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UnsatisfiableError while installing VIBRANT (glibc==2.27=0) #56

Open P-Leao opened 2 years ago

P-Leao commented 2 years ago

Hello everyone! While installing VIBRANT (conda install -c bioconda vibrant==1.2.0) The following error pops on the terminal:


`Found conflicts! Looking for incompatible packages.                                                                                                                failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.27=0
  - feature:|@/linux-64::__glibc==2.27=0

Your installed version is: 2.27`

My environment at the moment of the installation is this:

(vibrant_env) pedro@helheim:~$ conda list
# packages in environment at /home/pedro/miniconda3/envs/vibrant_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
biopython                 1.68                     py35_0    bioconda
ca-certificates           2021.10.8            ha878542_0    conda-forge
certifi                   2018.8.24             py35_1001    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dbus                      1.13.18              hb2f20db_0    anaconda
expat                     2.4.1                h9c3ff4c_0    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
glib                      2.56.2               hd408876_0    anaconda
gst-plugins-base          1.14.0               hbbd80ab_1    anaconda
gstreamer                 1.14.0               hb453b48_1    anaconda
hmmer                     3.3.2                h1b792b2_1    bioconda
icu                       58.2              hf484d3e_1000    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
joblib                    0.14.1                   pypi_0    pypi
jpeg                      9d                   h36c2ea0_0    conda-forge
kiwisolver                1.1.0                    pypi_0    pypi
lerc                      3.0                  h9c3ff4c_0    conda-forge
libdeflate                1.8                  h7f98852_0    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            7.5.0               h14aa051_19    conda-forge
libgfortran4              7.5.0               h14aa051_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libidn2                   2.3.2                h7f98852_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libtiff                   4.3.0                h6f004c6_2    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxml2                   2.9.9                h13577e0_2    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib                3.0.3                    pypi_0    pypi
mkl                       2021.4.0           h8d4b97c_729    conda-forge
mkl_fft                   1.0.9                    py35_0    conda-forge
mkl_random                1.0.1                    py35_0    conda-forge
mmtf-python               1.0.2                    py35_0    bioconda
msgpack-python            0.5.6            py35h2d50403_3    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
numpy                     1.18.5                   pypi_0    pypi
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
pandas                    0.25.3                   pypi_0    pypi
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pickle-mixin              1.0.2                    pypi_0    pypi
pillow                    5.3.0            py35hc736899_0    conda-forge
pip                       20.3.4             pyhd8ed1ab_0    conda-forge
prodigal                  2.6.3                h779adbc_3    bioconda
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.9.2            py35h05f1152_2    anaconda
python                    3.5.6                h12debd9_1
python-dateutil           2.8.2                    pypi_0    pypi
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
qt                        5.9.7                h5867ecd_1    anaconda
readline                  8.1                  h46c0cb4_0    conda-forge
reportlab                 3.5.8            py35h77bcf2c_0    conda-forge
scikit-learn              0.21.3                   pypi_0    pypi
scipy                     1.4.1                    pypi_0    pypi
seaborn                   0.9.1                    pypi_0    pypi
setuptools                40.4.3                   py35_0    conda-forge
sip                       4.19.8          py35hf484d3e_1000    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.36.0               h9cd32fc_2    conda-forge
statsmodels               0.9.0                    py35_0    conda-forge
tbb                       2021.3.0             h4bd325d_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tornado                   5.1.1            py35h470a237_0    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

Please let me know if you have any idea what is going on here, and how I could solve it. Feel free to ask for more information too.

Thanks!

KrisKieft commented 2 years ago

Hi,

Unfortunately I'm not too familiar with conda environments. My suggestion is to rather install via GitHub clone as that tends to not result in any issues. You could then create an environment for VIBRANT:

conda create -n vibrant python=3 pandas numpy scikit-learn=0.21.3 prodigal hmmer biopython matplotlib seaborn conda activate vibrant to activate the environment conda deactivate to deactivate the environment

In this case it's not installing via conda so you'll still need to provide the path to VIBRANT_run.py or add it to your PATH.

P-Leao commented 2 years ago

Thanks Kris!

It words fine! I created a conda environment with the requested dependencies, and them installed VIBRANT via GitHub.