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conda-forge / r-vroom-feedstock

A conda-smithy repository for r-vroom.
BSD 3-Clause "New" or "Revised" License
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vroom.so fails to load with GLIBCXX_3.4.30 on Ubuntu 18.04 #26

Closed gdevenyi closed 1 year ago

gdevenyi commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

Trying to use read_csv (which I presume depends on vroom somewhere), I get the following error:

> data <- read_csv("13100768.csv")
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/gdevenyi/mambaforge/envs/R/lib/R/library/vroom/libs/vroom.so':
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/gdevenyi/mambaforge/envs/R/lib/R/library/vroom/libs/vroom.so)

Installed packages

# packages in environment at /home/gdevenyi/mambaforge/envs/R:
#
# Name                    Version                   Build  Channel
_ipython_minor_entry_point 8.7.0                hb6b4a82_0    conda-forge
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.11.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
binutils_impl_linux-64    2.39                 he00db2b_1    conda-forge
binutils_linux-64         2.39                h5fc0e48_11    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    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           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contextlib2               21.6.0                   pypi_0    pypi
cryptography              38.0.4          py310h600f1e7_0    conda-forge
curl                      7.87.0               hdc1c0ab_0    conda-forge
debugpy                   1.6.4           py310hd8f1fbe_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docopt                    0.6.2                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
fftw                      3.3.10          nompi_hf0379b8_106    conda-forge
flit-core                 3.8.0              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                2.14.1               hc2a2eb6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
gcc_linux-64              12.2.0              h4798a0e_11    conda-forge
gdk-pixbuf                2.42.8               h9fd3ed7_2    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    12.2.0              h55be85b_19    conda-forge
gfortran_linux-64         12.2.0              h307d370_11    conda-forge
ghostscript               9.54.0               h27087fc_2    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
gitdb                     4.0.10             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.30             pyhd8ed1ab_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  6.0.2                h99bc08f_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h64030ff_2    conda-forge
gxx_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
gxx_linux-64              12.2.0              hb41e900_11    conda-forge
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagemagick               7.1.0_56        pl5321h0dc3a92_0    conda-forge
importlib-metadata        5.2.0              pyha770c72_0    conda-forge
importlib_resources       5.10.1             pyhd8ed1ab_1    conda-forge
internetarchive           3.0.0                    pypi_0    pypi
ipykernel                 6.19.4             pyh210e3f2_0    conda-forge
ipython                   8.7.0              pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.4              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonpatch                 1.32                     pypi_0    pypi
jsonpointer               2.3                      pypi_0    pypi
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-server-mathjax    0.2.6              pyh5bfe37b_1    conda-forge
jupyter_client            7.4.8              pyhd8ed1ab_0    conda-forge
jupyter_core              5.1.1           py310hff52083_0    conda-forge
jupyter_events            0.5.0              pyhd8ed1ab_1    conda-forge
jupyter_server            2.0.6              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.3              pyhd8ed1ab_0    conda-forge
jupyterlab                3.5.2              pyhd8ed1ab_0    conda-forge
jupyterlab-git            0.41.0             pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.17.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
ld_impl_linux-64          2.39                 hcc3a1bd_1    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   7.87.0               hdc1c0ab_0    conda-forge
libdeflate                1.14                 h166bdaf_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     12.2.0              h3b97bd3_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgd                     2.3.3                h5aea950_4    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgit2                   1.5.0                hdb3ecda_1    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.47.0               hff17c54_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
librsvg                   2.54.4               h7abd40a_0    conda-forge
libsanitizer              12.2.0              h46fd767_19    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-devel_linux-64  12.2.0              h3b97bd3_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.5.0                h82bc61c_0    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.44.2               h166bdaf_0    conda-forge
libwebp                   1.2.4                h1daa5a0_1    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.3               h7463322_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.1.1           py310h5764c6d_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.7              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.7              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.7              pyhd8ed1ab_0    conda-forge
nbdime                    3.1.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.1              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
nlopt                     2.7.1           py310h3342525_3    conda-forge
nodejs                    18.12.1              h8839609_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numpy                     1.24.0          py310h08bbf29_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.0.7                h0b41bf4_1    conda-forge
packaging                 22.0               pyhd8ed1ab_0    conda-forge
pandoc                    2.19.2               h32600fe_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.12              hd33c08f_1    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              2.6.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
psutil                    5.9.4           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.2          py310h5764c6d_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.8          h4a9ceb5_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.4              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytz                      2022.7             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h5764c6d_5    conda-forge
pyzmq                     24.0.1          py310h330234f_1    conda-forge
r-abind                   1.4_5           r42hc72bb7e_1004    conda-forge
r-alphavantager           0.1.2             r42hc72bb7e_2    conda-forge
r-anytime                 0.3.9             r42h7525677_1    conda-forge
r-askpass                 1.1               r42h06615bd_3    conda-forge
r-assertthat              0.2.1             r42hc72bb7e_3    conda-forge
r-backports               1.4.1             r42h06615bd_1    conda-forge
r-base                    4.2.2                ha7d60f8_3    conda-forge
r-base64enc               0.1_3           r42h06615bd_1005    conda-forge
r-bayestestr              0.13.0            r42hc72bb7e_1    conda-forge
r-bh                      1.78.0_0          r42hc72bb7e_1    conda-forge
r-bit                     4.0.5             r42h06615bd_0    conda-forge
r-bit64                   4.0.5             r42h06615bd_1    conda-forge
r-blob                    1.2.3             r42hc72bb7e_1    conda-forge
r-boot                    1.3_28.1          r42hc72bb7e_0    conda-forge
r-brew                    1.0_8             r42hc72bb7e_1    conda-forge
r-brio                    1.1.3             r42h06615bd_1    conda-forge
r-broom                   1.0.2             r42hc72bb7e_0    conda-forge
r-bslib                   0.4.2             r42hc72bb7e_0    conda-forge
r-cachem                  1.0.6             r42h06615bd_1    conda-forge
r-callr                   3.7.3             r42hc72bb7e_0    conda-forge
r-car                     3.1_1             r42hc72bb7e_0    conda-forge
r-cardata                 3.0_5             r42hc72bb7e_1    conda-forge
r-caret                   6.0_93            r42h06615bd_1    conda-forge
r-cellranger              1.1.0           r42hc72bb7e_1005    conda-forge
r-checkmate               2.1.0             r42h06615bd_1    conda-forge
r-class                   7.3_20            r42h06615bd_1    conda-forge
r-cli                     3.5.0             r42h38f115c_1    conda-forge
r-cliapp                  0.1.1             r42hc72bb7e_1    conda-forge
r-clipr                   0.8.0             r42hc72bb7e_1    conda-forge
r-clock                   0.6.1             r42h7525677_1    conda-forge
r-cluster                 2.1.4             r42h8da6f51_0    conda-forge
r-codetools               0.2_18            r42hc72bb7e_1    conda-forge
r-collections             0.3.6             r42h06615bd_0    conda-forge
r-colorspace              2.0_3             r42h06615bd_1    conda-forge
r-commonmark              1.8.1             r42h06615bd_0    conda-forge
r-confintr                0.2.0             r42hc72bb7e_1    conda-forge
r-conquer                 1.3.1             r42h37cf8d7_0    conda-forge
r-corrplot                0.92              r42hc72bb7e_1    conda-forge
r-cowplot                 1.1.1             r42hc72bb7e_1    conda-forge
r-cpp11                   0.4.3             r42hc72bb7e_0    conda-forge
r-crayon                  1.5.2             r42hc72bb7e_1    conda-forge
r-credentials             1.3.2             r42hc72bb7e_1    conda-forge
r-crosstalk               1.2.0             r42hc72bb7e_1    conda-forge
r-crul                    1.3               r42h785f33e_1    conda-forge
r-curl                    4.3.3             r42h06615bd_1    conda-forge
r-cyclocomp               1.1.0           r42hc72bb7e_1005    conda-forge
r-data.table              1.14.6            r42h06615bd_0    conda-forge
r-datawizard              0.6.5             r42hc72bb7e_0    conda-forge
r-dbi                     1.1.3             r42hc72bb7e_1    conda-forge
r-dbplyr                  2.2.1             r42hc72bb7e_1    conda-forge
r-deldir                  1.0_6             r42h8da6f51_1    conda-forge
r-desc                    1.4.2             r42hc72bb7e_1    conda-forge
r-devtools                2.4.5             r42hc72bb7e_1    conda-forge
r-diffobj                 0.3.5             r42h06615bd_1    conda-forge
r-digest                  0.6.31            r42h38f115c_0    conda-forge
r-downlit                 0.4.2             r42hc72bb7e_1    conda-forge
r-dplyr                   1.0.10            r42h7525677_1    conda-forge
r-dtplyr                  1.2.2             r42hc72bb7e_2    conda-forge
r-e1071                   1.7_12            r42h7525677_0    conda-forge
r-effects                 4.2_2             r42hc72bb7e_1    conda-forge
r-ellipsis                0.3.2             r42h06615bd_1    conda-forge
r-essentials              4.2             r42hd8ed1ab_2003    conda-forge
r-estimability            1.4.1             r42hc72bb7e_1    conda-forge
r-evaluate                0.19              r42hc72bb7e_0    conda-forge
r-fansi                   1.0.3             r42h06615bd_1    conda-forge
r-farver                  2.1.1             r42h7525677_1    conda-forge
r-fastmap                 1.1.0             r42h7525677_1    conda-forge
r-filelock                1.0.2           r42h06615bd_1003    conda-forge
r-fontawesome             0.4.0             r42hc72bb7e_0    conda-forge
r-forcats                 0.5.2             r42hc72bb7e_1    conda-forge
r-foreach                 1.5.2             r42hc72bb7e_1    conda-forge
r-forecast                8.19              r42h37cf8d7_0    conda-forge
r-foreign                 0.8_84            r42h133d619_0    conda-forge
r-formatr                 1.13              r42hc72bb7e_0    conda-forge
r-fracdiff                1.5_2             r42h64d53c3_0    conda-forge
r-fs                      1.5.2             r42h7525677_2    conda-forge
r-furrr                   0.3.1             r42hc72bb7e_1    conda-forge
r-future                  1.30.0            r42hc72bb7e_0    conda-forge
r-future.apply            1.10.0            r42hc72bb7e_0    conda-forge
r-gargle                  1.2.1             r42hc72bb7e_1    conda-forge
r-gdtools                 0.2.4             r42h287fb7f_1    conda-forge
r-generics                0.1.3             r42hc72bb7e_1    conda-forge
r-gert                    1.5.0             r42h163148b_3    conda-forge
r-gghighlight             0.4.0             r42hc72bb7e_0    conda-forge
r-ggplot2                 3.4.0             r42hc72bb7e_1    conda-forge
r-ggpmisc                 0.5.2             r42hc72bb7e_0    conda-forge
r-ggpp                    0.5.0             r42hc72bb7e_0    conda-forge
r-ggpubr                  0.5.0             r42hc72bb7e_0    conda-forge
r-ggrepel                 0.9.2             r42h7525677_0    conda-forge
r-ggsci                   2.9             r42hc72bb7e_1004    conda-forge
r-ggsignif                0.6.4             r42hc72bb7e_0    conda-forge
r-gh                      1.3.1             r42hc72bb7e_1    conda-forge
r-gistr                   0.9.0             r42hc72bb7e_1    conda-forge
r-gitcreds                0.1.2             r42hc72bb7e_1    conda-forge
r-glmnet                  4.1_2             r42h8da6f51_1    conda-forge
r-globals                 0.16.2            r42hc72bb7e_0    conda-forge
r-glue                    1.6.2             r42h06615bd_1    conda-forge
r-goftest                 1.2_3             r42h06615bd_1    conda-forge
r-googledrive             2.0.0             r42hc72bb7e_1    conda-forge
r-googlesheets4           1.0.1             r42h785f33e_1    conda-forge
r-gower                   1.0.1             r42h133d619_0    conda-forge
r-gridextra               2.3             r42hc72bb7e_1004    conda-forge
r-gtable                  0.3.1             r42hc72bb7e_1    conda-forge
r-hardhat                 1.2.0             r42hc72bb7e_1    conda-forge
r-haven                   2.5.1             r42h7525677_0    conda-forge
r-hexbin                  1.28.2            r42h8da6f51_1    conda-forge
r-highr                   0.10              r42hc72bb7e_0    conda-forge
r-hms                     1.1.2             r42hc72bb7e_1    conda-forge
r-htmltools               0.5.4             r42h38f115c_0    conda-forge
r-htmlwidgets             1.6.0             r42hc72bb7e_0    conda-forge
r-httpcode                0.3.0             r42ha770c72_2    conda-forge
r-httpgd                  1.3.0             r42he46e8b9_1    conda-forge
r-httpuv                  1.6.7             r42h38f115c_0    conda-forge
r-httr                    1.4.4             r42hc72bb7e_1    conda-forge
r-ids                     1.0.1             r42hc72bb7e_2    conda-forge
r-ini                     0.3.1           r42hc72bb7e_1004    conda-forge
r-insight                 0.18.8            r42hc72bb7e_0    conda-forge
r-ipred                   0.9_13            r42h06615bd_1    conda-forge
r-irdisplay               1.1               r42hd8ed1ab_1    conda-forge
r-irkernel                1.3.1             r42h785f33e_0    conda-forge
r-isoband                 0.2.7             r42h38f115c_1    conda-forge
r-iterators               1.0.14            r42hc72bb7e_1    conda-forge
r-janitor                 2.1.0             r42hc72bb7e_1    conda-forge
r-jquerylib               0.1.4             r42hc72bb7e_1    conda-forge
r-jsonlite                1.8.4             r42h133d619_0    conda-forge
r-jtools                  2.2.1             r42hc72bb7e_0    conda-forge
r-kableextra              1.3.4             r42hc72bb7e_1    conda-forge
r-kernsmooth              2.23_20           r42hd009a43_1    conda-forge
r-knitr                   1.41              r42hc72bb7e_0    conda-forge
r-labeling                0.4.2             r42hc72bb7e_2    conda-forge
r-languageserver          0.3.14            r42h06615bd_1    conda-forge
r-later                   1.3.0             r42h7525677_1    conda-forge
r-lattice                 0.20_45           r42h06615bd_1    conda-forge
r-lava                    1.7.0             r42hc72bb7e_0    conda-forge
r-lazyeval                0.2.2             r42h06615bd_3    conda-forge
r-lifecycle               1.0.3             r42hc72bb7e_1    conda-forge
r-lintr                   3.0.2             r42hc72bb7e_0    conda-forge
r-listenv                 0.9.0             r42hc72bb7e_0    conda-forge
r-lme4                    1.1_31            r42h7525677_0    conda-forge
r-lmertest                3.1_3             r42hc72bb7e_1    conda-forge
r-lmodel2                 1.7_3             r42hc72bb7e_1    conda-forge
r-lmtest                  0.9_40            r42h8da6f51_1    conda-forge
r-lobstr                  1.1.2             r42h38f115c_2    conda-forge
r-lpsolve                 5.6.17            r42h06615bd_0    conda-forge
r-lubridate               1.9.0             r42h133d619_0    conda-forge
r-magick                  2.7.3             r42h7525677_1    conda-forge
r-magrittr                2.0.3             r42h06615bd_1    conda-forge
r-maps                    3.4.1             r42h06615bd_1    conda-forge
r-maptools                1.1_6             r42h133d619_0    conda-forge
r-mass                    7.3_58.1          r42h06615bd_1    conda-forge
r-matrix                  1.5_3             r42h5f7b363_0    conda-forge
r-matrixmodels            0.5_1             r42hc72bb7e_0    conda-forge
r-matrixstats             0.63.0            r42h06615bd_0    conda-forge
r-memoise                 2.0.1             r42hc72bb7e_1    conda-forge
r-mgcv                    1.8_41            r42h5f7b363_0    conda-forge
r-mime                    0.12              r42h06615bd_1    conda-forge
r-miniui                  0.1.1.1         r42hc72bb7e_1003    conda-forge
r-minqa                   1.2.5             r42hb13c81a_0    conda-forge
r-mitools                 2.4               r42hc72bb7e_3    conda-forge
r-modeldata               1.0.1             r42hc72bb7e_1    conda-forge
r-modelmetrics            1.2.2.2           r42h7525677_2    conda-forge
r-modelr                  0.1.10            r42hc72bb7e_0    conda-forge
r-modelsummary            1.2.0             r42hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r42hc72bb7e_1005    conda-forge
r-nlme                    3.1_161           r42hac0b197_0    conda-forge
r-nloptr                  2.0.3             r42hb13c81a_1    conda-forge
r-nnet                    7.3_18            r42h06615bd_1    conda-forge
r-numderiv                2016.8_1.1        r42hc72bb7e_4    conda-forge
r-openssl                 2.0.5             r42habfbb5e_0    conda-forge
r-openxlsx                4.2.5.1           r42h7525677_0    conda-forge
r-padr                    0.6.2             r42h38f115c_1    conda-forge
r-pak                     0.3.1             r42hc72bb7e_1    conda-forge
r-pander                  0.6.5             r42h7525677_1    conda-forge
r-parallelly              1.33.0            r42hc72bb7e_0    conda-forge
r-parameters              0.20.0            r42hc72bb7e_0    conda-forge
r-pbdzmq                  0.3_8             r42h616c82a_0    conda-forge
r-pbkrtest                0.5.1             r42hc72bb7e_1    conda-forge
r-performance             0.10.1            r42hc72bb7e_0    conda-forge
r-performanceanalytics    2.0.4             r42h06615bd_2    conda-forge
r-pillar                  1.8.1             r42hc72bb7e_1    conda-forge
r-pkgbuild                1.4.0             r42hc72bb7e_0    conda-forge
r-pkgcache                2.0.4             r42hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r42hc72bb7e_2    conda-forge
r-pkgdown                 2.0.7             r42hc72bb7e_0    conda-forge
r-pkgload                 1.3.2             r42hc72bb7e_0    conda-forge
r-plotly                  4.10.1            r42hc72bb7e_0    conda-forge
r-plyr                    1.8.8             r42h7525677_0    conda-forge
r-polyclip                1.10_4            r42h7525677_0    conda-forge
r-polycub                 0.8.1             r42h06615bd_0    conda-forge
r-polynom                 1.4_1             r42hc72bb7e_1    conda-forge
r-praise                  1.0.0           r42hc72bb7e_1006    conda-forge
r-prettycode              1.1.0             r42hc72bb7e_2    conda-forge
r-prettyunits             1.1.1             r42hc72bb7e_2    conda-forge
r-proc                    1.18.0            r42h7525677_1    conda-forge
r-processx                3.8.0             r42h06615bd_0    conda-forge
r-prodlim                 2019.11.13        r42h7525677_2    conda-forge
r-profvis                 0.3.7             r42h06615bd_1    conda-forge
r-progress                1.2.2             r42hc72bb7e_3    conda-forge
r-progressr               0.12.0            r42hc72bb7e_0    conda-forge
r-promises                1.2.0.1           r42h7525677_1    conda-forge
r-proxy                   0.4_27            r42h06615bd_1    conda-forge
r-pryr                    0.1.5             r42h7525677_1    conda-forge
r-ps                      1.7.2             r42h06615bd_0    conda-forge
r-purrr                   1.0.0             r42h133d619_0    conda-forge
r-quadprog                1.5_8             r42hd009a43_4    conda-forge
r-quandl                  2.11.0            r42hc72bb7e_1    conda-forge
r-quantmod                0.4.20            r42hc72bb7e_1    conda-forge
r-quantreg                5.94              r42hb361e29_1    conda-forge
r-r.cache                 0.16.0            r42hc72bb7e_1    conda-forge
r-r.methodss3             1.8.2             r42hc72bb7e_1    conda-forge
r-r.oo                    1.25.0            r42hc72bb7e_1    conda-forge
r-r.utils                 2.12.2            r42hc72bb7e_0    conda-forge
r-r6                      2.5.1             r42hc72bb7e_1    conda-forge
r-ragg                    1.2.4             r42hd65d3ba_1    conda-forge
r-randomforest            4.7_1.1           r42h8da6f51_1    conda-forge
r-rappdirs                0.3.3             r42h06615bd_1    conda-forge
r-rapportools             1.1               r42hc72bb7e_1    conda-forge
r-rbokeh                  0.5.2             r42hc72bb7e_2    conda-forge
r-rcmdcheck               1.4.0             r42h785f33e_1    conda-forge
r-rcolorbrewer            1.1_3             r42h785f33e_1    conda-forge
r-rcpp                    1.0.9             r42h7525677_2    conda-forge
r-rcpparmadillo           0.11.4.2.1        r42h9f5de39_0    conda-forge
r-rcppeigen               0.3.3.9.3         r42h9f5de39_0    conda-forge
r-rcpproll                0.3.0           r42h7525677_1003    conda-forge
r-readr                   2.1.3             r42h7525677_1    conda-forge
r-readxl                  1.4.1             r42h3ebcfa7_1    conda-forge
r-recipes                 1.0.3             r42hc72bb7e_0    conda-forge
r-recommended             4.2             r42hd8ed1ab_1005    conda-forge
r-rematch                 1.0.1           r42hc72bb7e_1005    conda-forge
r-rematch2                2.1.2             r42hc72bb7e_2    conda-forge
r-remotes                 2.4.2             r42hc72bb7e_1    conda-forge
r-repr                    1.1.4             r42h785f33e_1    conda-forge
r-reprex                  2.0.2             r42hc72bb7e_1    conda-forge
r-reshape                 0.8.9             r42hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r42h7525677_2    conda-forge
r-rex                     1.2.1             r42hc72bb7e_1    conda-forge
r-riingo                  0.3.1             r42hc72bb7e_1    conda-forge
r-rio                     0.5.29            r42hc72bb7e_1    conda-forge
r-rlang                   1.0.6             r42h7525677_1    conda-forge
r-rmarkdown               2.19              r42hc72bb7e_0    conda-forge
r-roxygen2                7.2.3             r42h38f115c_0    conda-forge
r-rpart                   4.1.19            r42h06615bd_0    conda-forge
r-rprojroot               2.0.3             r42hc72bb7e_1    conda-forge
r-rsample                 1.1.1             r42hc72bb7e_1    conda-forge
r-rstatix                 0.7.1             r42hc72bb7e_0    conda-forge
r-rstudioapi              0.14              r42hc72bb7e_1    conda-forge
r-rversions               2.1.2             r42hc72bb7e_1    conda-forge
r-rvest                   1.0.3             r42hc72bb7e_1    conda-forge
r-sass                    0.4.4             r42h7525677_0    conda-forge
r-scales                  1.2.1             r42hc72bb7e_1    conda-forge
r-selectr                 0.4_2             r42hc72bb7e_2    conda-forge
r-sessioninfo             1.2.2             r42hc72bb7e_1    conda-forge
r-shape                   1.4.6             r42ha770c72_1    conda-forge
r-shiny                   1.7.4             r42h785f33e_0    conda-forge
r-slider                  0.3.0             r42h06615bd_0    conda-forge
r-snakecase               0.11.0            r42hc72bb7e_3    conda-forge
r-sourcetools             0.1.7           r42h7525677_1003    conda-forge
r-sp                      1.5_1             r42h06615bd_0    conda-forge
r-sparsem                 1.81              r42h8da6f51_1    conda-forge
r-spatial                 7.3_15            r42h06615bd_1    conda-forge
r-spatstat                3.0_2             r42hc72bb7e_0    conda-forge
r-spatstat.core           2.4_4             r42h7525677_1    conda-forge
r-spatstat.data           3.0_0             r42hc72bb7e_0    conda-forge
r-spatstat.explore        3.0_5             r42h06615bd_0    conda-forge
r-spatstat.geom           3.0_3             r42h06615bd_0    conda-forge
r-spatstat.linnet         3.0_3             r42h06615bd_0    conda-forge
r-spatstat.model          3.0_2             r42h06615bd_0    conda-forge
r-spatstat.random         3.0_1             r42h7525677_0    conda-forge
r-spatstat.sparse         3.0_0             r42h06615bd_0    conda-forge
r-spatstat.utils          3.0_1             r42h06615bd_0    conda-forge
r-splus2r                 1.3_3             r42h8da6f51_1    conda-forge
r-squarem                 2021.1            r42hc72bb7e_1    conda-forge
r-statmod                 1.4.37            r42hc3ea6d6_1    conda-forge
r-stringdist              0.9.10            r42h06615bd_0    conda-forge
r-stringi                 1.7.8             r42h30a9eb7_1    conda-forge
r-stringr                 1.5.0             r42h785f33e_0    conda-forge
r-styler                  1.8.1             r42hc72bb7e_0    conda-forge
r-summarytools            1.0.1             r42hc72bb7e_1    conda-forge
r-surveillance            1.20.3            r42h7525677_0    conda-forge
r-survey                  4.1_1             r42hc72bb7e_1    conda-forge
r-survival                3.4_0             r42h06615bd_1    conda-forge
r-svglite                 2.1.0             r42h7525677_1    conda-forge
r-sys                     3.4.1             r42h06615bd_0    conda-forge
r-systemfonts             1.0.4             r42h0ff29ef_1    conda-forge
r-tables                  0.9.10            r42hc72bb7e_0    conda-forge
r-tensor                  1.5             r42hc72bb7e_1004    conda-forge
r-testthat                3.1.6             r42h38f115c_0    conda-forge
r-textshaping             0.3.6             r42hbb20487_4    conda-forge
r-tibble                  3.1.8             r42h06615bd_1    conda-forge
r-tidyquant               1.0.6             r42h785f33e_0    conda-forge
r-tidyr                   1.2.1             r42h7525677_1    conda-forge
r-tidyselect              1.2.0             r42hc72bb7e_0    conda-forge
r-tidyverse               1.3.2             r42hc72bb7e_1    conda-forge
r-timechange              0.1.1             r42h38f115c_1    conda-forge
r-timedate                4021.107          r42hc72bb7e_0    conda-forge
r-timetk                  2.8.2             r42hc72bb7e_0    conda-forge
r-tinytex                 0.43              r42hc72bb7e_0    conda-forge
r-triebeard               0.3.0           r42h7525677_1005    conda-forge
r-tseries                 0.10_52           r42hd009a43_0    conda-forge
r-tsfeatures              1.1               r42hc72bb7e_1    conda-forge
r-ttr                     0.24.3            r42h06615bd_1    conda-forge
r-tzdb                    0.3.0             r42h7525677_1    conda-forge
r-urca                    1.3_3             r42h8da6f51_0    conda-forge
r-urlchecker              1.0.1             r42hc72bb7e_1    conda-forge
r-urltools                1.7.3             r42h7525677_3    conda-forge
r-usethis                 2.1.6             r42hc72bb7e_1    conda-forge
r-utf8                    1.2.2             r42h06615bd_1    conda-forge
r-uuid                    1.1_0             r42h06615bd_1    conda-forge
r-vctrs                   0.5.1             r42h7525677_0    conda-forge
r-viridislite             0.4.1             r42hc72bb7e_1    conda-forge
r-vroom                   1.6.0             r42h7525677_1    conda-forge
r-waldo                   0.4.0             r42hc72bb7e_1    conda-forge
r-warp                    0.2.0             r42h06615bd_2    conda-forge
r-webshot                 0.5.4             r42hc72bb7e_1    conda-forge
r-whisker                 0.4.1             r42hc72bb7e_0    conda-forge
r-withr                   2.5.0             r42hc72bb7e_1    conda-forge
r-xfun                    0.36              r42h38f115c_0    conda-forge
r-xml2                    1.3.3             r42h044e5c7_2    conda-forge
r-xmlparsedata            1.0.5             r42hc72bb7e_1    conda-forge
r-xopen                   1.0.0           r42hc72bb7e_1004    conda-forge
r-xtable                  1.8_4             r42hc72bb7e_4    conda-forge
r-xts                     0.12.2            r42h06615bd_0    conda-forge
r-yaml                    2.3.6             r42h06615bd_0    conda-forge
r-zip                     2.2.2             r42h06615bd_0    conda-forge
r-zoo                     1.8_11            r42h06615bd_1    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
ripgrep                   13.0.0               h2f28480_2    conda-forge
schema                    0.7.5                    pypi_0    pypi
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.6.3             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
testpath                  0.6.0              pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
tqdm                      4.64.0                   pypi_0    pypi
traitlets                 5.8.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
urllib3                   1.26.13            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.5              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                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.11.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge

Environment info

active environment : R
    active env location : /home/gdevenyi/mambaforge/envs/R
            shell level : 1
       user config file : /home/gdevenyi/.condarc
 populated config files : /home/gdevenyi/mambaforge/.condarc
                          /home/gdevenyi/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __cuda=12.0=0
                          __linux=5.4.0=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/gdevenyi/mambaforge  (writable)
      conda av data dir : /home/gdevenyi/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/nvidia/linux-64
                          https://conda.anaconda.org/nvidia/noarch
                          https://conda.anaconda.org/rapidsai/linux-64
                          https://conda.anaconda.org/rapidsai/noarch
                          https://conda.anaconda.org/simpleitk/linux-64
                          https://conda.anaconda.org/simpleitk/noarch
                          https://conda.anaconda.org/mrtrix3/linux-64
                          https://conda.anaconda.org/mrtrix3/noarch
                          https://conda.anaconda.org/itk/linux-64
                          https://conda.anaconda.org/itk/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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
          package cache : /home/gdevenyi/mambaforge/pkgs
                          /home/gdevenyi/.conda/pkgs
       envs directories : /home/gdevenyi/mambaforge/envs
                          /home/gdevenyi/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.4.0-135-generic neon/18.04 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
gdevenyi commented 1 year ago

Closing because I found that the a system-installed rstudio-desktop breaks environment in such a way that conda doesn't work properly. Using conda installed rstudio fixed it.

mfansler commented 1 year ago

Closing because I found that the a system-installed rstudio-desktop breaks environment in such a way that conda doesn't work properly. Using conda installed rstudio fixed it.

I'd be interested to hear this elaborated on. I have used native RStudio (on MacOS) with Conda R environments heavily for at least two years and never encountered such an issue.

gdevenyi commented 1 year ago

Okay, I've dug into this a bit more, and found:

If I upgrade to 2022.12.0-353 from deb, I get this now: image

Looks to me like whatever build config rstudio upstream is using is hard-coding paths somewhere where are interfering with loading of non-system R.

gdevenyi commented 1 year ago

https://github.com/rstudio/rstudio/issues/12508