AddOnTargetScores unable to run due to error with creating conda environment

[nicodemus88]

Hi developers,
I am having troubles running the AddOnTargetScores command as it produces an error while creating the conda environment. The error seems to be due to incompatible packages as below.

> testSpacer <- addOnTargetScores(testSpacer, methods = c("deephf", "deepspcas9"))
[addOnTargetScores] Adding deephf scores. 

/nemo/project/home/tanb/.cache/R/ExperimentHub
  does not exist, create directory? (yes/no): yes
  |======================================================================| 100%

snapshotDate(): 2022-10-31
see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh'
Content type 'application/x-sh' length 76120962 bytes (72.6 MB)
==================================================
downloaded 72.6 MB

PREFIX=/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                              
Solving environment: done

## Package Plan ##

  environment location: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py38h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py38h06a4308_2
    - cffi==1.15.0=py38hd667e15_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py38h7f8727e_0
    - conda==4.12.0=py38h06a4308_0
    - cryptography==36.0.0=py38h9ce1e76_0
    - idna==3.3=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.3=h7f8727e_2
    - openssl==1.1.1n=h7f8727e_0
    - pip==21.2.4=py38h06a4308_0
    - pycosat==0.6.3=py38h7b6447c_1
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py38h06a4308_0
    - python==3.8.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py38h27cfd23_0
    - setuptools==61.2.0=py38h06a4308_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=hc218d9a_0
    - tk==8.6.11=h1ccaba5_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.12=h7f8727e_1


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py38h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py38hd667e15_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/linux-64::conda-4.12.0-py38h06a4308_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py38h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py38h9ce1e76_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.4-py38h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
  python             pkgs/main/linux-64::python-3.8.13-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py38h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py38h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1


Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
    You currently have a PYTHONPATH environment variable set. This may cause
    unexpected behavior when running the Python interpreter in Miniconda3.
    For best results, please verify that your PYTHONPATH only points to
    directories of packages that are compatible with the Python interpreter
    in Miniconda3: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0
+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'create' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' 'python=3.6' '--quiet' '-c' 'conda-forge' '-c' 'bioconda'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2016.9.26          |           py36_0         217 KB  conda-forge
    openssl-1.1.1v             |       hd590300_0         1.9 MB  conda-forge
    pip-20.0.2                 |           py36_1         1.9 MB  conda-forge
    python-3.6.15              |hb7a2778_0_cpython        38.4 MB  conda-forge
    setuptools-49.6.0          |   py36h5fab9bb_3         936 KB  conda-forge
    wheel-0.36.2               |     pyhd3deb0d_0          31 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        43.3 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2023.7.22-hbcca054_0
  certifi            conda-forge/linux-64::certifi-2016.9.26-py36_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.1.0-he5830b7_0
  libgomp            conda-forge/linux-64::libgomp-13.1.0-he5830b7_0
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libsqlite          conda-forge/linux-64::libsqlite-3.42.0-h2797004_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.1.0-hfd8a6a1_0
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
  ncurses            conda-forge/linux-64::ncurses-6.4-hcb278e6_0
  openssl            conda-forge/linux-64::openssl-1.1.1v-hd590300_0
  pip                conda-forge/linux-64::pip-20.0.2-py36_1
  python             conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.6-2_cp36m
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py36h5fab9bb_3
  sqlite             conda-forge/linux-64::sqlite-3.42.0-h2c6b66d_0
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0


Preparing transaction: ...working... 
done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'install' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' 'python=3.6'
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'install' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' '-c' 'conda-forge' '-c' 'bioconda' 'python=3.6' 'python=3.6' 'viennarna=2.4.5' 'absl-py=0.12.0' 'astor=0.8.1' 'biopython=1.71' 'bleach=1.5.0' 'certifi=2020.12.5' 'cycler=0.10.0' 'decorator=4.4.2' 'dotmap=1.2.20' 'gast=0.4.0' 'GPy=1.9.8' 'GPyOpt=1.2.6' 'grpcio=1.36.1' 'h5py=2.9.0' 'html5lib=0.9999999' 'importlib-metadata=3.7.2' 'Keras=2.1.6' 'kiwisolver=1.3.1' 'Mako=1.1.4' 'Markdown=3.3.4' 'MarkupSafe=1.1.1' 'matplotlib=3.1.1' 'numpy=1.14.0' 'pandas=0.25.3' 'paramz=0.9.5' 'pip=21.0.1' 'protobuf=3.15.5' 'pygpu=0.7.6' 'pyparsing=2.4.7' 'python-dateutil=2.8.1' 'pytz=2021.1' 'PyYAML=5.4.1' 'scikit-learn=0.19.1' 'scipy=1.1.0' 'setuptools=49.6.0' 'six=1.15.0' 'tensorboard=1.8.0' 'tensorflow=1.8.0' 'termcolor=1.1.0' 'Theano=1.0.5' 'tornado=6.1' 'typing-extensions=3.7.4.3' 'webencodings=0.5.1' 'Werkzeug=1.0.1' 'wheel=0.36.2' 'zipp=3.4.1'
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                           \                                   \ 

UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (python):

What follows after that code chunk is a long list of incompatible packages which ends with this code chunk.

Package libedit conflicts for:
sqlite -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']
python[version='3.6.*,3.6.*'] -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0
  - biopython=1.71 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
  - gpy=1.9.8 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - grpcio=1.36.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - h5py=2.9.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - keras=2.1.6 -> tensorflow -> __cuda
  - keras=2.1.6 -> tensorflow -> __glibc[version='>=2.17']
  - kiwisolver=1.3.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - libffi -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - libnsl -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - libstdcxx-ng -> __glibc[version='>=2.17']
  - libzlib -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - markupsafe=1.1.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - matplotlib=3.1.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - ncurses -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - numpy=1.14.0 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
  - openssl -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - pandas=0.25.3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - protobuf=3.15.5 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - pygpu=0.7.6 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - python[version='3.6.*,3.6.*'] -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - pyyaml=5.4.1 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - readline -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - scikit-learn=0.19.1 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
  - scipy=1.1.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - sqlite -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - tensorboard=1.8.0 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
  - tk -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - tornado=6.1 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - viennarna=2.4.5 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
  - xz -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

Note that strict channel priority may have removed packages required for satisfiability.

Error: one or more Python packages failed to install [error code 1]

Could you please advise how to fix this issue? Thank you.

[Jfortin1]

Hi @nicodemus88, we fixed a few bugs today in crisprScore; could you install version 1.7.2 of the devel branch of crisprScore to see if you have the same problems?

[Jfortin1]

@nicodemus88 Any updates from your side?