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libstdc++.so.6: version `GLIBCXX_3.4.26' not found on Linux
Asked Answered
rlinuxlibstdc++
P

2

7

I was trying to load Seurat package in rstudio and got this error

Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/wdata/msmuhammad/workbench/miniconda3/envs/test2/lib/R/library/Rcpp/libs/Rcpp.so':
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /wdata/msmuhammad/workbench/miniconda3/envs/test2/lib/R/library/Rcpp/libs/Rcpp.so)

I'm using rstudio on a conda environment

I found a question regarding same issue of not having version `GLIBCXX_3.4.26'. that led me to running this command

strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX

and I got this:

GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_DEBUG_MESSAGE_LENGTH

So, it doesn't have the required version and I can't install the libstdc++ from the terminal because that step requires the sudo command and I'm not one of the sudoers and I keep getting permission denied.

Ubuntu 18.04.6

Linux 4.15.0-154-generic

So, is there any solution for this issue other than the sudo command?

I tried this command with my conda environment

strings msmuhammad/workbench/miniconda3/envs/test2/lib/libstdc++.so.6 | grep GLIBCXX

and I got this

GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_3.4.29
GLIBCXX_DEBUG_MESSAGE_LENGTH
_ZNKSt14basic_ifstreamIcSt11char_traitsIcEE7is_openEv@GLIBCXX_3.4
_ZNSt13basic_istreamIwSt11char_traitsIwEE6ignoreEv@@GLIBCXX_3.4.5
_ZNKSbIwSt11char_traitsIwESaIwEE11_M_disjunctEPKw@GLIBCXX_3.4
_ZNKSt14basic_ifstreamIwSt11char_traitsIwEE7is_openEv@@GLIBCXX_3.4.5
GLIBCXX_3.4.21
GLIBCXX_3.4.9
_ZSt10adopt_lock@@GLIBCXX_3.4.11
GLIBCXX_3.4.10
GLIBCXX_3.4.16
GLIBCXX_3.4.1
_ZNSt19istreambuf_iteratorIcSt11char_traitsIcEEppEv@GLIBCXX_3.4
GLIBCXX_3.4.28
_ZNSs7_M_copyEPcPKcm@GLIBCXX_3.4
GLIBCXX_3.4.25
_ZNSt19istreambuf_iteratorIcSt11char_traitsIcEEppEv@@GLIBCXX_3.4.5
_ZNSs7_M_moveEPcPKcm@@GLIBCXX_3.4.5
_ZNKSt13basic_fstreamIwSt11char_traitsIwEE7is_openEv@GLIBCXX_3.4
_ZNKSt13basic_fstreamIcSt11char_traitsIcEE7is_openEv@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE4_Rep26_M_set_length_and_sharableEm@@GLIBCXX_3.4.5
_ZNSs4_Rep26_M_set_length_and_sharableEm@GLIBCXX_3.4
_ZSt10defer_lock@@GLIBCXX_3.4.11
_ZN10__gnu_norm15_List_node_base4swapERS0_S1_@@GLIBCXX_3.4
_ZNSs9_M_assignEPcmc@@GLIBCXX_3.4.5
_ZNKSbIwSt11char_traitsIwESaIwEE15_M_check_lengthEmmPKc@@GLIBCXX_3.4.5
_ZNKSt14basic_ifstreamIcSt11char_traitsIcEE7is_openEv@@GLIBCXX_3.4.5
_ZNSbIwSt11char_traitsIwESaIwEE7_M_moveEPwPKwm@GLIBCXX_3.4
GLIBCXX_3.4.24
_ZNVSt9__atomic011atomic_flag12test_and_setESt12memory_order@@GLIBCXX_3.4.11
GLIBCXX_3.4.20
_ZNSt11char_traitsIwE2eqERKwS2_@@GLIBCXX_3.4.5
GLIBCXX_3.4.12
_ZNSi6ignoreEv@@GLIBCXX_3.4.5
GLIBCXX_3.4.2
_ZNSt11char_traitsIcE2eqERKcS2_@@GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.15
_ZNKSt13basic_fstreamIcSt11char_traitsIcEE7is_openEv@@GLIBCXX_3.4.5
_ZNSs9_M_assignEPcmc@GLIBCXX_3.4
GLIBCXX_3.4.19
_ZNKSt14basic_ofstreamIwSt11char_traitsIwEE7is_openEv@GLIBCXX_3.4
_ZNSt19istreambuf_iteratorIwSt11char_traitsIwEEppEv@GLIBCXX_3.4
GLIBCXX_3.4.27
_ZN10__gnu_norm15_List_node_base7reverseEv@@GLIBCXX_3.4
_ZN10__gnu_norm15_List_node_base4hookEPS0_@@GLIBCXX_3.4
_ZNSt11char_traitsIwE2eqERKwS2_@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE7_M_copyEPwPKwm@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE7_M_copyEPwPKwm@@GLIBCXX_3.4.5
GLIBCXX_3.4.23
GLIBCXX_3.4.3
GLIBCXX_3.4.7
_ZNSi6ignoreEl@@GLIBCXX_3.4.5
_ZNKSbIwSt11char_traitsIwESaIwEE11_M_disjunctEPKw@@GLIBCXX_3.4.5
_ZNSt13basic_istreamIwSt11char_traitsIwEE6ignoreEv@GLIBCXX_3.4
_ZNKSt13basic_fstreamIwSt11char_traitsIwEE7is_openEv@@GLIBCXX_3.4.5
_ZNSbIwSt11char_traitsIwESaIwEE7_M_moveEPwPKwm@@GLIBCXX_3.4.5
GLIBCXX_3.4.18
_ZNSbIwSt11char_traitsIwESaIwEE4_Rep26_M_set_length_and_sharableEm@GLIBCXX_3.4
_ZNSt13basic_istreamIwSt11char_traitsIwEE6ignoreEl@@GLIBCXX_3.4.5
_ZSt15future_category@@GLIBCXX_3.4.14
_ZNSi6ignoreEl@GLIBCXX_3.4
GLIBCXX_3.4.29
_ZNSt11char_traitsIcE2eqERKcS2_@GLIBCXX_3.4
_ZNKSs15_M_check_lengthEmmPKc@GLIBCXX_3.4
_ZN10__gnu_norm15_List_node_base8transferEPS0_S1_@@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE9_M_assignEPwmw@GLIBCXX_3.4
_ZNVSt9__atomic011atomic_flag5clearESt12memory_order@@GLIBCXX_3.4.11
_ZNKSt14basic_ofstreamIcSt11char_traitsIcEE7is_openEv@@GLIBCXX_3.4.5
_ZNKSt14basic_ofstreamIcSt11char_traitsIcEE7is_openEv@GLIBCXX_3.4
_ZNSs7_M_moveEPcPKcm@GLIBCXX_3.4
_ZNSt13basic_istreamIwSt11char_traitsIwEE6ignoreEl@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE9_M_assignEPwmw@@GLIBCXX_3.4.5
_ZNKSbIwSt11char_traitsIwESaIwEE15_M_check_lengthEmmPKc@GLIBCXX_3.4
_ZNKSs11_M_disjunctEPKc@@GLIBCXX_3.4.5
_ZN10__gnu_norm15_List_node_base6unhookEv@@GLIBCXX_3.4
GLIBCXX_3.4.22
_ZNSt19istreambuf_iteratorIwSt11char_traitsIwEEppEv@@GLIBCXX_3.4.5
_ZNSi6ignoreEv@GLIBCXX_3.4
_ZNSs7_M_copyEPcPKcm@@GLIBCXX_3.4.5
GLIBCXX_3.4.8
GLIBCXX_3.4.13
_ZSt11try_to_lock@@GLIBCXX_3.4.11
_ZNKSt14basic_ofstreamIwSt11char_traitsIwEE7is_openEv@@GLIBCXX_3.4.5
GLIBCXX_3.4.17
GLIBCXX_3.4.4
_ZNKSs15_M_check_lengthEmmPKc@@GLIBCXX_3.4.5
_ZNKSt14basic_ifstreamIwSt11char_traitsIwEE7is_openEv@GLIBCXX_3.4
_ZNSs4_Rep26_M_set_length_and_sharableEm@@GLIBCXX_3.4.5
GLIBCXX_3.4.26
_ZNKSs11_M_disjunctEPKc@GLIBCXX_3.4

It seems that the package is updated and the required version is there in the conda environment directory but for some reason rstudio doesn't check that file.

How to make sure that rstudio looks at that directory?

The output of conda info is as below

     active environment : test2
    active env location : /wdata/msmuhammad/workbench/miniconda3/envs/test2
            shell level : 3
       user config file : /home/msmuhammad/.condarc
 populated config files : /home/msmuhammad/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __cuda=9.1=0
                          __linux=4.15.0=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /wdata/msmuhammad/workbench/miniconda3  (writable)
      conda av data dir : /wdata/msmuhammad/workbench/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/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 : /wdata/msmuhammad/workbench/miniconda3/pkgs
                          /home/msmuhammad/.conda/pkgs
       envs directories : /wdata/msmuhammad/workbench/miniconda3/envs
                          /home/msmuhammad/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Linux/4.15.0-154-generic ubuntu/18.04.6 glibc/2.27
                UID:GID : 2449533:900053705
             netrc file : None
           offline mode : False

and conda list output was as below

# packages in environment at /wdata/msmuhammad/workbench/miniconda3/envs/test2:
#
# 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
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_1    conda-forge
bwidget                   1.9.14               ha770c72_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2021.7.5             h06a4308_1  
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
curl                      7.79.0               hea6ffbf_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_8    conda-forge
gcc_linux-64              9.4.0                h391b98a_1    conda-forge
gettext                   0.21.0               hf68c758_0  
gfortran_impl_linux-64    9.4.0                h0003116_8    conda-forge
gfortran_linux-64         9.4.0                hf0ab688_1    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
graphite2                 1.3.14               h23475e2_0  
gsl                       2.6                  he838d99_2    conda-forge
gxx_impl_linux-64         9.4.0                h03d3576_8    conda-forge
gxx_linux-64              9.4.0                h0316aca_1    conda-forge
harfbuzz                  2.9.1                h83ec7ef_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_14    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libcurl                   7.79.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20210714         h7f8727e_0  
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h9c3ff4c_2    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-devel_linux-64     9.4.0                hd854feb_8    conda-forge
libgcc-ng                 11.2.0               h1d223b6_8    conda-forge
libgfortran-ng            11.2.0               h69a702a_8    conda-forge
libgfortran5              11.2.0               h5c6108e_8    conda-forge
libglib                   2.68.4               h174f98d_1    conda-forge
libgomp                   11.2.0               h1d223b6_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libsanitizer              9.4.0                h79bfe98_8    conda-forge
libssh2                   1.10.0               ha56f1ee_0    conda-forge
libstdcxx-devel_linux-64  9.4.0                hd854feb_8    conda-forge
libstdcxx-ng              11.2.0               he4da1e4_8    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.12               h72842e0_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                   1.1.1l               h7f98852_0    conda-forge
pango                     1.48.10              hb8ff022_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
r                         4.1             r41hd8ed1ab_1004    conda-forge
r-abind                   1.4_5           r41hc72bb7e_1003    conda-forge
r-askpass                 1.1               r41hcfec24a_2    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_2    conda-forge
r-backports               1.2.1             r41hcfec24a_0    conda-forge
r-base                    4.1.0                hb67fd72_2    conda-forge
r-base64enc               0.1_3           r41hcfec24a_1004    conda-forge
r-bh                      1.75.0_0          r41hc72bb7e_0    conda-forge
r-bitops                  1.0_7             r41hcfec24a_0    conda-forge
r-boot                    1.3_28            r41hc72bb7e_0    conda-forge
r-brio                    1.1.2             r41hcfec24a_0    conda-forge
r-bslib                   0.3.0             r41hc72bb7e_0    conda-forge
r-cachem                  1.0.6             r41hcfec24a_0    conda-forge
r-callr                   3.7.0             r41hc72bb7e_0    conda-forge
r-catools                 1.18.2            r41h03ef668_0    conda-forge
r-class                   7.3_19            r41hcfec24a_0    conda-forge
r-cli                     3.0.1             r41h03ef668_1    conda-forge
r-cluster                 2.1.2             r41h859d828_0    conda-forge
r-codetools               0.2_18            r41hc72bb7e_0    conda-forge
r-colorspace              2.0_2             r41hcfec24a_0    conda-forge
r-commonmark              1.7             r41hcfec24a_1002    conda-forge
r-cowplot                 1.1.1             r41hc72bb7e_0    conda-forge
r-crayon                  1.4.1             r41hc72bb7e_0    conda-forge
r-crosstalk               1.1.1             r41hc72bb7e_0    conda-forge
r-curl                    4.3.2             r41hcfec24a_0    conda-forge
r-data.table              1.14.0            r41hcfec24a_0    conda-forge
r-deldir                  0.2_10            r41h859d828_0    conda-forge
r-desc                    1.3.0             r41hc72bb7e_0    conda-forge
r-diffobj                 0.3.4             r41hcfec24a_0    conda-forge
r-digest                  0.6.27            r41h03ef668_0    conda-forge
r-dplyr                   1.0.7             r41h03ef668_0    conda-forge
r-dqrng                   0.3.0             r41h03ef668_0    conda-forge
r-ellipsis                0.3.2             r41hcfec24a_0    conda-forge
r-evaluate                0.14              r41hc72bb7e_2    conda-forge
r-fansi                   0.4.2             r41hcfec24a_0    conda-forge
r-farver                  2.1.0             r41h03ef668_0    conda-forge
r-fastmap                 1.1.0             r41h03ef668_0    conda-forge
r-fitdistrplus            1.1_5             r41hc72bb7e_0    conda-forge
r-fnn                     1.1.3             r41h03ef668_2    conda-forge
r-foreign                 0.8_81            r41hcfec24a_0    conda-forge
r-fs                      1.5.0             r41h03ef668_0    conda-forge
r-future                  1.22.1            r41hc72bb7e_0    conda-forge
r-future.apply            1.8.1             r41hc72bb7e_0    conda-forge
r-generics                0.1.0             r41hc72bb7e_0    conda-forge
r-ggplot2                 3.3.5             r41hc72bb7e_0    conda-forge
r-ggrepel                 0.9.1             r41h03ef668_0    conda-forge
r-ggridges                0.5.3             r41hc72bb7e_0    conda-forge
r-globals                 0.14.0            r41hc72bb7e_0    conda-forge
r-glue                    1.4.2             r41hcfec24a_0    conda-forge
r-goftest                 1.2_2             r41hcfec24a_1    conda-forge
r-gplots                  3.1.1             r41hc72bb7e_0    conda-forge
r-gridextra               2.3             r41hc72bb7e_1003    conda-forge
r-gtable                  0.3.0             r41hc72bb7e_3    conda-forge
r-gtools                  3.9.2             r41hcfec24a_0    conda-forge
r-here                    1.0.1             r41hc72bb7e_0    conda-forge
r-hexbin                  1.28.2            r41h859d828_0    conda-forge
r-htmltools               0.5.2             r41h03ef668_0    conda-forge
r-htmlwidgets             1.5.4             r41hc72bb7e_0    conda-forge
r-httpuv                  1.6.3             r41h03ef668_0    conda-forge
r-httr                    1.4.2             r41hc72bb7e_0    conda-forge
r-ica                     1.0_2             r41hc72bb7e_2    conda-forge
r-igraph                  1.2.6             r41he0372cf_1    conda-forge
r-irlba                   2.3.3             r41he454529_3    conda-forge
r-isoband                 0.2.5             r41h03ef668_0    conda-forge
r-jquerylib               0.1.4             r41hc72bb7e_0    conda-forge
r-jsonlite                1.7.2             r41hcfec24a_0    conda-forge
r-kernsmooth              2.23_20           r41h742201e_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_0    conda-forge
r-later                   1.2.0             r41h03ef668_0    conda-forge
r-lattice                 0.20_44           r41hcfec24a_0    conda-forge
r-lazyeval                0.2.2             r41hcfec24a_2    conda-forge
r-leiden                  0.3.9             r41hc72bb7e_0    conda-forge
r-lifecycle               1.0.0             r41hc72bb7e_0    conda-forge
r-listenv                 0.8.0             r41hc72bb7e_1    conda-forge
r-lmtest                  0.9_38            r41h859d828_1    conda-forge
r-lsei                    1.3_0             r41h92ddd45_1    conda-forge
r-magrittr                2.0.1             r41hcfec24a_1    conda-forge
r-mass                    7.3_54            r41hcfec24a_0    conda-forge
r-matrix                  1.3_4             r41he454529_0    conda-forge
r-matrixstats             0.61.0            r41hcfec24a_0    conda-forge
r-mgcv                    1.8_36            r41he454529_0    conda-forge
r-mime                    0.11              r41hcfec24a_0    conda-forge
r-miniui                  0.1.1.1         r41hc72bb7e_1002    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1003    conda-forge
r-nlme                    3.1_153           r41h859d828_0    conda-forge
r-nnet                    7.3_16            r41hcfec24a_0    conda-forge
r-npsurv                  0.5_0             r41hc72bb7e_0    conda-forge
r-openssl                 1.4.5             r41he36bf35_0    conda-forge
r-parallelly              1.28.1            r41hc72bb7e_0    conda-forge
r-patchwork               1.1.1             r41hc72bb7e_0    conda-forge
r-pbapply                 1.5_0             r41hc72bb7e_0    conda-forge
r-pillar                  1.6.2             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_1    conda-forge
r-pkgload                 1.2.2             r41h03ef668_0    conda-forge
r-plotly                  4.9.4.1           r41hc72bb7e_1    conda-forge
r-plyr                    1.8.6             r41h03ef668_1    conda-forge
r-png                     0.1_7           r41hcfec24a_1004    conda-forge
r-polyclip                1.10_0            r41h03ef668_2    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1004    conda-forge
r-processx                3.5.2             r41hcfec24a_0    conda-forge
r-promises                1.2.0.1           r41h03ef668_0    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-rann                    2.6.1             r41h03ef668_2    conda-forge
r-rappdirs                0.3.3             r41hcfec24a_0    conda-forge
r-rcolorbrewer            1.1_2           r41h785f33e_1003    conda-forge
r-rcpp                    1.0.7             r41h03ef668_0    conda-forge
r-rcppannoy               0.0.19            r41h03ef668_0    conda-forge
r-rcpparmadillo           0.10.6.0.0        r41h306847c_0    conda-forge
r-rcppeigen               0.3.3.9.1         r41h306847c_0    conda-forge
r-rcppparallel            5.1.4             r41h03ef668_0    conda-forge
r-rcppprogress            0.4.2             r41hc72bb7e_1    conda-forge
r-recommended             4.1             r41hd8ed1ab_1004    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r41h03ef668_1    conda-forge
r-reticulate              1.22              r41h03ef668_0    conda-forge
r-rlang                   0.4.11            r41hcfec24a_0    conda-forge
r-rocr                    1.0_11            r41hc72bb7e_1    conda-forge
r-rpart                   4.1_15            r41hcfec24a_2    conda-forge
r-rprojroot               2.0.2             r41hc72bb7e_0    conda-forge
r-rspectra                0.16_0            r41h306847c_4    conda-forge
r-rstudioapi              0.13              r41hc72bb7e_0    conda-forge
r-rtsne                   0.15              r41h6dc32e9_3    conda-forge
r-sass                    0.4.0             r41h03ef668_0    conda-forge
r-scales                  1.1.1             r41hc72bb7e_0    conda-forge
r-scattermore             0.7               r41hcfec24a_0    conda-forge
r-sctransform             0.3.2             r41h78ebb21_1    conda-forge
r-seurat                  4.0.4             r41h03ef668_0    conda-forge
r-seuratobject            4.0.2             r41h03ef668_0    conda-forge
r-shiny                   1.6.0             r41hc72bb7e_0    conda-forge
r-sitmo                   2.0.1             r41h03ef668_2    conda-forge
r-sourcetools             0.1.7           r41h9c3ff4c_1002    conda-forge
r-spatial                 7.3_14            r41hcfec24a_0    conda-forge
r-spatstat                2.2_0             r41hc72bb7e_0    conda-forge
r-spatstat.core           2.3_0             r41h03ef668_0    conda-forge
r-spatstat.data           2.1_0             r41hc72bb7e_0    conda-forge
r-spatstat.geom           2.2_2             r41hcfec24a_0    conda-forge
r-spatstat.linnet         2.3_0             r41hcfec24a_0    conda-forge
r-spatstat.sparse         2.0_0             r41hcfec24a_0    conda-forge
r-spatstat.utils          2.2_0             r41h7f98852_0    conda-forge
r-stringi                 1.7.4             r41hcabe038_0    conda-forge
r-stringr                 1.4.0             r41hc72bb7e_2    conda-forge
r-survival                3.2_13            r41hcfec24a_0    conda-forge
r-sys                     3.4               r41hcfec24a_0    conda-forge
r-tensor                  1.5             r41hc72bb7e_1003    conda-forge
r-testthat                3.0.4             r41h03ef668_0    conda-forge
r-tibble                  3.1.4             r41hcfec24a_0    conda-forge
r-tidyr                   1.1.3             r41h03ef668_0    conda-forge
r-tidyselect              1.1.1             r41hc72bb7e_0    conda-forge
r-utf8                    1.2.2             r41hcfec24a_0    conda-forge
r-uwot                    0.1.10            r41h03ef668_0    conda-forge
r-vctrs                   0.3.8             r41hcfec24a_1    conda-forge
r-viridislite             0.4.0             r41hc72bb7e_0    conda-forge
r-waldo                   0.3.1             r41hc72bb7e_0    conda-forge
r-withr                   2.4.2             r41hc72bb7e_0    conda-forge
r-xtable                  1.8_4             r41hc72bb7e_3    conda-forge
r-yaml                    2.2.1             r41hcfec24a_1    conda-forge
r-zoo                     1.8_9             r41hcfec24a_1    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
sysroot_linux-64          2.12                he073ed8_14    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tktable                   2.10                 hb7b940f_3    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-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            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge
Piggott answered 22/9, 2021 at 17:9 Comment(9)
Build your package from source, or ask your system administrator to upgrade your OS. – Pianoforte
Is everything installed through Conda? – Introrse
@Introrse yes, all through conda – Piggott
@Introrse I edited the question and added the output of these – Piggott
Thanks for adding that. How is RStudio configured to use the environment? Are you activating first, then launching? or manipulating env vars (e.g., RSTUDIO_WHICH_R)? Does everything work fine when just launching R from command line with activated environment? – Introrse
@Introrse yes, I activate the environment first and then launch rstudio. didn't manipulate env vars. yes, everything works fine if I launched R from the command line after activating the environment. I don't face any issues with loading Seurat in this case. – Piggott
Everything looks fine from what I am familiar with. I can only speculate there must be some additional environment variables that need to be set to get RStudio working in Linux (possibly LD*-related variables). I swear I've seen an answer where someone had a pure environment variable setup for Conda R env + native RStudio (and not just RSTUDIO_WHICH_R), but I cannot find it now. – Introrse
@Introrse is it this one you're talking about? #58923666 – Piggott
Exactly, I was just about to link it. Yeah, try setting LD_LIBRARY_PATH as part of when the environment gets activated. – Introrse
A
6

I had a similar issue. My system had the correct GLIBCXX_3.4.26 version in /usr/lib/x86_64-linux-gnu/libstdc++.so.6, but my conda environment did not:

ImportError: /mnt/nfs/home/[my_username]/miniconda3/envs/myenv/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /usr/lib/x86_64-linux-gnu/libLLVM-12.so.1)

In other similar questions' answers, many people suggested running

conda update libgcc

but my libgcc in my conda environment was already up to date, so this did not solve it.

The solution that fixed it for me was:

conda update libstdcxx-ng

(credit goes to the answer here: scipy not using anaconda's local lib for libgcc).

Arredondo answered 28/4, 2022 at 21:56 Comment(0)
R
4

As far as I understand problem is that your binary first checks system path and you conda path may or may not be on a lookup list.

Following worked for me:

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<your lib path> <your binary>
Rhaetic answered 28/10, 2021 at 18:32 Comment(2)
Can you elaborate on what is :<your lib path> <your binary> ? – Chilli
<your lib path> is where your CONDA supplied libstdc++.so.6 resides. <your binary> is the file you want to run. You can also omit <your binary>, but prepend export to the LD_LIBRARY_PATH=... command, and then run your command. – Morty

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