Docker image is broken

[oathbound01]

When trying to install the benchmark through Docker, the process fails when trying to install the first algorithm

[+] Building 115.5s (8/8) FINISHED                               docker:default
 => [internal] load build definition from Dockerfile                       0.0s
 => => transferring dockerfile: 1.82kB                                     0.0s
 => WARN: FromAsCasing: 'as' and 'FROM' keywords' casing do not match (li  0.0s
 => [internal] load metadata for docker.io/condaforge/mambaforge:4.11.0-2  0.5s
 => [internal] load .dockerignore                                          0.0s
 => => transferring context: 2B                                            0.0s
 => [1/4] FROM docker.io/condaforge/mambaforge:4.11.0-2@sha256:6a79f20170  0.0s
 => [internal] load build context                                          0.2s
 => => transferring context: 84.04MB                                       0.2s
 => CACHED [2/4] RUN apt update && apt install -y     default-jdk     rsy  0.0s
 => [3/4] COPY . .                                                         0.7s
 => ERROR [4/4] RUN bash install.sh                                      113.9s
------                                                                          
 > [4/4] RUN bash install.sh:                                                   
0.501 installing base srbench environment                                       
24.42 Transaction                                                               
24.42                                                                           
24.42   Prefix: /opt/conda/envs/srbench                                         
24.42 
24.42   Updating specs:
24.42 
24.42    - python
24.42    - scikit-learn
24.42    - pandas
24.42    - numpy
24.42    - jupyter
24.42    - pytest
24.42    - matplotlib
24.42    - sympy
24.42    - ipdb
24.42    - seaborn
24.42    - pyyaml
24.42    - pip
24.42 
24.42 
24.45   Package                                 Version  Build                Channel                   Size
24.45 ────────────────────────────────────────────────────────────────────────────────────────────────────────
24.45   Install:
24.45 ────────────────────────────────────────────────────────────────────────────────────────────────────────
24.45 
24.45   + _libgcc_mutex                             0.1  conda_forge          conda-forge/linux-64       3kB
24.45   + _openmp_mutex                             4.5  2_gnu                conda-forge/linux-64      24kB
24.45   + alsa-lib                               1.2.12  h4ab18f5_0           conda-forge/linux-64     556kB
24.45   + anyio                             4.6.2.post1  pyhd8ed1ab_0         conda-forge/noarch       110kB
24.45   + argon2-cffi                            23.1.0  pyhd8ed1ab_0         conda-forge/noarch        19kB
24.45   + argon2-cffi-bindings                   21.2.0  py313h536fd9c_5      conda-forge/linux-64      35kB
24.45   + arrow                                   1.3.0  pyhd8ed1ab_0         conda-forge/noarch       100kB
24.45   + asttokens                               2.4.1  pyhd8ed1ab_0         conda-forge/noarch        29kB
24.45   + async-lru                               2.0.4  pyhd8ed1ab_0         conda-forge/noarch        15kB
24.45   + attrs                                  24.2.0  pyh71513ae_0         conda-forge/noarch        56kB
24.45   + babel                                  2.14.0  pyhd8ed1ab_0         conda-forge/noarch         8MB
24.45   + beautifulsoup4                         4.12.3  pyha770c72_0         conda-forge/noarch       118kB
24.45   + bleach                                  6.1.0  pyhd8ed1ab_0         conda-forge/noarch       131kB
24.45   + brotli                                  1.1.0  hb9d3cd8_2           conda-forge/linux-64      19kB
24.45   + brotli-bin                              1.1.0  hb9d3cd8_2           conda-forge/linux-64      19kB
24.45   + brotli-python                           1.1.0  py313h46c70d0_2      conda-forge/linux-64     350kB
24.45   + bzip2                                   1.0.8  h4bc722e_7           conda-forge/linux-64     253kB
24.45   + ca-certificates                     2024.8.30  hbcca054_0           conda-forge/linux-64     159kB
24.45   + cached-property                         1.5.2  hd8ed1ab_1           conda-forge/noarch         4kB
24.45   + cached_property                         1.5.2  pyha770c72_1         conda-forge/noarch        11kB
24.45   + cairo                                  1.18.0  hebfffa5_3           conda-forge/linux-64     984kB
24.45   + certifi                             2024.8.30  pyhd8ed1ab_0         conda-forge/noarch       164kB
24.45   + cffi                                   1.17.1  py313hfab6e84_0      conda-forge/linux-64     296kB
24.45   + charset-normalizer                      3.4.0  pyhd8ed1ab_0         conda-forge/noarch        47kB
24.45   + colorama                                0.4.6  pyhd8ed1ab_0         conda-forge/noarch        25kB
24.45   + comm                                    0.2.2  pyhd8ed1ab_0         conda-forge/noarch        12kB
24.45   + contourpy                               1.3.0  py313h33d0bda_2      conda-forge/linux-64     277kB
24.45   + cpython                                3.13.0  py313hd8ed1ab_100    conda-forge/noarch        46kB
24.45   + cycler                                 0.12.1  pyhd8ed1ab_0         conda-forge/noarch        13kB
24.45   + cyrus-sasl                             2.1.27  h54b06d7_7           conda-forge/linux-64     220kB
24.45   + dbus                                   1.13.6  h5008d03_3           conda-forge/linux-64     619kB
24.45   + debugpy                                 1.8.7  py313h46c70d0_0      conda-forge/linux-64       3MB
24.45   + decorator                               5.1.1  pyhd8ed1ab_0         conda-forge/noarch        12kB
24.45   + defusedxml                              0.7.1  pyhd8ed1ab_0         conda-forge/noarch        24kB
24.45   + double-conversion                       3.3.0  h59595ed_0           conda-forge/linux-64      79kB
24.45   + entrypoints                               0.4  pyhd8ed1ab_0         conda-forge/noarch         9kB
24.45   + exceptiongroup                          1.2.2  pyhd8ed1ab_0         conda-forge/noarch        20kB
24.45   + executing                               2.1.0  pyhd8ed1ab_0         conda-forge/noarch        28kB
24.45   + expat                                   2.6.3  h5888daf_0           conda-forge/linux-64     138kB
24.45   + font-ttf-dejavu-sans-mono                2.37  hab24e00_0           conda-forge/noarch       397kB
24.45   + font-ttf-inconsolata                    3.000  h77eed37_0           conda-forge/noarch        97kB
24.45   + font-ttf-source-code-pro                2.038  h77eed37_0           conda-forge/noarch       701kB
24.45   + font-ttf-ubuntu                          0.83  h77eed37_3           conda-forge/noarch         2MB
24.45   + fontconfig                             2.14.2  h14ed4e7_0           conda-forge/linux-64     272kB
24.45   + fonts-conda-ecosystem                       1  0                    conda-forge/noarch         4kB
24.45   + fonts-conda-forge                           1  0                    conda-forge/noarch         4kB
24.45   + fonttools                              4.54.1  py313h536fd9c_0      conda-forge/linux-64       3MB
24.45   + fqdn                                    1.5.1  pyhd8ed1ab_0         conda-forge/noarch        14kB
24.45   + freetype                               2.12.1  h267a509_2           conda-forge/linux-64     635kB
24.45   + gmp                                     6.3.0  hac33072_2           conda-forge/linux-64     460kB
24.45   + gmpy2                                   2.1.5  py313h11186cd_2      conda-forge/linux-64     212kB
24.45   + graphite2                              1.3.13  h59595ed_1003        conda-forge/linux-64      97kB
24.45   + h11                                    0.14.0  pyhd8ed1ab_0         conda-forge/noarch        48kB
24.45   + h2                                      4.1.0  pyhd8ed1ab_0         conda-forge/noarch        47kB
24.45   + harfbuzz                                9.0.0  hda332d3_1           conda-forge/linux-64       2MB
24.45   + hpack                                   4.0.0  pyh9f0ad1d_0         conda-forge/noarch        25kB
24.45   + httpcore                                1.0.6  pyhd8ed1ab_0         conda-forge/noarch        46kB
24.45   + httpx                                  0.27.2  pyhd8ed1ab_0         conda-forge/noarch        65kB
24.45   + hyperframe                              6.0.1  pyhd8ed1ab_0         conda-forge/noarch        15kB
24.45   + icu                                      75.1  he02047a_0           conda-forge/linux-64      12MB
24.45   + idna                                     3.10  pyhd8ed1ab_0         conda-forge/noarch        50kB
24.45   + importlib-metadata                      8.5.0  pyha770c72_0         conda-forge/noarch        29kB
24.45   + importlib_metadata                      8.5.0  hd8ed1ab_0           conda-forge/noarch         9kB
24.45   + importlib_resources                     6.4.5  pyhd8ed1ab_0         conda-forge/noarch        33kB
24.45   + iniconfig                               2.0.0  pyhd8ed1ab_0         conda-forge/noarch        11kB
24.45   + ipdb                                  0.13.13  pyhd8ed1ab_0         conda-forge/noarch        19kB
24.45   + ipykernel                              6.29.5  pyh3099207_0         conda-forge/noarch       119kB
24.45   + ipython                                8.28.0  pyh707e725_0         conda-forge/noarch       600kB
24.45   + ipywidgets                              8.1.5  pyhd8ed1ab_0         conda-forge/noarch       113kB
24.45   + isoduration                           20.11.0  pyhd8ed1ab_0         conda-forge/noarch        17kB
24.45   + jedi                                   0.19.1  pyhd8ed1ab_0         conda-forge/noarch       841kB
24.45   + jinja2                                  3.1.4  pyhd8ed1ab_0         conda-forge/noarch       112kB
24.45   + joblib                                  1.4.2  pyhd8ed1ab_0         conda-forge/noarch       220kB
24.45   + json5                                  0.9.25  pyhd8ed1ab_0         conda-forge/noarch        28kB
24.45   + jsonpointer                             3.0.0  py313h78bf25f_1      conda-forge/linux-64      18kB
24.45   + jsonschema                             4.23.0  pyhd8ed1ab_0         conda-forge/noarch        74kB
24.45   + jsonschema-specifications           2024.10.1  pyhd8ed1ab_0         conda-forge/noarch        16kB
24.45   + jsonschema-with-format-nongpl          4.23.0  hd8ed1ab_0           conda-forge/noarch         7kB
24.45   + jupyter                                 1.1.1  pyhd8ed1ab_0         conda-forge/noarch         9kB
24.45   + jupyter-lsp                             2.2.5  pyhd8ed1ab_0         conda-forge/noarch        56kB
24.45   + jupyter_client                          8.6.3  pyhd8ed1ab_0         conda-forge/noarch       106kB
24.45   + jupyter_console                         6.6.3  pyhd8ed1ab_0         conda-forge/noarch        26kB
24.45   + jupyter_core                            5.7.2  pyh31011fe_1         conda-forge/noarch        58kB
24.45   + jupyter_events                         0.10.0  pyhd8ed1ab_0         conda-forge/noarch        21kB
24.45   + jupyter_server                         2.14.2  pyhd8ed1ab_0         conda-forge/noarch       324kB
24.45   + jupyter_server_terminals                0.5.3  pyhd8ed1ab_0         conda-forge/noarch        20kB
24.45   + jupyterlab                              4.2.5  pyhd8ed1ab_0         conda-forge/noarch         7MB
24.45   + jupyterlab_pygments                     0.3.0  pyhd8ed1ab_1         conda-forge/noarch        19kB
24.45   + jupyterlab_server                      2.27.3  pyhd8ed1ab_0         conda-forge/noarch        49kB
24.45   + jupyterlab_widgets                     3.0.13  pyhd8ed1ab_0         conda-forge/noarch       186kB
24.45   + keyutils                                1.6.1  h166bdaf_0           conda-forge/linux-64     118kB
24.45   + kiwisolver                              1.4.7  py313h33d0bda_0      conda-forge/linux-64      71kB
24.45   + krb5                                   1.21.3  h659f571_0           conda-forge/linux-64       1MB
24.45   + lcms2                                    2.16  hb7c19ff_0           conda-forge/linux-64     245kB
24.45   + ld_impl_linux-64                         2.43  h712a8e2_1           conda-forge/linux-64     670kB
24.45   + lerc                                    4.0.0  h27087fc_0           conda-forge/linux-64     282kB
24.45   + libblas                                 3.9.0  24_linux64_openblas  conda-forge/linux-64      15kB
24.45   + libbrotlicommon                         1.1.0  hb9d3cd8_2           conda-forge/linux-64      69kB
24.45   + libbrotlidec                            1.1.0  hb9d3cd8_2           conda-forge/linux-64      33kB
24.45   + libbrotlienc                            1.1.0  hb9d3cd8_2           conda-forge/linux-64     282kB
24.45   + libcblas                                3.9.0  24_linux64_openblas  conda-forge/linux-64      15kB
24.45   + libclang-cpp19.1                       19.1.2  default_hb5137d0_1   conda-forge/linux-64      21MB
24.45   + libclang13                             19.1.2  default_h9c6a7e4_1   conda-forge/linux-64      12MB
24.45   + libcups                                 2.3.3  h4637d8d_4           conda-forge/linux-64       5MB
24.45   + libdeflate                               1.22  hb9d3cd8_0           conda-forge/linux-64      72kB
24.45   + libdrm                                2.4.123  hb9d3cd8_0           conda-forge/linux-64     303kB
24.45   + libedit                          3.1.20191231  he28a2e2_2           conda-forge/linux-64     124kB
24.45   + libegl                                  1.7.0  ha4b6fd6_1           conda-forge/linux-64      45kB
24.45   + libexpat                                2.6.3  h5888daf_0           conda-forge/linux-64      74kB
24.45   + libffi                                  3.4.2  h7f98852_5           conda-forge/linux-64      58kB
24.45   + libgcc                                 14.2.0  h77fa898_1           conda-forge/linux-64     849kB
24.45   + libgcc-ng                              14.2.0  h69a702a_1           conda-forge/linux-64      54kB
24.45   + libgfortran                            14.2.0  h69a702a_1           conda-forge/linux-64      54kB
24.45   + libgfortran-ng                         14.2.0  h69a702a_1           conda-forge/linux-64      54kB
24.45   + libgfortran5                           14.2.0  hd5240d6_1           conda-forge/linux-64       1MB
24.45   + libgl                                   1.7.0  ha4b6fd6_1           conda-forge/linux-64     134kB
24.45   + libglib                                2.82.2  h2ff4ddf_0           conda-forge/linux-64       4MB
24.45   + libglvnd                                1.7.0  ha4b6fd6_1           conda-forge/linux-64     132kB
24.45   + libglx                                  1.7.0  ha4b6fd6_1           conda-forge/linux-64      78kB
24.45   + libgomp                                14.2.0  h77fa898_1           conda-forge/linux-64     461kB
24.45   + libiconv                                 1.17  hd590300_2           conda-forge/linux-64     706kB
24.45   + libjpeg-turbo                           3.0.0  hd590300_1           conda-forge/linux-64     619kB
24.45   + liblapack                               3.9.0  24_linux64_openblas  conda-forge/linux-64      15kB
24.45   + libllvm19                              19.1.2  ha7bfdaf_0           conda-forge/linux-64      40MB
24.45   + libmpdec                                4.0.0  h4bc722e_0           conda-forge/linux-64      90kB
24.45   + libntlm                                   1.4  h7f98852_1002        conda-forge/linux-64      33kB
24.45   + libopenblas                            0.3.27  pthreads_hac2b453_1  conda-forge/linux-64       6MB
24.45   + libopengl                               1.7.0  ha4b6fd6_1           conda-forge/linux-64      50kB
24.45   + libpciaccess                             0.18  hd590300_0           conda-forge/linux-64      28kB
24.45   + libpng                                 1.6.44  hadc24fc_0           conda-forge/linux-64     291kB
24.45   + libpq                                    17.0  h04577a9_4           conda-forge/linux-64       3MB
24.45   + libsodium                              1.0.20  h4ab18f5_0           conda-forge/linux-64     206kB
24.45   + libsqlite                              3.46.1  hadc24fc_0           conda-forge/linux-64     865kB
24.45   + libstdcxx                              14.2.0  hc0a3c3a_1           conda-forge/linux-64       4MB
24.45   + libstdcxx-ng                           14.2.0  h4852527_1           conda-forge/linux-64      54kB
24.45   + libtiff                                 4.7.0  he137b08_1           conda-forge/linux-64     428kB
24.45   + libuuid                                2.38.1  h0b41bf4_0           conda-forge/linux-64      34kB
24.45   + libwebp-base                            1.4.0  hd590300_0           conda-forge/linux-64     439kB
24.45   + libxcb                                 1.17.0  h8a09558_0           conda-forge/linux-64     396kB
24.45   + libxkbcommon                            1.7.0  h2c5496b_1           conda-forge/linux-64     593kB
24.45   + libxml2                                2.12.7  he7c6b58_4           conda-forge/linux-64     707kB
24.45   + libxslt                                1.1.39  h76b75d6_0           conda-forge/linux-64     254kB
24.45   + libzlib                                 1.3.1  hb9d3cd8_2           conda-forge/linux-64      61kB
24.45   + markupsafe                              3.0.2  py313h8060acc_0      conda-forge/linux-64      25kB
24.45   + matplotlib                              3.9.2  py313h78bf25f_1      conda-forge/linux-64       9kB
24.45   + matplotlib-base                         3.9.2  py313h129903b_1      conda-forge/linux-64       8MB
24.45   + matplotlib-inline                       0.1.7  pyhd8ed1ab_0         conda-forge/noarch        15kB
24.45   + mistune                                 3.0.2  pyhd8ed1ab_0         conda-forge/noarch        66kB
24.45   + mpc                                     1.3.1  h24ddda3_1           conda-forge/linux-64     117kB
24.45   + mpfr                                    4.2.1  h90cbb55_3           conda-forge/linux-64     635kB
24.45   + mpmath                                  1.3.0  pyhd8ed1ab_0         conda-forge/noarch       438kB
24.45   + munkres                                 1.1.4  pyh9f0ad1d_0         conda-forge/noarch        12kB
24.45   + mysql-common                            9.0.1  h266115a_1           conda-forge/linux-64     640kB
24.45   + mysql-libs                              9.0.1  he0572af_1           conda-forge/linux-64       1MB
24.45   + nbclient                               0.10.0  pyhd8ed1ab_0         conda-forge/noarch        28kB
24.45   + nbconvert-core                         7.16.4  pyhd8ed1ab_1         conda-forge/noarch       190kB
24.45   + nbformat                               5.10.4  pyhd8ed1ab_0         conda-forge/noarch       101kB
24.45   + ncurses                                   6.5  he02047a_1           conda-forge/linux-64     889kB
24.45   + nest-asyncio                            1.6.0  pyhd8ed1ab_0         conda-forge/noarch        12kB
24.45   + notebook                                7.2.2  pyhd8ed1ab_0         conda-forge/noarch         4MB
24.45   + notebook-shim                           0.2.4  pyhd8ed1ab_0         conda-forge/noarch        17kB
24.45   + numpy                                   2.1.2  py313h4bf6692_0      conda-forge/linux-64       8MB
24.45   + openjpeg                                2.5.2  h488ebb8_0           conda-forge/linux-64     342kB
24.45   + openldap                                2.6.8  hedd0468_0           conda-forge/linux-64     780kB
24.45   + openssl                                 3.3.2  hb9d3cd8_0           conda-forge/linux-64       3MB
24.45   + overrides                               7.7.0  pyhd8ed1ab_0         conda-forge/noarch        30kB
24.45   + packaging                                24.1  pyhd8ed1ab_0         conda-forge/noarch        50kB
24.45   + pandas                                  2.2.3  py313ha87cce1_1      conda-forge/linux-64      15MB
24.45   + pandocfilters                           1.5.0  pyhd8ed1ab_0         conda-forge/noarch        12kB
24.45   + parso                                   0.8.4  pyhd8ed1ab_0         conda-forge/noarch        75kB
24.45   + patsy                                   0.5.6  pyhd8ed1ab_0         conda-forge/noarch       187kB
24.45   + pcre2                                   10.44  hba22ea6_2           conda-forge/linux-64     952kB
24.45   + pexpect                                 4.9.0  pyhd8ed1ab_0         conda-forge/noarch        54kB
24.45   + pickleshare                             0.7.5  py_1003              conda-forge/noarch         9kB
24.45   + pillow                                 11.0.0  py313h2d7ed13_0      conda-forge/linux-64      42MB
24.45   + pip                                      24.2  pyh145f28c_1         conda-forge/noarch         1MB
24.45   + pixman                                 0.43.2  h59595ed_0           conda-forge/linux-64     387kB
24.45   + pkgutil-resolve-name                   1.3.10  pyhd8ed1ab_1         conda-forge/noarch        11kB
24.45   + platformdirs                            4.3.6  pyhd8ed1ab_0         conda-forge/noarch        21kB
24.45   + pluggy                                  1.5.0  pyhd8ed1ab_0         conda-forge/noarch        24kB
24.45   + prometheus_client                      0.21.0  pyhd8ed1ab_0         conda-forge/noarch        49kB
24.45   + prompt-toolkit                         3.0.48  pyha770c72_0         conda-forge/noarch       270kB
24.45   + prompt_toolkit                         3.0.48  hd8ed1ab_0           conda-forge/noarch         7kB
24.45   + psutil                                  6.0.0  py313h536fd9c_2      conda-forge/linux-64     498kB
24.45   + pthread-stubs                             0.4  hb9d3cd8_1002        conda-forge/linux-64       8kB
24.45   + ptyprocess                              0.7.0  pyhd3deb0d_0         conda-forge/noarch        17kB
24.45   + pure_eval                               0.2.3  pyhd8ed1ab_0         conda-forge/noarch        17kB
24.45   + pycparser                                2.22  pyhd8ed1ab_0         conda-forge/noarch       105kB
24.45   + pygments                               2.18.0  pyhd8ed1ab_0         conda-forge/noarch       879kB
24.45   + pyparsing                               3.2.0  pyhd8ed1ab_1         conda-forge/noarch        92kB
24.45   + pyside6                                 6.8.0  py313h5f61773_1      conda-forge/linux-64      11MB
24.45   + pysocks                                 1.7.1  pyha2e5f31_6         conda-forge/noarch        19kB
24.45   + pytest                                  8.3.3  pyhd8ed1ab_0         conda-forge/noarch       258kB
24.45   + python                                 3.13.0  h9ebbce0_100_cp313   conda-forge/linux-64      33MB
24.45   + python-dateutil                         2.9.0  pyhd8ed1ab_0         conda-forge/noarch       223kB
24.45   + python-fastjsonschema                  2.20.0  pyhd8ed1ab_0         conda-forge/noarch       226kB
24.45   + python-json-logger                      2.0.7  pyhd8ed1ab_0         conda-forge/noarch        13kB
24.45   + python-tzdata                          2024.2  pyhd8ed1ab_0         conda-forge/noarch       143kB
24.45   + python_abi                               3.13  5_cp313              conda-forge/linux-64       6kB
24.45   + pytz                                   2024.1  pyhd8ed1ab_0         conda-forge/noarch       189kB
24.45   + pyyaml                                  6.0.2  py313h536fd9c_1      conda-forge/linux-64     206kB
24.45   + pyzmq                                  26.2.0  py313h8e95178_3      conda-forge/linux-64     385kB
24.45   + qhull                                  2020.2  h434a139_5           conda-forge/linux-64     553kB
24.45   + qt6-main                                6.8.0  h6e8976b_0           conda-forge/linux-64      51MB
24.45   + readline                                  8.2  h8228510_1           conda-forge/linux-64     281kB
24.45   + referencing                            0.35.1  pyhd8ed1ab_0         conda-forge/noarch        42kB
24.45   + requests                               2.32.3  pyhd8ed1ab_0         conda-forge/noarch        59kB
24.45   + rfc3339-validator                       0.1.4  pyhd8ed1ab_0         conda-forge/noarch         8kB
24.45   + rfc3986-validator                       0.1.1  pyh9f0ad1d_0         conda-forge/noarch         8kB
24.45   + rpds-py                                0.20.0  py313h920b4c0_1      conda-forge/linux-64     334kB
24.45   + scikit-learn                            1.5.2  py313h8ef605b_1      conda-forge/linux-64      10MB
24.45   + scipy                                  1.14.1  py313h902d034_0      conda-forge/linux-64      18MB
24.45   + seaborn                                0.13.2  hd8ed1ab_2           conda-forge/noarch         7kB
24.45   + seaborn-base                           0.13.2  pyhd8ed1ab_2         conda-forge/noarch       235kB
24.45   + send2trash                              1.8.3  pyh0d859eb_0         conda-forge/noarch        23kB
24.45   + setuptools                             75.1.0  pyhd8ed1ab_0         conda-forge/noarch       777kB
24.45   + six                                    1.16.0  pyh6c4a22f_0         conda-forge/noarch        14kB
24.45   + sniffio                                 1.3.1  pyhd8ed1ab_0         conda-forge/noarch        15kB
24.45   + soupsieve                                 2.5  pyhd8ed1ab_1         conda-forge/noarch        37kB
24.45   + stack_data                              0.6.2  pyhd8ed1ab_0         conda-forge/noarch        26kB
24.45   + statsmodels                            0.14.4  py313ha014f3b_0      conda-forge/linux-64      12MB
24.45   + sympy                                  1.13.3  pyh2585a3b_104       conda-forge/noarch         5MB
24.45   + terminado                              0.18.1  pyh0d859eb_0         conda-forge/noarch        22kB
24.45   + threadpoolctl                           3.5.0  pyhc1e730c_0         conda-forge/noarch        24kB
24.45   + tinycss2                                1.3.0  pyhd8ed1ab_0         conda-forge/noarch        25kB
24.45   + tk                                     8.6.13  noxft_h4845f30_101   conda-forge/linux-64       3MB
24.45   + toml                                   0.10.2  pyhd8ed1ab_0         conda-forge/noarch        18kB
24.45   + tomli                                   2.0.2  pyhd8ed1ab_0         conda-forge/noarch        18kB
24.45   + tornado                                 6.4.1  py313h536fd9c_1      conda-forge/linux-64     863kB
24.45   + traitlets                              5.14.3  pyhd8ed1ab_0         conda-forge/noarch       110kB
24.45   + types-python-dateutil          2.9.0.20241003  pyhff2d567_0         conda-forge/noarch        22kB
24.45   + typing-extensions                      4.12.2  hd8ed1ab_0           conda-forge/noarch        10kB
24.45   + typing_extensions                      4.12.2  pyha770c72_0         conda-forge/noarch        40kB
24.45   + typing_utils                            0.1.0  pyhd8ed1ab_0         conda-forge/noarch        14kB
24.45   + tzdata                                  2024b  hc8b5060_0           conda-forge/noarch       122kB
24.45   + uri-template                            1.3.0  pyhd8ed1ab_0         conda-forge/noarch        24kB
24.45   + urllib3                                 2.2.3  pyhd8ed1ab_0         conda-forge/noarch        98kB
24.45   + wayland                                1.23.1  h3e06ad9_0           conda-forge/linux-64     322kB
24.45   + wcwidth                                0.2.13  pyhd8ed1ab_0         conda-forge/noarch        33kB
24.45   + webcolors                              24.8.0  pyhd8ed1ab_0         conda-forge/noarch        18kB
24.45   + webencodings                            0.5.1  pyhd8ed1ab_2         conda-forge/noarch        16kB
24.45   + websocket-client                        1.8.0  pyhd8ed1ab_0         conda-forge/noarch        47kB
24.45   + widgetsnbextension                     4.0.13  pyhd8ed1ab_0         conda-forge/noarch       899kB
24.45   + xcb-util                                0.4.1  hb711507_2           conda-forge/linux-64      20kB
24.45   + xcb-util-cursor                         0.1.5  hb9d3cd8_0           conda-forge/linux-64      20kB
24.45   + xcb-util-image                          0.4.0  hb711507_2           conda-forge/linux-64      25kB
24.45   + xcb-util-keysyms                        0.4.1  hb711507_0           conda-forge/linux-64      14kB
24.45   + xcb-util-renderutil                    0.3.10  hb711507_0           conda-forge/linux-64      17kB
24.45   + xcb-util-wm                             0.4.2  hb711507_0           conda-forge/linux-64      52kB
24.45   + xkeyboard-config                         2.43  hb9d3cd8_0           conda-forge/linux-64     389kB
24.45   + xorg-libice                             1.1.1  hb9d3cd8_1           conda-forge/linux-64      58kB
24.45   + xorg-libsm                              1.2.4  he73a12e_1           conda-forge/linux-64      28kB
24.45   + xorg-libx11                            1.8.10  h4f16b4b_0           conda-forge/linux-64     838kB
24.45   + xorg-libxau                            1.0.11  hb9d3cd8_1           conda-forge/linux-64      15kB
24.45   + xorg-libxcomposite                      0.4.6  hb9d3cd8_2           conda-forge/linux-64      14kB
24.45   + xorg-libxcursor                         1.2.2  hb9d3cd8_0           conda-forge/linux-64      32kB
24.45   + xorg-libxdamage                         1.1.6  hb9d3cd8_0           conda-forge/linux-64      13kB
24.45   + xorg-libxdmcp                           1.1.5  hb9d3cd8_0           conda-forge/linux-64      20kB
24.45   + xorg-libxext                            1.3.6  hb9d3cd8_0           conda-forge/linux-64      50kB
24.45   + xorg-libxfixes                          6.0.1  hb9d3cd8_0           conda-forge/linux-64      20kB
24.45   + xorg-libxi                              1.8.2  hb9d3cd8_0           conda-forge/linux-64      47kB
24.45   + xorg-libxrandr                          1.5.4  hb9d3cd8_0           conda-forge/linux-64      30kB
24.45   + xorg-libxrender                        0.9.11  hb9d3cd8_1           conda-forge/linux-64      38kB
24.45   + xorg-libxtst                            1.2.5  hb9d3cd8_3           conda-forge/linux-64      33kB
24.45   + xorg-libxxf86vm                         1.1.5  hb9d3cd8_4           conda-forge/linux-64      18kB
24.45   + xorg-xorgproto                         2024.1  hb9d3cd8_1           conda-forge/linux-64     565kB
24.45   + xz                                      5.2.6  h166bdaf_0           conda-forge/linux-64     418kB
24.45   + yaml                                    0.2.5  h7f98852_2           conda-forge/linux-64      89kB
24.45   + zeromq                                  4.3.5  h3b0a872_6           conda-forge/linux-64     336kB
24.45   + zipp                                   3.20.2  pyhd8ed1ab_0         conda-forge/noarch        21kB
24.45   + zlib                                    1.3.1  hb9d3cd8_2           conda-forge/linux-64      92kB
24.45   + zstandard                              0.23.0  py313h80202fe_1      conda-forge/linux-64     424kB
24.45   + zstd                                    1.5.6  ha6fb4c9_0           conda-forge/linux-64     555kB
24.45 
24.45   Summary:
24.45 
24.45   Install: 273 packages
24.45 
24.45   Total download: 399MB
24.45 
24.45 ────────────────────────────────────────────────────────────────────────────────────────────────────────
24.45 
65.09 
65.09 
65.09 Looking for: ['python', 'scikit-learn', 'pandas', 'numpy', 'jupyter', 'pytest', 'matplotlib', 'sympy', 'ipdb', 'seaborn', 'pyyaml', 'pip']
65.09 
65.09 
65.09 Preparing transaction: ...working... done
66.23 Verifying transaction: ...working... done
70.42 Executing transaction: ...working... done
83.46 Installing pip dependencies: ...working... Ran pip subprocess with arguments:
84.82 ['/opt/conda/envs/srbench/bin/python', '-m', 'pip', 'install', '-U', '-r', '/condaenv.2r8myj5q.requirements.txt']
84.82 Pip subprocess output:
84.82 Collecting pmlb==1.0.1.post3 (from -r /condaenv.2r8myj5q.requirements.txt (line 1))
84.82   Downloading pmlb-1.0.1.post3-py3-none-any.whl.metadata (1.7 kB)
84.82 Collecting pytest-order (from -r /condaenv.2r8myj5q.requirements.txt (line 2))
84.82   Downloading pytest_order-1.3.0-py3-none-any.whl.metadata (7.7 kB)
84.82 Requirement already satisfied: pandas>=1.0.5 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2.2.3)
84.82 Requirement already satisfied: requests>=2.24.0 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2.32.3)
84.82 Requirement already satisfied: pyyaml>=5.3.1 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (6.0.2)
84.82 Requirement already satisfied: pytest>=6.2.4 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pytest-order->-r /condaenv.2r8myj5q.requirements.txt (line 2)) (8.3.3)
84.82 Requirement already satisfied: numpy>=1.26.0 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pandas>=1.0.5->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2.1.2)
84.82 Requirement already satisfied: python-dateutil>=2.8.2 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pandas>=1.0.5->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2.9.0)
84.82 Requirement already satisfied: pytz>=2020.1 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pandas>=1.0.5->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2024.1)
84.82 Requirement already satisfied: tzdata>=2022.7 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pandas>=1.0.5->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2024.2)
84.82 Requirement already satisfied: iniconfig in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pytest>=6.2.4->pytest-order->-r /condaenv.2r8myj5q.requirements.txt (line 2)) (2.0.0)
84.82 Requirement already satisfied: packaging in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pytest>=6.2.4->pytest-order->-r /condaenv.2r8myj5q.requirements.txt (line 2)) (24.1)
84.82 Requirement already satisfied: pluggy<2,>=1.5 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from pytest>=6.2.4->pytest-order->-r /condaenv.2r8myj5q.requirements.txt (line 2)) (1.5.0)
84.82 Requirement already satisfied: charset-normalizer<4,>=2 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from requests>=2.24.0->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (3.4.0)
84.82 Requirement already satisfied: idna<4,>=2.5 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from requests>=2.24.0->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (3.10)
84.82 Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from requests>=2.24.0->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2.2.3)
84.82 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from requests>=2.24.0->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (2024.8.30)
84.82 Requirement already satisfied: six>=1.5 in /opt/conda/envs/srbench/lib/python3.13/site-packages (from python-dateutil>=2.8.2->pandas>=1.0.5->pmlb==1.0.1.post3->-r /condaenv.2r8myj5q.requirements.txt (line 1)) (1.16.0)
84.82 Downloading pmlb-1.0.1.post3-py3-none-any.whl (19 kB)
84.82 Downloading pytest_order-1.3.0-py3-none-any.whl (14 kB)
84.82 Installing collected packages: pytest-order, pmlb
84.82 Successfully installed pmlb-1.0.1.post3 pytest-order-1.3.0
84.82 
84.82 done
84.82 #
84.82 # To activate this environment, use
84.82 #
84.82 #     $ conda activate srbench
84.82 #
84.82 # To deactivate an active environment, use
84.82 #
84.82 #     $ conda deactivate
84.82 
85.40 no change     /opt/conda/condabin/conda
85.40 no change     /opt/conda/bin/conda
85.40 no change     /opt/conda/bin/conda-env
85.40 no change     /opt/conda/bin/activate
85.40 no change     /opt/conda/bin/deactivate
85.40 no change     /opt/conda/etc/profile.d/conda.sh
85.40 no change     /opt/conda/etc/fish/conf.d/conda.fish
85.40 no change     /opt/conda/shell/condabin/Conda.psm1
85.40 no change     /opt/conda/shell/condabin/conda-hook.ps1
85.40 no change     /opt/conda/lib/python3.9/site-packages/xontrib/conda.xsh
85.40 no change     /opt/conda/etc/profile.d/conda.csh
85.40 modified      /root/.bashrc
85.40 
85.40 ==> For changes to take effect, close and re-open your current shell. <==
85.40 
85.42 ////////////////////////////////////////
85.42 installing these SR methods:
85.42 afp bingo e2et eplex eql feat ffx geneticengine gpgomea gplearn gpzgd itea operon ps-tree pysr qlattice rils-rols tir
85.42 ////////////////////////////////////////
85.42 vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
85.42 .................... Installing afp ...
85.43 build_clone_base_env: yes
85.43 ........................................
85.43 Cloning base environment
85.43 ........................................
87.84 Source:      /opt/conda/envs/srbench
87.84 Destination: /opt/conda/envs/srbench-afp
87.84 Packages: 273
87.84 Files: 39
87.84 Preparing transaction: ...working... done
88.96 Verifying transaction: ...working... done
93.20 Executing transaction: ...working... done
106.1 #
106.1 # To activate this environment, use
106.1 #
106.1 #     $ conda activate srbench-afp
106.1 #
106.1 # To deactivate an active environment, use
106.1 #
106.1 #     $ conda deactivate
106.1 
106.3 Update alg env from environment.yml
106.3 ........................................
106.5 conda-forge/linux-64                                         Using cache
106.5 conda-forge/noarch                                           Using cache
112.8 
112.8 
112.8 Looking for: ['python=3', 'eigen=3.3.7', 'boost=1.74.0', 'scikit-learn', 'pandas=1.1', 'pip']
112.8 
112.8 
112.8 Encountered problems while solving:
112.8   - nothing provides _python_rc needed by python-3.13.0rc1-h3b4618f_0_cp313t
112.8 
------
Dockerfile:45
--------------------
  43 |     SHELL ["/bin/bash", "-c"]
  44 |     COPY . .
  45 | >>> RUN bash install.sh 
  46 |     
--------------------
ERROR: failed to solve: process "/bin/bash -c bash install.sh" did not complete successfully: exit code: 1

For some reason it looks like it's trying to pull from a release candidate version of Python, breaking the entire thing in the process.

I've tried running

conda clean --all --yes
conda config --set channel_priority strict

to no avail. I've also tried manually updating some dependencies, both in the base_environment.yml and the specific environment.yml, but every time I fix something, I end up breaking something else.

It would seem that the fix is simpler than I imagine, yet any combination I try doesn't work.

[oathbound01]

I should point out that the issue is very likely not with the Dockerfile or the Docker installation per se, but rather with the install.sh process and the various environment.yml dependencies and/or the channel used for the conda packages

[gAldeia]

Hi @oathbound01 !

I am not really sure what may be causing your installation issue.

Are you using the correct branch (docker-compose)?

There is a CI workflow that tries to build and test all containers here https://github.com/cavalab/srbench/blob/docker-compose/.github/workflows/ci-docker.yml. You can also check the logs when trying to build AFP, which seems to be the first algorithm that fails in your local machine https://github.com/cavalab/srbench/actions/runs/11374625817/job/31643734527

[gAldeia]

I also noticed that Python 3.13 was released earlier this month, with led to building errors with some algorithms. I had to fix python to 3.12 for one algorithm in order to install it, but the pipeline worked for the others.

[oathbound01]

Are you using the correct branch (docker-compose)?

No, I was not using that branch, since it's not mentioned anywhere, and the user-guide.md simply directs me towards the standard Dockerfile that is present in the main branch.

Having said that, not even that branch seems to work: the standard Dockerfile not only uses broken/dead proxies but also fails to create the mamba environment:

 > [ 4/23] RUN mamba env create -f base_environment.yml:
1.034 
1.034 CondaValueError: prefix already exists: /opt/conda
1.034 
------

Commenting that line, the Dockerfile STILL fails since it's looking for install.sh which doesn't exist.

 > [ 4/22] RUN bash install.sh  afp:
0.264 bash: install.sh: No such file or directory

Even switching to the (intended?) install_algorithm.sh file doesn't work, since it's trying to use micromamba and it doesn't seem to be installed in the Docker image:

0.233 SUBNAME: afp ; SUBFOLDER: ./afp                                                                                                                                                     
0.233 vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv                                                                                                     
0.233 .................... Installing afp ...                                                                                                                                             
0.233 ........................................                                                                                                                                            
0.233 Creating environment
0.233 ........................................
0.234 install_algorithm.sh: line 33: micromamba: command not found

Also using the docker-compose file created with the appropriate script seems to fail:

 => [eql 5/6] RUN bash install_algorithm.sh eql     && micromamba clean  206.1s
 => [itea 5/6] RUN bash install_algorithm.sh itea     && micromamba cle  206.0s
 => CANCELED [bingo 5/6] RUN bash install_algorithm.sh bingo     && mic  205.1s
 => [ffx 5/6] RUN bash install_algorithm.sh ffx     && micromamba clean  205.9s
 => [ps-tree 5/6] RUN bash install_algorithm.sh ps-tree     && micromam  205.8s
 => [eplex 5/6] RUN bash install_algorithm.sh eplex     && micromamba c  205.8s
 => [afp 5/6] RUN bash install_algorithm.sh afp     && micromamba clean  205.7s
 => CANCELED [rils-rols 5/6] RUN bash install_algorithm.sh rils-rols     204.2s
 => [gpgomea 5/6] RUN bash install_algorithm.sh gpgomea     && micromam  205.6s
 => ERROR [feat 5/6] RUN bash install_algorithm.sh feat     && micromam  202.1s
 => [qlattice 5/6] RUN bash install_algorithm.sh qlattice     && microm  205.4s
 => [operon 5/6] RUN bash install_algorithm.sh operon     && micromamba  205.3s
 => [gplearn 5/6] RUN bash install_algorithm.sh gplearn     && micromam  205.3s
 => [geneticengine 5/6] RUN bash install_algorithm.sh geneticengine      205.2s
 => [e2et 5/6] RUN bash install_algorithm.sh e2et     && micromamba cle  205.2s
 => [pysr 5/6] RUN bash install_algorithm.sh pysr     && micromamba cle  205.1s
 => [gpzgd 5/6] RUN bash install_algorithm.sh gpzgd     && micromamba c  205.1s
 => [tir 3/7] WORKDIR /install                                             0.5s
 => [tir 4/7] COPY --chown=mambauser:mambauser base_environment.yml insta  0.3s
 => [tir 5/7] COPY --chown=mambauser:mambauser ./algorithms/tir ./tir      0.2s
 => [tir 6/7] RUN bash install_algorithm.sh tir     && micromamba clean  108.9s
------
 > [feat 5/6] RUN bash install_algorithm.sh feat     && micromamba clean --all --yes:
2.196 SUBNAME: feat ; SUBFOLDER: ./feat
2.196 vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
2.196 .................... Installing feat ...
2.196 ........................................
2.196 Creating environment
2.196 ........................................
2.196 using ./feat/environment.yml ... 
200.9 error    libmamba Could not solve for environment specs
200.9     The following packages are incompatible
200.9     ├─ cmake 3.28.2**  does not exist (perhaps a typo or a missing channel);
200.9     ├─ ninja 1.11.1**  does not exist (perhaps a typo or a missing channel);
200.9     ├─ pybind11 2.11.1**  does not exist (perhaps a typo or a missing channel);
200.9     ├─ pybind11_json 0.2.13**  does not exist (perhaps a typo or a missing channel);
200.9     └─ shogun-cpp 6.1.4**  does not exist (perhaps a typo or a missing channel).
200.9 critical libmamba Could not solve for environment specs
------
failed to solve: process "/usr/local/bin/_dockerfile_shell.sh bash install_algorithm.sh $ALGORITHM     && micromamba clean --all --yes" did not complete successfully: exit code: 1

Also, I don't see how Actions has much of anything to do with this, I just want to test out the algorithms inside of a Docker container. At this point, I'm not sure if I'm doing something wrong or if the whole process is just very broken, but in any case a more detailed guide on what I'm REALLY supposed to do wouldn't hurt

[folivetti]

Hi @oathbound01 we're sorry for this inconvenience. We're now in the middle of setting things up for a new version of srbench (the docker images is meant to be part of that new version) so things may not yet be working as intended.
AFTER we finish setting things up, we will merge the current working branch to main and update the documentation.

Notice that this project is being maintained by very few volunteers with limited time (at this point I would say only @gAldeia is actively working on that) so things may not run as fast as we wish!

We will look into this issue and let you know when we figure it out what's going on. In the meantime I ask you for your patience and, if you figure things out on your end, please let us know and prepare a PR. The success of such projects depend on the whole community working together as a team :-)

[gAldeia]

Hey @oathbound01,

If you're looking for a stable version of the master branch, there’s a release that should work: v2.0 release.

If you want to use the Docker images, you'll need to switch to the docker-compose branch. You are right --- there's no mention of this in the main branch, so I will update the README.md to include it. Switching to this branch should resolve your issues, as GitHub Actions can successfully build and test all images, including new algorithms staged for benchmarking.

As @folivetti mentioned, it is still a WIP.

[gAldeia]

There is a small guide on how to use the docker here https://github.com/cavalab/srbench/blob/docker-compose/docs/user_guide.md#for-docker-users

[oathbound01]

switching to this branch should resolve your issues, as GitHub Actions can successfully build and test all images, including new algorithms staged for benchmarking.

Unfortunately, switching to that branch has not solved my issues, as you can see with the error above. And I don't really know what is causing this, especially when Actions seems to be working fine, especially considering that I've tried following its workflow (which is the same as the guide you linked me) as closely as I could, yet the build just fails.

If you're looking for a stable version of the master branch, there’s a release that should work: v2.0 release.

The stable release is also giving me issues, but to be fair I think it's just conda being conda and refusing to cooperate on my Fedora machine. I might try it on Arch to see if I can get things moving again, although at this point I'm pretty disheartened and might just wait for the Docker image to be done

[gAldeia]

I haven't tested it on other operating systems yet. So far, I've managed to get it running in my WSL environment (which can be a bit tricky at times) and on an Ubuntu machine.

A last resource: instead of building it, try to pull it from docherhub.

I know the CI handles DockerHub uploads, but it's tied to William's account, so I don't have the credentials. This means it's not fully up to date, though some algorithms are available: SRBench on DockerHub.

In the meantime, I'll look into the micromamba issue you mentioned. Thanks for bringing it up!