7 conda-forge
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
geos 3.13.0 h5888daf_0 conda-forge
geotiff 1.7.4 h3551947_0 conda-forge
gfortran_impl_linux-64 15.2.0 h1b0a18f_7 conda-forge
ghostscript 10.06.0 hecca717_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.84.0 h07242d1_0 conda-forge
glib-tools 2.84.0 h4833e2c_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 h6a678d5_0
graphite2 1.3.14 hecca717_2 conda-forge
graphviz 12.2.1 h5ae0cbf_1 conda-forge
gsl 2.7 he838d99_0 conda-forge
gtk3 3.24.43 hd6cba2e_1 conda-forge
gts 0.7.6 hb67d8dd_3
gxx_impl_linux-64 15.2.0 h54ccb8d_7 conda-forge
harfbuzz 11.0.0 h76408a6_0 conda-forge
hdf5 1.14.5 h2b7332f_2
hicolor-icon-theme 0.17 h06a4308_2
icu 75.1 he02047a_0 conda-forge
idna 3.7 py310h06a4308_0
imagemagick 7.1.1_41 imagemagick_hcfc5581_0 conda-forge
ipykernel 6.30.1 py310h06a4308_0
ipython 8.30.0 py310h06a4308_0
jbig 2.1 hdba287a_0
jedi 0.19.2 py310h06a4308_0
jinja2 3.1.6 py310h06a4308_0
json-c 0.18 h6688a6e_0 conda-forge
jsonschema 4.25.0 py310h06a4308_0
jsonschema-specifications 2023.7.1 py310h06a4308_0
jupyter_client 8.6.3 py310h06a4308_0
jupyter_core 5.8.1 py310h06a4308_0
jupyter_events 0.12.0 py310h06a4308_0
jupyter_server 2.17.0 pyhcf101f3_0 conda-forge
jupyter_server_terminals 0.5.3 py310h06a4308_0
jupyterlab_pygments 0.3.0 py310h06a4308_0
kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.40 h12ee557_0
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20250512.1 cxx17_hba17884_0 conda-forge
libarchive 3.7.7 hadbb8c3_0 conda-forge
libavif16 1.3.0 h6395336_2 conda-forge
libblas 3.9.0 37_h4a7cf45_openblas conda-forge
libcblas 3.9.0 37_h0358290_openblas conda-forge
libcups 2.3.3 hb8b1518_5 conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libde265 1.0.15 h00ab1b0_0 conda-forge
libdeflate 1.22 hb9d3cd8_0 conda-forge
libdrm 2.4.125 hb03c661_1 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 h5eee18b_2
libegl-devel 1.7.0 h5eee18b_2
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.4.4 h6a678d5_1
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 h767d61c_7 conda-forge
libgcc-devel_linux-64 15.2.0 h73f6952_107 conda-forge
libgcc-ng 15.2.0 h69a702a_7 conda-forge
libgd 2.3.3 h6f5c62b_11 conda-forge
libgdal-core 3.10.0 h7250d82_5 conda-forge
libgfortran 15.2.0 h69a702a_7 conda-forge
libgfortran-ng 15.2.0 h69a702a_7 conda-forge
libgfortran5 15.2.0 hcd61629_7 conda-forge
libgit2 1.8.4 hd24f944_1 conda-forge
libgl 1.7.0 h5eee18b_2
libgl-devel 1.7.0 h5eee18b_2
libglib 2.84.0 h2ff4ddf_0 conda-forge
libglvnd 1.7.0 h5eee18b_2
libglx 1.7.0 h5eee18b_2
libglx-devel 1.7.0 h5eee18b_2
libgomp 15.2.0 h767d61c_7 conda-forge
libheif 1.18.2 gpl_hffcb242_100 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
libkml 1.3.0 haa4a5bd_1022 conda-forge
liblapack 3.9.0 37_h47877c9_openblas conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_2 conda-forge
libpciaccess 0.18 h5eee18b_0
libpng 1.6.50 h421ea60_1 conda-forge
librsvg 2.58.4 h49af25d_2 conda-forge
librttopo 1.1.0 h97f6797_17 conda-forge
libsanitizer 15.2.0 hb13aed2_7 conda-forge
libsodium 1.0.18 h7b6447c_0
libspatialite 5.1.0 h1b4f908_12 conda-forge
libsqlite 3.50.4 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h8f9b012_7 conda-forge
libstdcxx-devel_linux-64 15.2.0 h73f6952_107 conda-forge
libstdcxx-ng 15.2.0 h4852527_7 conda-forge
libtiff 4.7.0 he137b08_1 conda-forge
libudunits2 2.2.28 h40f5838_3 conda-forge
libuuid 2.41.2 he9a06e4_0 conda-forge
libwebp 1.6.0 h9635ea4_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h9b100fa_0
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.8.0 hc4a0caf_0 conda-forge
libxml2 2.13.5 hb346dea_0 conda-forge
libzlib 1.3.1 hb25bd0a_0
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h280c20c_1002 conda-forge
make 4.4.1 hb9d3cd8_2 conda-forge
markupsafe 3.0.2 py310h5eee18b_0
matplotlib-inline 0.1.7 py310h06a4308_0
minizip 4.0.7 h401b404_0 conda-forge
mistune 3.1.2 py310h06a4308_0
nb_conda_kernels 2.5.2 py310h06a4308_1
nbclient 0.10.2 py310h06a4308_0
nbconvert-core 7.16.6 py310h06a4308_0
nbformat 5.10.4 py310h06a4308_0
ncurses 6.5 h7934f7d_0
nest-asyncio 1.6.0 py310h06a4308_0
openjpeg 2.5.2 h0d4d230_1
openssl 3.5.4 h26f9b46_0 conda-forge
overrides 7.4.0 py310h06a4308_0
packaging 25.0 py310h06a4308_0
pandoc 3.8 h06a4308_0
pandocfilters 1.5.1 py310h06a4308_0
pango 1.56.3 h9ac818e_1 conda-forge
parso 0.8.4 py310h06a4308_0
pcre2 10.44 hc749103_2 conda-forge
perl 5.32.1 0_h5eee18b_perl5
pexpect 4.9.0 py310h06a4308_0
pip 25.2 pyhc872135_1
pixman 0.46.4 h54a6638_1 conda-forge
pkg-config 0.29.2 h1bed415_8
platformdirs 4.3.7 py310h06a4308_0
proj 9.5.1 h0054346_0 conda-forge
prometheus_client 0.21.1 py310h06a4308_0
prompt-toolkit 3.0.52 py310h06a4308_0
prompt_toolkit 3.0.52 hd3eb1b0_0
psutil 5.9.0 py310h5eee18b_1
pthread-stubs 0.3 h0ce48e5_1
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.3 py310h06a4308_0
pycparser 2.23 py310h06a4308_0
pygments 2.19.1 py310h06a4308_0
python 3.10.15 h4a871b0_2_cpython conda-forge
python-dateutil 2.9.0post0 py310h06a4308_2
python-fastjsonschema 2.20.0 py310h06a4308_0
python-json-logger 3.2.1 py310h06a4308_0
pyyaml 6.0.2 py310h5eee18b_0
pyzmq 26.2.0 py310h6a678d5_0
r-askpass 1.2.1 r44h54b55ab_1 conda-forge
r-assertthat 0.2.1 r44hc72bb7e_6 conda-forge
r-base 4.4.1 h64c9cd0_16 conda-forge
r-base64enc 0.1_3 r44h54b55ab_1008 conda-forge
r-bit 4.6.0 r44h54b55ab_1 conda-forge
r-bit64 4.6.0_1 r44h54b55ab_1 conda-forge
r-brio 1.1.5 r44h54b55ab_2 conda-forge
r-bslib 0.9.0 r44hc72bb7e_1 conda-forge
r-cachem 1.1.0 r44h54b55ab_2 conda-forge
r-callr 3.7.6 r44hc72bb7e_2 conda-forge
r-class 7.3_23 r44h54b55ab_1 conda-forge
r-classint 0.4_11 r44heaba542_1 conda-forge
r-cli 3.6.5 r44h3697838_1 conda-forge
r-clipr 0.8.0 r44hc72bb7e_4 conda-forge
r-cpp11 0.5.2 r44h785f33e_2 conda-forge
r-crayon 1.5.3 r44hc72bb7e_2 conda-forge
r-credentials 2.0.3 r44hc72bb7e_1 conda-forge
r-curl 7.0.0 r44h10955f1_1 conda-forge
r-dbi 1.2.3 r44hc72bb7e_2 conda-forge
r-desc 1.4.3 r44hc72bb7e_2 conda-forge
r-digest 0.6.37 r44h3697838_1 conda-forge
r-downlit 0.4.4 r44hc72bb7e_2 conda-forge
r-dplyr 1.1.4 r44h3697838_2 conda-forge
r-e1071 1.7_16 r44h3697838_1 conda-forge
r-ellipsis 0.3.2 r44h54b55ab_4 conda-forge
r-evaluate 1.0.5 r44hc72bb7e_1 conda-forge
r-fansi 1.0.6 r44h54b55ab_2 conda-forge
r-fastmap 1.2.0 r44h3697838_2 conda-forge
r-fontawesome 0.5.3 r44hc72bb7e_1 conda-forge
r-fs 1.6.6 r44h3697838_1 conda-forge
r-generics 0.1.4 r44hc72bb7e_1 conda-forge
r-gert 2.1.4 r44h017ce79_0 conda-forge
r-gh 1.5.0 r44hc72bb7e_1 conda-forge
r-gitcreds 0.1.2 r44hc72bb7e_4 conda-forge
r-glue 1.8.0 r44h54b55ab_1 conda-forge
r-here 1.0.2 r44hc72bb7e_0 conda-forge
r-highr 0.11 r44hc72bb7e_2 conda-forge
r-hms 1.1.3 r44hc72bb7e_3 conda-forge
r-htmltools 0.5.8.1 r44h3697838_2 conda-forge
r-httr2 1.2.1 r44hc72bb7e_1 conda-forge
r-igraph 2.0.3 r44h510f1ce_1 conda-forge
r-ini 0.3.1 r44hc72bb7e_1007 conda-forge
r-jquerylib 0.1.4 r44hc72bb7e_4 conda-forge
r-jsonlite 2.0.0 r44h54b55ab_1 conda-forge
r-kernsmooth 2.23_26 r44ha0a88a1_1 conda-forge
r-knitr 1.50 r44hc72bb7e_1 conda-forge
r-lattice 0.22_7 r44h54b55ab_1 conda-forge
r-leiden 0.4.3.1 r44hc72bb7e_2 conda-forge
r-lifecycle 1.0.4 r44hc72bb7e_2 conda-forge
r-magick 2.8.5 r44h93ab643_0 conda-forge
r-magrittr 2.0.4 r44h54b55ab_0 conda-forge
r-mass 7.3_65 r44h54b55ab_0 conda-forge
r-matrix 1.7_4 r44h0e4624f_1 conda-forge
r-memoise 2.0.1 r44hc72bb7e_4 conda-forge
r-mime 0.13 r44h54b55ab_1 conda-forge
r-openssl 2.3.4 r44h50f7d53_0 conda-forge
r-pillar 1.11.1 r44hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_5 conda-forge
r-pkgdown 2.1.3 r44hc72bb7e_1 conda-forge
r-png 0.1_8 r44h6b2d295_3 conda-forge
r-prettyunits 1.2.0 r44hc72bb7e_2 conda-forge
r-processx 3.8.6 r44h54b55ab_1 conda-forge
r-progress 1.2.3 r44hc72bb7e_2 conda-forge
r-proxy 0.4_27 r44h54b55ab_4 conda-forge
r-ps 1.9.1 r44h54b55ab_1 conda-forge
r-purrr 1.1.0 r44h54b55ab_1 conda-forge
r-r6 2.6.1 r44hc72bb7e_1 conda-forge
r-ragg 1.5.0 r44h9f1dc4d_1 conda-forge
r-rappdirs 0.3.3 r44h54b55ab_4 conda-forge
r-rcpp 1.1.0 r44h3697838_1 conda-forge
r-rcpptoml 0.2.3 r44h3697838_1 conda-forge
r-readr 2.1.5 r44h3697838_2 conda-forge
r-reticulate 1.43.0 r44h3697838_1 conda-forge
r-rlang 1.1.6 r44h3697838_1 conda-forge
r-rmarkdown 2.30 r44hc72bb7e_0 conda-forge
r-rprojroot 2.1.1 r44hc72bb7e_1 conda-forge
r-rstudioapi 0.17.1 r44hc72bb7e_1 conda-forge
r-s2 1.1.9 r44h7d5736c_3 conda-forge
r-sass 0.4.10 r44h3697838_1 conda-forge
r-sf 1.0_19 r44h4d3cc04_2 conda-forge
r-sys 3.4.3 r44h54b55ab_1 conda-forge
r-systemfonts 1.3.1 r44h74f4acd_0 conda-forge
r-textshaping 0.4.0 r44ha47bcaa_2 conda-forge
r-tibble 3.3.0 r44h54b55ab_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_2 conda-forge
r-tinytex 0.57 r44hc72bb7e_1 conda-forge
r-tzdb 0.5.0 r44h3697838_2 conda-forge
r-units 1.0_0 r44h3697838_0 conda-forge
r-usethis 3.2.1 r44hc72bb7e_1 conda-forge
r-utf8 1.2.6 r44h54b55ab_1 conda-forge
r-vctrs 0.6.5 r44h3697838_2 conda-forge
r-vroom 1.6.6 r44h3697838_0 conda-forge
r-whisker 0.4.1 r44hc72bb7e_3 conda-forge
r-withr 3.0.2 r44hc72bb7e_1 conda-forge
r-wk 0.9.4 r44h3697838_2 conda-forge
r-xfun 0.53 r44h3697838_1 conda-forge
r-xml2 1.3.6 r44h8194278_2 conda-forge
r-yaml 2.3.10 r44h54b55ab_1 conda-forge
r-zip 2.3.3 r44h54b55ab_1 conda-forge
rav1e 0.7.1 h8fae777_3 conda-forge
readline 8.3 hc2a1206_0
referencing 0.30.2 py310h06a4308_0
rfc3339-validator 0.1.4 py310h06a4308_0
rfc3986-validator 0.1.1 py310h06a4308_0
rpds-py 0.22.3 py310h4aa5aa6_0
sed 4.9 h6688a6e_0 conda-forge
send2trash 1.8.2 py310h06a4308_1
setuptools 80.9.0 py310h06a4308_0
six 1.17.0 py310h06a4308_0
snappy 1.2.2 h03e3b7b_0 conda-forge
sniffio 1.3.0 py310h06a4308_0
soupsieve 2.5 py310h06a4308_0
sqlite 3.50.2 hb25bd0a_1
stack_data 0.6.3 py310h06a4308_0
svt-av1 3.1.2 hecca717_0 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
terminado 0.18.1 py310h06a4308_0
tinycss2 1.4.0 py310h06a4308_0
tk 8.6.15 h54e0aa7_0
tktable 2.10 h8d826fa_7 conda-forge
tornado 6.5.1 py310h5eee18b_0
traitlets 5.14.3 py310h06a4308_0
typing-extensions 4.15.0 py310h06a4308_0
typing_extensions 4.15.0 py310h06a4308_0
tzdata 2025b h04d1e81_0
udunits2 2.2.28 h40f5838_3 conda-forge
uriparser 0.9.8 hac33072_0 conda-forge
wayland 1.24.0 hdac8c69_0
wcwidth 0.2.13 py310h06a4308_0
webencodings 0.5.1 py310h06a4308_1
websocket-client 1.8.0 py310h06a4308_0
wheel 0.45.1 py310h06a4308_0
x265 3.5 h924138e_3 conda-forge
xerces-c 3.2.5 h988505b_2 conda-forge
xkeyboard-config 2.44 h5eee18b_0
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h9b100fa_1
xorg-libxau 1.0.12 h9b100fa_0
xorg-libxcomposite 0.4.6 h9b100fa_2
xorg-libxcursor 1.2.3 h9b100fa_0
xorg-libxdamage 1.1.6 h9b100fa_0
xorg-libxdmcp 1.1.5 h9b100fa_0
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 h9b100fa_0
xorg-libxi 1.8.2 h9b100fa_0
xorg-libxinerama 1.1.5 h50385e7_1
xorg-libxrandr 1.5.4 h9b100fa_0
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 h9b100fa_3
xorg-libxxf86vm 1.1.6 h9b100fa_0
xorg-xorgproto 2024.1 h5eee18b_1
xz 5.6.4 h5eee18b_1
yaml 0.2.5 h7b6447c_0
zeromq 4.3.5 h6a678d5_0
zlib 1.3.1 hb25bd0a_0
zstd 1.5.7 hb8e6e7a_2 conda-forge

Thx!

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