'libstdc++.so.6: version `GLIBCXX_3.4.26' not found on Linux
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
Solution 1:[1]
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).
Solution 2:[2]
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>
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|---|
| Solution 1 | |
| Solution 2 | Aleksey Vlasenko |