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The Fast Cross-Platform Package Manager
https://mamba.readthedocs.io
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error while loading shared libraries without specifying the LD_LIBRARY_PATH #3331

Open zhangyz1997 opened 1 week ago

zhangyz1997 commented 1 week ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Micromamba

Search tried in issue tracker

Yes

Latest version of Mamba

Tried in Conda?

I didn't try

Describe your issue

I frequently encounter an error stating “error while loading shared libraries” when using packages installed on micromamba. This issue occurs across multiple packages, and creating a new environment does not resolve it. Temporarily setting LD_LIBRARY_PATH to the lib directory under the environment path seems to fix the issue. There are no additional errors during the package installation and environment activation process. I am running this on an HPC compute node that uses the CentOS 7 system.

mamba info / micromamba info

libmamba version : 1.5.8
     micromamba version : 1.5.8
           curl version : libcurl/8.6.0 OpenSSL/3.2.1 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5
       envs directories : /home/zhangyz1997/micromamba/envs
          package cache : /home/zhangyz1997/micromamba/pkgs
                          /home/zhangyz1997/.mamba/pkgs
            environment : rliger (active)
           env location : /home/zhangyz1997/micromamba/envs/rliger
      user config files : /home/zhangyz1997/.mambarc
 populated config files : /home/zhangyz1997/.condarc
       virtual packages : __unix=0=0
                          __linux=3.10.0=0
                          __glibc=2.17=0
                          __archspec=1=x86_64-v4
               channels : https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/noarch
                          https://conda.anaconda.org/nodefaults/linux-64
                          https://conda.anaconda.org/nodefaults/noarch
       base environment : /home/zhangyz1997/micromamba
               platform : linux-64

Logs

No response

environment.yml

name: rliger
channels:
- bioconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- binutils_impl_linux-64=2.40=ha1999f0_7
- bioconductor-biocgenerics=0.48.1=r43hdfd78af_2
- bioconductor-complexheatmap=2.18.0=r43hdfd78af_0
- bioconductor-iranges=2.36.0=r43ha9d7317_2
- bioconductor-s4vectors=0.40.2=r43ha9d7317_2
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=hd590300_5
- c-ares=1.28.1=hd590300_0
- ca-certificates=2024.6.2=hbcca054_0
- cairo=1.18.0=hbb29018_2
- curl=8.8.0=he654da7_0
- expat=2.6.2=h59595ed_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_2
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=h267a509_2
- fribidi=1.0.10=h36c2ea0_0
- gcc_impl_linux-64=13.2.0=h9eb54c0_13
- gfortran_impl_linux-64=13.2.0=h9efe08d_13
- glpk=5.0=h445213a_0
- gmp=6.3.0=hac33072_2
- graphite2=1.3.13=h59595ed_1003
- gxx_impl_linux-64=13.2.0=h2a599c4_13
- harfbuzz=8.5.0=hfac3d4d_0
- hdf5=1.14.3=nompi_hdf9ad27_105
- icu=73.2=h59595ed_0
- kernel-headers_linux-64=2.6.32=he073ed8_17
- keyutils=1.6.1=h166bdaf_0
- krb5=1.21.2=h659d440_0
- ld_impl_linux-64=2.40=hf3520f5_7
- lerc=4.0.0=h27087fc_0
- libaec=1.1.3=h59595ed_0
- libblas=3.9.0=22_linux64_openblas
- libcurl=8.8.0=hca28451_0
- libdeflate=1.20=hd590300_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=hd590300_2
- libexpat=2.6.2=h59595ed_0
- libffi=3.4.2=h7f98852_5
- libgcc-devel_linux-64=13.2.0=hdb50d1a_113
- libgcc-ng=13.2.0=h77fa898_13
- libgfortran-ng=13.2.0=h69a702a_13
- libgfortran5=13.2.0=h3d2ce59_13
- libglib=2.80.2=h8a4344b_1
- libgomp=13.2.0=h77fa898_13
- libiconv=1.17=hd590300_2
- libjpeg-turbo=3.0.0=hd590300_1
- liblapack=3.9.0=22_linux64_openblas
- libnghttp2=1.58.0=h47da74e_1
- libopenblas=0.3.27=pthreads_h413a1c8_0
- libpng=1.6.43=h2797004_0
- libsanitizer=13.2.0=h6ddb7a1_13
- libssh2=1.11.0=h0841786_0
- libstdcxx-devel_linux-64=13.2.0=hdb50d1a_113
- libstdcxx-ng=13.2.0=hc0a3c3a_13
- libtiff=4.6.0=h1dd3fc0_3
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.4.0=hd590300_0
- libxcb=1.16=hd590300_0
- libxml2=2.12.7=hc051c1a_1
- libzlib=1.3.1=h4ab18f5_1
- make=4.3=hd18ef5c_1
- ncurses=6.5=h59595ed_0
- openssl=3.3.1=h4ab18f5_0
- pango=1.54.0=h84a9a3c_0
- pcre2=10.44=h0f59acf_0
- pixman=0.43.2=h59595ed_0
- pthread-stubs=0.4=h36c2ea0_1001
- r-base=4.3.3=h8ee917f_2
- r-bh=1.84.0_0=r43hc72bb7e_0
- r-bit=4.0.5=r43h57805ef_1
- r-bit64=4.0.5=r43h57805ef_2
- r-circlize=0.4.16=r43hc72bb7e_0
- r-cli=3.6.3=r43ha18555a_0
- r-clue=0.3_65=r43h57805ef_0
- r-cluster=2.1.6=r43h61816a4_0
- r-codetools=0.2_20=r43hc72bb7e_0
- r-colorspace=2.1_0=r43h57805ef_1
- r-cowplot=1.1.3=r43hc72bb7e_0
- r-cpp11=0.4.7=r43hc72bb7e_0
- r-crayon=1.5.3=r43hc72bb7e_0
- r-digest=0.6.36=r43ha18555a_0
- r-doparallel=1.0.17=r43hc72bb7e_2
- r-dplyr=1.1.4=r43ha503ecb_0
- r-dqrng=0.3.2=r43ha503ecb_0
- r-ellipsis=0.3.2=r43h57805ef_2
- r-fansi=1.0.6=r43h57805ef_0
- r-farver=2.1.2=r43ha18555a_0
- r-fnn=1.1.4=r43ha503ecb_0
- r-foreach=1.5.2=r43hc72bb7e_2
- r-generics=0.1.3=r43hc72bb7e_2
- r-getoptlong=1.0.5=r43hc72bb7e_2
- r-ggplot2=3.5.1=r43hc72bb7e_0
- r-ggrepel=0.9.5=r43ha503ecb_0
- r-globaloptions=0.1.2=r43ha770c72_2
- r-glue=1.7.0=r43h57805ef_0
- r-gridextra=2.3=r43hc72bb7e_1005
- r-grr=0.9.5=r43ha503ecb_1006
- r-gtable=0.3.5=r43hc72bb7e_0
- r-hdf5r=1.3.10=r43h0e8ca13_0
- r-ica=1.0_3=r43hc72bb7e_2
- r-igraph=2.0.3=r43hbec7d4a_0
- r-irlba=2.3.5.1=r43h316c678_2
- r-isoband=0.2.7=r43ha503ecb_2
- r-iterators=1.0.14=r43hc72bb7e_2
- r-labeling=0.4.3=r43hc72bb7e_0
- r-lattice=0.22_6=r43h57805ef_0
- r-leidenalg=1.1.3=r43ha503ecb_0
- r-lifecycle=1.0.4=r43hc72bb7e_0
- r-liger=2.0.1=r43hd0834be_0
- r-magrittr=2.0.3=r43h57805ef_2
- r-mass=7.3_60=r43h57805ef_1
- r-matrix=1.6_5=r43h316c678_0
- r-matrix.utils=0.9.8=r43hc72bb7e_3
- r-matrixstats=1.3.0=r43h57805ef_0
- r-mclust=6.1=r43hd9ac46e_0
- r-mgcv=1.9_1=r43h316c678_0
- r-munsell=0.5.1=r43hc72bb7e_0
- r-nlme=3.1_165=r43hbcb9c34_0
- r-pbmcapply=1.5.1=r43h57805ef_2
- r-pillar=1.9.0=r43hc72bb7e_1
- r-pkgconfig=2.0.3=r43hc72bb7e_3
- r-plyr=1.8.9=r43ha503ecb_0
- r-png=0.1_8=r43h81d01c5_1
- r-proc=1.18.5=r43ha503ecb_0
- r-r6=2.5.1=r43hc72bb7e_2
- r-rann=2.6.1=r43ha503ecb_4
- r-rcolorbrewer=1.1_3=r43h785f33e_2
- r-rcpp=1.0.12=r43h7df8631_0
- r-rcppannoy=0.0.22=r43ha503ecb_0
- r-rcpparmadillo=0.12.8.4.0=r43h58a4165_0
- r-rcppeigen=0.3.4.0.0=r43h08d816e_0
- r-rcppprogress=0.4.2=r43hc72bb7e_3
- r-rjson=0.2.21=r43ha503ecb_3
- r-rlang=1.1.4=r43ha18555a_0
- r-rtsne=0.17=r43h7ce84a7_0
- r-scales=1.3.0=r43hc72bb7e_0
- r-sccore=1.0.5=r43ha503ecb_0
- r-shape=1.4.6.1=r43ha770c72_0
- r-sitmo=2.0.2=r43ha503ecb_2
- r-tibble=3.2.1=r43h57805ef_2
- r-tidyselect=1.2.1=r43hc72bb7e_0
- r-utf8=1.2.4=r43h57805ef_0
- r-uwot=0.1.16=r43ha503ecb_0
- r-vctrs=0.6.5=r43ha503ecb_0
- r-viridis=0.6.5=r43hc72bb7e_0
- r-viridislite=0.4.2=r43hc72bb7e_1
- r-withr=3.0.0=r43hc72bb7e_0
- readline=8.2=h8228510_1
- sed=4.8=he412f7d_0
- sysroot_linux-64=2.12=he073ed8_17
- tk=8.6.13=noxft_h4845f30_101
- tktable=2.10=h0c5db8f_5
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.9=hb711507_1
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-libxt=1.3.0=hd590300_1
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.6=h166bdaf_0
- zlib=1.3.1=h4ab18f5_1
- zstd=1.5.6=ha6fb4c9_0

~/.condarc

channels:
  - conda-forge
  - nodefaults
show_channel_urls: true
custom_channels:
  conda-forge: https://mirrors.bfsu.edu.cn/anaconda/cloud
  bioconda: https://mirrors.bfsu.edu.cn/anaconda/cloud
  menpo: https://mirrors.bfsu.edu.cn/anaconda/cloud
  pytorch: https://mirrors.bfsu.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.bfsu.edu.cn/anaconda/cloud
  nvidia: https://mirrors.sustech.edu.cn/anaconda-extra/cloud