I am using both R and python for a research project. The computations and all analyses are done in a remote server which I access using SSH. I do not have root privileges to the server.
I have a Conda virtual environment for the project. My usual workflow is connecting to the server through the SSH features of Visual Studio Code and then editing code and running it in the terminal iteratively (using the Remote - SSH extension from Microsoft). When editing Python scripts, everything works great: I can edit the files and run them in the terminal with no error messages and so on.
However, as soon as I start editing an R script, I get some weird error messages although I believe R is correctly set up. See the output of a quick check (out of a simple Terminal shell):
The Conda environment I am working on is r_conda. It shows that it sees R and it's loading it from the correct binary. Even radian seems to be correctly installed in the Conda environment.
When I open an R file in VS Code, I get the following errors:
I am using this R extension.
I have already edited the settings of the extension to point it to the correct binaries:
Does anyone know what is going on? How to solve this?
Following the suggestion from @merv, here is what is installed in the r_conda environment:
(r_conda) [rgr6291@klc0201 ~]$ conda list
# packages in environment at /home/rgr6291/.conda/envs/r_conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_4 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cairo 1.16.0 ha00ac49_1009 conda-forge
cffi 1.15.0 pypi_0 pypi
curl 7.81.0 h494985f_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 hba837de_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gcc_linux-64 9.4.0 h391b98a_4 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_11 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_4 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gxx_linux-64 9.4.0 h0316aca_4 conda-forge
harfbuzz 3.2.0 hb4a5f5f_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
krb5 1.19.2 h48eae69_3 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 12_linux64_openblas conda-forge
libcblas 3.9.0 12_linux64_openblas conda-forge
libcurl 7.81.0 h494985f_0 conda-forge
libdeflate 1.8 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libgcc-ng 11.2.0 h1d223b6_11 conda-forge
libgfortran-ng 11.2.0 h69a702a_11 conda-forge
libgfortran5 11.2.0 h5c6108e_11 conda-forge
libglib 2.70.2 h174f98d_1 conda-forge
libgomp 11.2.0 h1d223b6_11 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 12_linux64_openblas conda-forge
libnghttp2 1.43.0 ha19adfc_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsanitizer 9.4.0 h79bfe98_11 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge
libtiff 4.3.0 h6f004c6_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.1 h7f98852_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lineedit 0.1.6 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
openssl 3.0.0 h7f98852_2 conda-forge
pandoc 2.17 h7f98852_0 conda-forge
pango 1.50.3 h9967ed3_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
python 3.10.2 h543edf9_0_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
r-askpass 1.1 r41hcfec24a_2 conda-forge
r-assertthat 0.2.1 r41hc72bb7e_2 conda-forge
r-backports 1.4.1 r41hcfec24a_0 conda-forge
r-base 4.1.2 h2553ce4_1 conda-forge
r-base64enc 0.1_3 r41hcfec24a_1004 conda-forge
r-bayestestr 0.11.5 r41hc72bb7e_0 conda-forge
r-bit 4.0.4 r41hcfec24a_0 conda-forge
r-bit64 4.0.5 r41hcfec24a_0 conda-forge
r-blob 1.2.2 r41hc72bb7e_0 conda-forge
r-brio 1.1.3 r41hcfec24a_0 conda-forge
r-broom 0.7.11 r41hc72bb7e_0 conda-forge
r-callr 3.7.0 r41hc72bb7e_0 conda-forge
r-cellranger 1.1.0 r41hc72bb7e_1004 conda-forge
r-checkmate 2.0.0 r41hcfec24a_1 conda-forge
r-cli 3.1.0 r41h03ef668_0 conda-forge
r-clipr 0.7.1 r41hc72bb7e_0 conda-forge
r-colorspace 2.0_2 r41hcfec24a_0 conda-forge
r-cpp11 0.4.2 r41hc72bb7e_0 conda-forge
r-crayon 1.4.2 r41hc72bb7e_0 conda-forge
r-curl 4.3.2 r41hcfec24a_0 conda-forge
r-data.table 1.14.2 r41hcfec24a_0 conda-forge
r-datawizard 0.2.2 r41hc72bb7e_0 conda-forge
r-dbi 1.1.2 r41hc72bb7e_0 conda-forge
r-dbplyr 2.1.1 r41hc72bb7e_0 conda-forge
r-desc 1.4.0 r41hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r41hcfec24a_0 conda-forge
r-digest 0.6.29 r41h03ef668_0 conda-forge
r-dplyr 1.0.7 r41h03ef668_0 conda-forge
r-dtplyr 1.2.0 r41hc72bb7e_0 conda-forge
r-ellipsis 0.3.2 r41hcfec24a_0 conda-forge
r-evaluate 0.14 r41hc72bb7e_2 conda-forge
r-fansi 1.0.2 r41hcfec24a_0 conda-forge
r-farver 2.1.0 r41h03ef668_0 conda-forge
r-fastmap 1.1.0 r41h03ef668_0 conda-forge
r-forcats 0.5.1 r41hc72bb7e_0 conda-forge
r-fs 1.5.2 r41h03ef668_0 conda-forge
r-gargle 1.2.0 r41hc72bb7e_0 conda-forge
r-gdtools 0.2.3 r41h42e24d8_0 conda-forge
r-generics 0.1.1 r41hc72bb7e_0 conda-forge
r-ggplot2 3.3.5 r41hc72bb7e_0 conda-forge
r-ggsci 2.9 r41hc72bb7e_1003 conda-forge
r-glue 1.6.0 r41hcfec24a_0 conda-forge
r-googledrive 2.0.0 r41hc72bb7e_0 conda-forge
r-googlesheets4 1.0.0 r41h785f33e_0 conda-forge
r-gtable 0.3.0 r41hc72bb7e_3 conda-forge
r-haven 2.4.3 r41h2713e49_0 conda-forge
r-here 1.0.1 r41hc72bb7e_0 conda-forge
r-highr 0.9 r41hc72bb7e_0 conda-forge
r-hms 1.1.1 r41hc72bb7e_0 conda-forge
r-htmltools 0.5.2 r41h03ef668_0 conda-forge
r-httr 1.4.2 r41hc72bb7e_0 conda-forge
r-ids 1.0.1 r41hc72bb7e_1 conda-forge
r-insight 0.15.0 r41hc72bb7e_0 conda-forge
r-isoband 0.2.5 r41h03ef668_0 conda-forge
r-jquerylib 0.1.4 r41hc72bb7e_0 conda-forge
r-jsonlite 1.7.3 r41hcfec24a_0 conda-forge
r-kableextra 1.3.4 r41hc72bb7e_0 conda-forge
r-knitr 1.37 r41hc72bb7e_1 conda-forge
r-labeling 0.4.2 r41hc72bb7e_1 conda-forge
r-lattice 0.20_45 r41hcfec24a_0 conda-forge
r-lifecycle 1.0.1 r41hc72bb7e_0 conda-forge
r-lubridate 1.8.0 r41h03ef668_0 conda-forge
r-magrittr 2.0.1 r41hcfec24a_1 conda-forge
r-mass 7.3_55 r41hcfec24a_0 conda-forge
r-matrix 1.4_0 r41he454529_0 conda-forge
r-mgcv 1.8_38 r41he454529_0 conda-forge
r-mime 0.12 r41hcfec24a_0 conda-forge
r-modelr 0.1.8 r41hc72bb7e_0 conda-forge
r-modelsummary 0.9.5 r41hc72bb7e_0 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1004 conda-forge
r-nlme 3.1_155 r41h859d828_0 conda-forge
r-openssl 1.4.6 r41he82ab30_0 conda-forge
r-parameters 0.16.0 r41hc72bb7e_0 conda-forge
r-performance 0.8.0 r41hc72bb7e_0 conda-forge
r-pillar 1.6.4 r41hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_1 conda-forge
r-pkgload 1.2.4 r41h03ef668_0 conda-forge
r-praise 1.0.0 r41hc72bb7e_1005 conda-forge
r-prettyunits 1.1.1 r41hc72bb7e_1 conda-forge
r-processx 3.5.2 r41hcfec24a_0 conda-forge
r-progress 1.2.2 r41hc72bb7e_2 conda-forge
r-ps 1.6.0 r41hcfec24a_0 conda-forge
r-purrr 0.3.4 r41hcfec24a_1 conda-forge
r-r6 2.5.1 r41hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r41hcfec24a_0 conda-forge
r-rcolorbrewer 1.1_2 r41h785f33e_1003 conda-forge
r-rcpp 1.0.8 r41h03ef668_0 conda-forge
r-readr 2.1.1 r41h03ef668_0 conda-forge
r-readxl 1.3.1 r41h2713e49_4 conda-forge
r-rematch 1.0.1 r41hc72bb7e_1004 conda-forge
r-rematch2 2.1.2 r41hc72bb7e_1 conda-forge
r-reprex 2.0.1 r41hc72bb7e_0 conda-forge
r-rlang 0.4.12 r41hcfec24a_0 conda-forge
r-rmarkdown 2.11 r41hc72bb7e_1 conda-forge
r-rprojroot 2.0.2 r41hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r41hc72bb7e_0 conda-forge
r-rvest 1.0.2 r41hc72bb7e_0 conda-forge
r-sandwich 3.0_1 r41hc72bb7e_0 conda-forge
r-scales 1.1.1 r41hc72bb7e_0 conda-forge
r-selectr 0.4_2 r41hc72bb7e_1 conda-forge
r-stringi 1.7.6 r41h337692f_1 conda-forge
r-stringr 1.4.0 r41hc72bb7e_2 conda-forge
r-svglite 2.0.0 r41h03ef668_0 conda-forge
r-sys 3.4 r41hcfec24a_0 conda-forge
r-systemfonts 1.0.3 r41hef9c87a_0 conda-forge
r-tables 0.9.6 r41hc72bb7e_0 conda-forge
r-testthat 3.1.1 r41h03ef668_0 conda-forge
r-tibble 3.1.6 r41hcfec24a_0 conda-forge
r-tidyr 1.1.4 r41h03ef668_0 conda-forge
r-tidyselect 1.1.1 r41hc72bb7e_0 conda-forge
r-tidyverse 1.3.1 r41hc72bb7e_0 conda-forge
r-tinytex 0.36 r41hc72bb7e_0 conda-forge
r-tzdb 0.2.0 r41h03ef668_0 conda-forge
r-utf8 1.2.2 r41hcfec24a_0 conda-forge
r-uuid 1.0_3 r41hcfec24a_0 conda-forge
r-vctrs 0.3.8 r41hcfec24a_1 conda-forge
r-viridislite 0.4.0 r41hc72bb7e_0 conda-forge
r-vroom 1.5.7 r41h03ef668_0 conda-forge
r-waldo 0.3.1 r41hc72bb7e_0 conda-forge
r-webshot 0.5.2 r41hc72bb7e_1 conda-forge
r-withr 2.4.3 r41hc72bb7e_0 conda-forge
r-xfun 0.29 r41h03ef668_0 conda-forge
r-xml2 1.3.3 r41h03ef668_0 conda-forge
r-yaml 2.2.1 r41hcfec24a_1 conda-forge
r-zoo 1.8_9 r41hcfec24a_1 conda-forge
radian 0.5.12 pyhd8ed1ab_0 conda-forge
rchitect 0.3.35 pypi_0 pypi
readline 8.1 h46c0cb4_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 60.5.0 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
tzdata 2021e he74cb21_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.1 ha95c52a_0 conda-forge