Error while loading conda entry point: conda-libmamba-solver (/lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found #544
Comments
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Can you please add the details requested by the issue template? They will help us assess the system conditions which seem to be affecting your installation. Report the output of:
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the same problem i have encountered: Error while loading conda entry point: conda-libmamba-solver (/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /data3/lgb_data_softwear/miniconda/lib/python3.10/site-packages/libmambapy/bindings.cpython-310-x86_64-linux-gnu.so)) ### conda info populated config files : /home/Lvgongbo/.condarc conda list -n base packages in environment at /data3/lgb_data_softwear/miniconda:Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge conda config --show-sources
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Thanks. Can you post also the output of |
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```
$ env | sort
CONDA_BACKUP_JAVA_HOME=:-:-:-:-:-:-:-:-:-:-
CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=:-:-:-:-:-:-:-:-:-:-
CONDA_DEFAULT_ENV=base
CONDA_EXE=/data3/lgb_data_softwear/miniconda/bin/conda
CONDA_PREFIX=/data3/lgb_data_softwear/miniconda
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/data3/lgb_data_softwear/miniconda/bin/python
CONDA_SHLVL=1
DISPLAY=localhost:13.0
GSETTINGS_SCHEMA_DIR=/data3/lgb_data_softwear/miniconda/share/glib-2.0/schemas
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
GTDBTK_DATA_PATH=/data3/lgb_data_softwear/miniconda/envs/gtdbtk/share/gtdbtk-2.4.0/db
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/Lvgongbo
HOSTNAME=localhost.localdomain
JAVA_HOME=/data3/lgb_data_softwear/miniconda
JAVA_LD_LIBRARY_PATH=/data3/lgb_data_softwear/miniconda/lib/server
LANG=en_US.UTF-8
LC_ALL=C
LD_LIBRARY_PATH=/data3/lgb_data_softwear/miniconda/lib:
LESSOPEN=||/usr/bin/lesspipe.sh %s
LOGNAME=Lvgongbo
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL=/var/spool/mail/Lvgongbo
PATH=/data3/lgb_data_softwear/miniconda/bin:/data3/lgb_data_softwear/datebase_lgb/metaWRAP/bin:/usr/bin
PERL5LIB=:/data3/lgb_data_softwear/softwear_lgb/MOCAT/src
PWD=/home/Lvgongbo
RSTUDIO_WHICH_R=/data3/lgb_data_softwear/miniconda/bin/R
SDLAST_ID=1198
SELINUX_LEVEL_REQUESTED=
SELINUX_ROLE_REQUESTED=
SELINUX_USE_CURRENT_RANGE=
SHELL=/bin/bash
SHLVL=1
SINGLEM_METAPACKAGE_PATH=/data3/lgb_data_softwear/nosZ_Reference_amino_acid/singlem/bin/OUTPUT_DIRECTORY/S3.2.1.GTDB_r214.metapackage_20231006.smpkg.zb
SSH_CLIENT=172.19.250.184 11272 22
SSH_CONNECTION=172.19.250.184 11272 172.19.251.232 22
SSH_TTY=/dev/pts/3
TERM=xterm
USER=Lvgongbo
XDG_DATA_DIRS=/home/Lvgongbo/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_RUNTIME_DIR=/run/user/1010
XDG_SESSION_ID=98663
_=/usr/bin/env
_CE_CONDA=
_CE_M=
```
thanks!!!!!!!!!!!!!!!!
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Yes, I do see a |
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after i unset it:
conda info
Error while loading conda entry point: conda-libmamba-solver (/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /data3/lgb_data_softwear/miniconda/lib/python3.10/site-packages/libmambapy/bindings.cpython-310-x86_64-linux-gnu.so))
active environment : base
active env location : /data3/lgb_data_softwear/miniconda
shell level : 1
user config file : /home/Lvgongbo/.condarc
populated config files : /home/Lvgongbo/.condarc
conda version : 24.9.1
conda-build version : not installed
python version : 3.10.13.final.0
solver : classic
virtual packages : __archspec=1=zen2
__conda=24.9.1=0
__glibc=2.17=0
__linux=3.10.0=0
__unix=0=0
base environment : /data3/lgb_data_softwear/miniconda (writable)
conda av data dir : /data3/lgb_data_softwear/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/ursky/linux-64
https://conda.anaconda.org/ursky/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
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /data3/lgb_data_softwear/miniconda/pkgs
/home/Lvgongbo/.conda/pkgs
envs directories : /data3/lgb_data_softwear/miniconda/envs
/home/Lvgongbo/.conda/envs
platform : linux-64
user-agent : conda/24.9.1 requests/2.32.3 CPython/3.10.13 Linux/3.10.0-1160.90.1.el7.x86_64 centos/7.9.2009 glibc/2.17
UID:GID : 1010:1010
netrc file : None
offline mode : False
At 2024-10-15 22:21:01, "jaimergp" ***@***.***> wrote:
Yes, I do see a LD_LIBRARY_PATH entry. Can you try to unset it? You shouldn't need that.
unset LD_LIBRARY_PATH
conda info
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Not sure why it's trying to load stuff from |
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I have fixed this problem by downgrading the version of conda: conda install -c bioconda conda=24.3.0! Hope this method can be work for others!!! |
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I had a similar error and found that the The following resolved my issue (where my conda is installed to hope this helps. |
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This is probably an issue related to mamba-org/mamba#3423 |
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Hi~ o(*￣▽￣*)ブ， it works！！！！！！！！！！ thanks for your help！ Have a good day.
At 2024-11-08 05:07:56, "mmsteven" ***@***.***> wrote:
I had a similar error and found that the .so was not getting linked correctly so in my <conda-prefix>/lib directory. I only had the libstdc++.so.6.0.33 file and was missing the so.6 link
The following resolved my issue (where my conda is installed to /mnt/hostname/users/data/miniconda3)
cd /mnt/hostname/users/data/miniconda3/lib
ln -s libstdc++.so.6.0.33 libstdc++.so.6
hope this helps.
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Hi:
I have an unsolvable problem when running this code.I get this error message whenever I try to do anything with conda.
How can I solve it?
Best
XI Li
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