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conda-forge / pymol-open-source-feedstock

A conda-smithy repository for pymol-open-source.
BSD 3-Clause "New" or "Revised" License
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Unable to install pymol-open-source after upgrading micromamba to v2 #31

Open ori-scala opened 1 month ago

ori-scala commented 1 month ago

Solution to issue cannot be found in the documentation.

Issue

Hi, I've tried to upgrade from micromamba 1.5.10 to 2.0.2 and got the following error when trying to install pymol-open-source

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ pymol-open-source does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

Installed packages



### Environment info

    active environment : luca-env
    active env location : /home/ubuntu/anaconda3/envs/luca-env
            shell level : 2
       user config file : /home/ubuntu/.condarc
 populated config files :
          conda version : 24.1.2
    conda-build version : 24.1.2
         python version : 3.11.7.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=x86_64_v4
                          __conda=24.1.2=0
                          __glibc=2.35=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /home/ubuntu/anaconda3  (writable)
      conda av data dir : /home/ubuntu/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : 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 : /home/ubuntu/anaconda3/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/anaconda3/envs
                          /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/24.1.2 requests/2.31.0 CPython/3.11.7 Linux/6.8.0-1016-aws ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.6 aau/0.4.3 c/DLe7N-WupybK0xXeNwdHbw s/HhYkbKcgqJCW6dRe9XMN7A e/--4_dFc0gL1OEAPkwffxBw
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
bkpoon commented 1 month ago

Can you add -c conda-forge to your command? From your conda info output, it looks like you only have the defaults channel.

ori-scala commented 1 month ago

Sorry, I'm using a dockerfile:

FROM ubuntu:22.04

# Install base utilities
RUN apt-get update && \
    apt-get install -y curl libgl1 libglx-mesa0 bzip2 && \
    apt-get clean autoremove --yes && \
    rm -rf /var/lib/{apt,dpkg,cache,log} && \
    rm -rf /root/.cache

# Install micromamba
ENV MAMBA_ROOT_PREFIX=/opt/conda
RUN mkdir -p $MAMBA_ROOT_PREFIX && chmod 777 $MAMBA_ROOT_PREFIX
RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/2.0.2 | tar -xvj bin/micromamba && \
    touch /root/.bashrc && \
    ./bin/micromamba shell init --shell bash --root-prefix /opt/conda && \
    grep -v '[ -z "\$PS1" ] && return' /root/.bashrc  > /opt/conda/bashrc && \
    apt-get clean autoremove --yes && \
    rm -rf /var/lib/{apt,dpkg,cache,log} && \
    rm -rf /root/.cache

# Install env
RUN micromamba env create --name my-env --file environment.yml --root-prefix /opt/conda --yes

The contents of environment.yml is:

channels:
  - defaults
  - conda-forge

dependencies:
  - python=3.12.3
  - pymol-open-source

Note that changing 2.0.2 to 1.5.10 makes it work.

bkpoon commented 1 month ago

In that case, remove the - defaults line in your environment.yml. Generally, you should not mix the defaults channel with the conda-forge channel.

ori-scala commented 1 month ago

Tried with the yml file below:

dependencies:
  - defaults::python=3.12.3
  - bioconda::cd-hit
#  - conda-forge::pymol-open-source
  - conda-forge::python-kaleido

And it works. Uncommenting the pymol-open-source makes it fail again with the same issue. Removing the defaults:: from the second line generates the following error:

python =3.12.3 does not exist (perhaps a typo or a missing channel)
bkpoon commented 1 month ago

Can you try this environment file?

channels:
  - conda-forge

dependencies:
  - python=3.12.3
  - bioconda::cd-hit
  - pymol-open-source
  - python-kaleido

When I try this, the solved environment is the following

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache

Transaction

  Prefix: /opt/conda/envs/abc

  Updating specs:

   - python=3.12.3
   - bioconda::cd-hit
   - pymol-open-source
   - python-kaleido

  Package                           Version  Build                Channel           Size
──────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                       0.1  conda_forge          conda-forge        3kB
  + _openmp_mutex                       4.5  2_gnu                conda-forge       24kB
  + alsa-lib                         1.2.12  h4ab18f5_0           conda-forge      556kB
  + attr                              2.5.1  h166bdaf_1           conda-forge       71kB
  + blosc                            1.21.5  hc2324a3_1           conda-forge       49kB
  + bzip2                             1.0.8  h4bc722e_7           conda-forge     Cached
  + c-ares                           1.32.3  h4bc722e_0           conda-forge     Cached
  + ca-certificates               2024.8.30  hbcca054_0           conda-forge     Cached
  + cairo                            1.18.0  h3faef2a_0           conda-forge      982kB
  + cd-hit                            4.8.1  h43eeafb_10          bioconda         238kB
  + dbus                             1.13.6  h5008d03_3           conda-forge      619kB
  + expat                             2.6.3  h5888daf_0           conda-forge      138kB
  + font-ttf-dejavu-sans-mono          2.37  hab24e00_0           conda-forge      397kB
  + font-ttf-inconsolata              3.000  h77eed37_0           conda-forge       97kB
  + font-ttf-source-code-pro          2.038  h77eed37_0           conda-forge      701kB
  + font-ttf-ubuntu                    0.83  h77eed37_3           conda-forge        2MB
  + fontconfig                       2.14.2  h14ed4e7_0           conda-forge      272kB
  + fonts-conda-ecosystem                 1  0                    conda-forge        4kB
  + fonts-conda-forge                     1  0                    conda-forge        4kB
  + freetype                         2.12.1  h267a509_2           conda-forge      635kB
  + gettext                          0.22.5  he02047a_3           conda-forge      479kB
  + gettext-tools                    0.22.5  he02047a_3           conda-forge        3MB
  + glew                              2.1.0  h9c3ff4c_2           conda-forge      663kB
  + glib                             2.80.2  hf974151_0           conda-forge      600kB
  + glib-tools                       2.80.2  hb6ce0ca_0           conda-forge      114kB
  + glm                             0.9.9.8  h00ab1b0_0           conda-forge      218kB
  + graphite2                        1.3.13  h59595ed_1003        conda-forge       97kB
  + gst-plugins-base                 1.24.4  h9ad1361_0           conda-forge        3MB
  + gstreamer                        1.24.4  haf2f30d_0           conda-forge        2MB
  + harfbuzz                          8.5.0  hfac3d4d_0           conda-forge        2MB
  + hdf4                             4.2.15  h2a13503_7           conda-forge      757kB
  + hdf5                             1.14.3  nompi_hdf9ad27_105   conda-forge        4MB
  + icu                                73.2  h59595ed_0           conda-forge       12MB
  + kaleido-core                      0.2.1  h3644ca4_0           conda-forge       62MB
  + keyutils                          1.6.1  h166bdaf_0           conda-forge     Cached
  + krb5                             1.21.3  h659f571_0           conda-forge     Cached
  + lame                              3.100  h166bdaf_1003        conda-forge      508kB
  + ld_impl_linux-64                   2.43  h712a8e2_1           conda-forge     Cached
  + libaec                            1.1.3  h59595ed_0           conda-forge       35kB
  + libasprintf                      0.22.5  he8f35ee_3           conda-forge       43kB
  + libasprintf-devel                0.22.5  he8f35ee_3           conda-forge       34kB
  + libblas                           3.9.0  24_linux64_openblas  conda-forge       15kB
  + libcap                             2.69  h0f662aa_0           conda-forge      101kB
  + libcblas                          3.9.0  24_linux64_openblas  conda-forge       15kB
  + libclang-cpp15                   15.0.7  default_h127d8a8_5   conda-forge       17MB
  + libclang13                       18.1.7  default_h087397f_0   conda-forge       11MB
  + libcups                           2.3.3  h4637d8d_4           conda-forge        5MB
  + libcurl                           8.8.0  hca28451_1           conda-forge      410kB
  + libedit                    3.1.20191231  he28a2e2_2           conda-forge     Cached
  + libev                              4.33  hd590300_2           conda-forge     Cached
  + libevent                         2.1.12  hf998b51_1           conda-forge      427kB
  + libexpat                          2.6.3  h5888daf_0           conda-forge     Cached
  + libffi                            3.4.2  h7f98852_5           conda-forge     Cached
  + libflac                           1.4.3  h59595ed_0           conda-forge      394kB
  + libgcc                           14.2.0  h77fa898_1           conda-forge     Cached
  + libgcc-ng                        14.2.0  h69a702a_1           conda-forge       54kB
  + libgcrypt                        1.11.0  h4ab18f5_1           conda-forge      684kB
  + libgettextpo                     0.22.5  he02047a_3           conda-forge      171kB
  + libgettextpo-devel               0.22.5  he02047a_3           conda-forge       37kB
  + libgfortran                      14.2.0  h69a702a_1           conda-forge       54kB
  + libgfortran-ng                   14.2.0  h69a702a_1           conda-forge       54kB
  + libgfortran5                     14.2.0  hd5240d6_1           conda-forge        1MB
  + libglib                          2.80.2  hf974151_0           conda-forge        4MB
  + libglu                            9.0.0  hac7e632_1003        conda-forge      331kB
  + libgomp                          14.2.0  h77fa898_1           conda-forge     Cached
  + libgpg-error                       1.50  h4f305b6_0           conda-forge      274kB
  + libiconv                           1.17  hd590300_2           conda-forge     Cached
  + libjpeg-turbo                     3.0.0  hd590300_1           conda-forge      619kB
  + liblapack                         3.9.0  24_linux64_openblas  conda-forge       15kB
  + libllvm15                        15.0.7  hb3ce162_4           conda-forge       33MB
  + libllvm18                        18.1.7  hb77312f_0           conda-forge       38MB
  + libnetcdf                         4.9.2  nompi_h135f659_114   conda-forge      849kB
  + libnghttp2                       1.58.0  h47da74e_1           conda-forge     Cached
  + libnsl                            2.0.1  hd590300_0           conda-forge     Cached
  + libogg                            1.3.5  h4ab18f5_0           conda-forge      206kB
  + libopenblas                      0.3.27  pthreads_hac2b453_1  conda-forge        6MB
  + libopus                           1.3.1  h7f98852_1           conda-forge      261kB
  + libpng                           1.6.43  h2797004_0           conda-forge      288kB
  + libpq                              16.4  h2d7952a_3           conda-forge        3MB
  + libsndfile                        1.2.2  hc60ed4a_1           conda-forge      354kB
  + libsqlite                        3.46.0  hde9e2c9_0           conda-forge      865kB
  + libssh2                          1.11.0  h0841786_0           conda-forge     Cached
  + libstdcxx                        14.2.0  hc0a3c3a_1           conda-forge     Cached
  + libstdcxx-ng                     14.2.0  h4852527_1           conda-forge       54kB
  + libsystemd0                       256.7  h2774228_0           conda-forge      410kB
  + libuuid                          2.38.1  h0b41bf4_0           conda-forge     Cached
  + libvorbis                         1.3.7  h9c3ff4c_0           conda-forge      286kB
  + libxcb                             1.15  h0b41bf4_0           conda-forge      384kB
  + libxcrypt                        4.4.36  hd590300_1           conda-forge     Cached
  + libxkbcommon                      1.7.0  h662e7e4_0           conda-forge      594kB
  + libxml2                          2.12.7  hc051c1a_1           conda-forge      705kB
  + libzip                           1.10.1  h2629f0a_3           conda-forge      107kB
  + libzlib                          1.2.13  h4ab18f5_6           conda-forge       62kB
  + lz4-c                             1.9.4  hcb278e6_0           conda-forge     Cached
  + mathjax                           2.7.7  ha770c72_3           conda-forge       22MB
  + mpg123                           1.32.6  h59595ed_0           conda-forge      492kB
  + mysql-common                      8.3.0  hf1915f5_4           conda-forge      785kB
  + mysql-libs                        8.3.0  hca2cd23_4           conda-forge        2MB
  + ncurses                             6.5  he02047a_1           conda-forge     Cached
  + nspr                               4.35  h27087fc_0           conda-forge      227kB
  + nss                               3.100  hca3bf56_0           conda-forge        2MB
  + numpy                             2.1.2  py312h58c1407_0      conda-forge        8MB
  + openssl                           3.3.2  hb9d3cd8_0           conda-forge     Cached
  + packaging                          24.1  pyhd8ed1ab_0         conda-forge     Cached
  + pcre2                             10.43  hcad00b1_0           conda-forge      951kB
  + pip                                24.2  pyh8b19718_1         conda-forge     Cached
  + pixman                           0.43.2  h59595ed_0           conda-forge      387kB
  + ply                                3.11  pyhd8ed1ab_2         conda-forge       49kB
  + pmw                               2.0.1  py312h7900ff3_1008   conda-forge      631kB
  + pthread-stubs                       0.4  hb9d3cd8_1002        conda-forge        8kB
  + pulseaudio-client                  17.0  hb77b528_0           conda-forge      758kB
  + pymol-open-source                 3.0.0  py312h3c651bb_8      conda-forge        7MB
  + pyqt                             5.15.9  py312h949fe66_5      conda-forge        5MB
  + pyqt5-sip                       12.12.2  py312h30efb56_5      conda-forge       86kB
  + python                           3.12.3  hab00c5b_0_cpython   conda-forge       32MB
  + python-kaleido                    0.2.1  pyhd8ed1ab_0         conda-forge       18kB
  + python_abi                         3.12  5_cp312              conda-forge        6kB
  + qt-main                          5.15.8  hc9dc06e_21          conda-forge       61MB
  + readline                            8.2  h8228510_1           conda-forge     Cached
  + setuptools                       75.1.0  pyhd8ed1ab_0         conda-forge     Cached
  + sip                              6.7.12  py312h30efb56_0      conda-forge      576kB
  + snappy                            1.2.1  ha2e4443_0           conda-forge       42kB
  + sqlite                           3.46.0  h6d4b2fc_0           conda-forge      860kB
  + tk                               8.6.13  noxft_h4845f30_101   conda-forge     Cached
  + toml                             0.10.2  pyhd8ed1ab_0         conda-forge       18kB
  + tomli                             2.0.2  pyhd8ed1ab_0         conda-forge       18kB
  + tzdata                            2024b  hc8b5060_0           conda-forge     Cached
  + wheel                            0.44.0  pyhd8ed1ab_0         conda-forge     Cached
  + xcb-util                          0.4.0  hd590300_1           conda-forge       20kB
  + xcb-util-image                    0.4.0  h8ee46fc_1           conda-forge       24kB
  + xcb-util-keysyms                  0.4.0  h8ee46fc_1           conda-forge       14kB
  + xcb-util-renderutil               0.3.9  hd590300_1           conda-forge       17kB
  + xcb-util-wm                       0.4.1  h8ee46fc_1           conda-forge       52kB
  + xkeyboard-config                   2.42  h4ab18f5_0           conda-forge      389kB
  + xorg-kbproto                      1.0.7  hb9d3cd8_1003        conda-forge       30kB
  + xorg-libice                       1.1.1  hb9d3cd8_1           conda-forge       58kB
  + xorg-libsm                        1.2.4  he73a12e_1           conda-forge       28kB
  + xorg-libx11                       1.8.9  h8ee46fc_0           conda-forge      828kB
  + xorg-libxau                      1.0.11  hb9d3cd8_1           conda-forge       15kB
  + xorg-libxdmcp                     1.1.5  hb9d3cd8_0           conda-forge       20kB
  + xorg-libxext                      1.3.4  h0b41bf4_2           conda-forge       50kB
  + xorg-libxrender                  0.9.11  hd590300_0           conda-forge       38kB
  + xorg-renderproto                 0.11.1  hb9d3cd8_1003        conda-forge       12kB
  + xorg-xextproto                    7.3.0  hb9d3cd8_1004        conda-forge       31kB
  + xorg-xf86vidmodeproto             2.3.1  hb9d3cd8_1004        conda-forge       26kB
  + xorg-xproto                      7.0.31  hb9d3cd8_1008        conda-forge       73kB
  + xz                                5.2.6  h166bdaf_0           conda-forge     Cached
  + zlib                             1.2.13  h4ab18f5_6           conda-forge       93kB
  + zstd                              1.5.6  ha6fb4c9_0           conda-forge     Cached

  Summary:

  Install: 149 packages

  Total download: 372MB

──────────────────────────────────────────────────────────────────────────────────────────

Dry run. Not executing the transaction.

Version 3.12.3 does exist for python on the conda-forge channel as well as newer versions. Maybe only use 3.12 for your python specification if things continue to fail. Also, avoid specifying the channel before the package name. I think there is some issue with micromamba and memory usage when there are too many of those. Alternatively, use a pre-2.0 version of micromamba.