[ Started: 2023-11-20 12:55:23 CET ]
[ liana v0.1.13 for BioC-3.18 from https://github.com/saezlab/liana@master ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘liana’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘liana_cc2tensor.Rmd’ using rmarkdown
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Contains 1 files.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 12:56:03] [TRACE]   [OmnipathR] Cache locked: FALSE
PREFIX=/home/omnipath/.cache/R/basilisk/1.15.1/0
Unpacking payload ...

  0%|          | 0/40 [00:00<?, ?it/s]
Extracting : libffi-3.3-he6710b0_2.conda:   0%|          | 0/40 [00:00<?, ?it/s]
Extracting : libffi-3.3-he6710b0_2.conda:   2%|▎         | 1/40 [00:00<00:04,  8.87it/s]
Extracting : cffi-1.15.0-py39hd667e15_1.conda:   2%|▎         | 1/40 [00:00<00:04,  8.87it/s]
Extracting : readline-8.1.2-h7f8727e_1.conda:   5%|▌         | 2/40 [00:00<00:04,  8.87it/s] 
Extracting : _libgcc_mutex-0.1-main.conda:   8%|▊         | 3/40 [00:00<00:04,  8.87it/s]   
Extracting : certifi-2021.10.8-py39h06a4308_2.conda:  10%|█         | 4/40 [00:00<00:04,  8.87it/s]
Extracting : zlib-1.2.12-h7f8727e_1.conda:  12%|█▎        | 5/40 [00:00<00:03,  8.87it/s]          
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda:  15%|█▌        | 6/40 [00:00<00:03,  8.87it/s]
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda:  18%|█▊        | 7/40 [00:00<00:00, 36.04it/s]
Extracting : tzdata-2022a-hda174b7_0.conda:  18%|█▊        | 7/40 [00:00<00:00, 36.04it/s]            
Extracting : yaml-0.2.5-h7b6447c_0.conda:  20%|██        | 8/40 [00:00<00:00, 36.04it/s]  
Extracting : cryptography-36.0.0-py39h9ce1e76_0.conda:  22%|██▎       | 9/40 [00:00<00:00, 36.04it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda:  25%|██▌       | 10/40 [00:00<00:00, 36.04it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda:  28%|██▊       | 11/40 [00:00<00:00, 35.60it/s]
Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda:  28%|██▊       | 11/40 [00:00<00:00, 35.60it/s]    
Extracting : conda-package-handling-1.8.1-py39h7f8727e_0.conda:  30%|███       | 12/40 [00:00<00:00, 35.60it/s]
Extracting : xz-5.2.5-h7b6447c_0.conda:  32%|███▎      | 13/40 [00:00<00:00, 35.60it/s]                        
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda:  35%|███▌      | 14/40 [00:00<00:00, 35.60it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda:  38%|███▊      | 15/40 [00:00<00:00, 34.55it/s]
Extracting : ncurses-6.3-h7f8727e_2.conda:  38%|███▊      | 15/40 [00:00<00:00, 34.55it/s]   
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda:  40%|████      | 16/40 [00:00<00:00, 34.55it/s]
Extracting : pysocks-1.7.1-py39h06a4308_0.conda:  42%|████▎     | 17/40 [00:00<00:00, 34.55it/s]
Extracting : libgomp-9.3.0-h5101ec6_17.conda:  45%|████▌     | 18/40 [00:00<00:00, 34.55it/s]   
Extracting : pip-21.2.4-py39h06a4308_0.conda:  48%|████▊     | 19/40 [00:00<00:00, 34.55it/s]
Extracting : pip-21.2.4-py39h06a4308_0.conda:  50%|█████     | 20/40 [00:00<00:00, 25.63it/s]
Extracting : ca-certificates-2022.3.29-h06a4308_1.conda:  50%|█████     | 20/40 [00:00<00:00, 25.63it/s]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda:  52%|█████▎    | 21/40 [00:00<00:00, 25.63it/s]            
Extracting : openssl-1.1.1n-h7f8727e_0.conda:  55%|█████▌    | 22/40 [00:00<00:00, 25.63it/s]
Extracting : idna-3.3-pyhd3eb1b0_0.conda:  57%|█████▊    | 23/40 [00:00<00:00, 25.63it/s]    
Extracting : tk-8.6.11-h1ccaba5_0.conda:  60%|██████    | 24/40 [00:00<00:00, 25.63it/s] 
Extracting : setuptools-61.2.0-py39h06a4308_0.conda:  62%|██████▎   | 25/40 [00:00<00:00, 25.63it/s]
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  65%|██████▌   | 26/40 [00:00<00:00, 25.63it/s]     
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  68%|██████▊   | 27/40 [00:00<00:00, 35.94it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda:  68%|██████▊   | 27/40 [00:00<00:00, 35.94it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda:  70%|███████   | 28/40 [00:00<00:00, 35.94it/s]
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda:  72%|███████▎  | 29/40 [00:00<00:00, 35.94it/s]
Extracting : python-3.9.12-h12debd9_0.conda:  75%|███████▌  | 30/40 [00:01<00:00, 35.94it/s]      
Extracting : sqlite-3.38.2-hc218d9a_0.conda:  78%|███████▊  | 31/40 [00:01<00:00, 35.94it/s]
Extracting : sqlite-3.38.2-hc218d9a_0.conda:  80%|████████  | 32/40 [00:01<00:00, 22.32it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  80%|████████  | 32/40 [00:01<00:00, 22.32it/s]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda:  82%|████████▎ | 33/40 [00:01<00:00, 22.32it/s]
Extracting : conda-4.12.0-py39h06a4308_0.conda:  85%|████████▌ | 34/40 [00:01<00:00, 22.32it/s]  
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  88%|████████▊ | 35/40 [00:01<00:00, 22.32it/s]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda:  90%|█████████ | 36/40 [00:01<00:00, 22.32it/s]              
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda:  92%|█████████▎| 37/40 [00:01<00:00, 22.32it/s]
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  95%|█████████▌| 38/40 [00:01<00:00, 22.32it/s]
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2:  98%|█████████▊| 39/40 [00:01<00:00, 22.32it/s]       
                                                                                             
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/omnipath/.cache/R/basilisk/1.15.1/0

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py39h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py39h06a4308_2
    - cffi==1.15.0=py39hd667e15_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=py39h7f8727e_0
    - conda==4.12.0=py39h06a4308_0
    - cryptography==36.0.0=py39h9ce1e76_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=py39h06a4308_0
    - pycosat==0.6.3=py39h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py39h06a4308_0
    - python==3.9.12=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py39h27cfd23_0
    - setuptools==61.2.0=py39h06a4308_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
    - tzdata==2022a=hda174b7_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-py39h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_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-py39h06a4308_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-py39h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_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-py39h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
  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-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.12-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-py39h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_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
  tzdata             pkgs/main/noarch::tzdata-2022a-hda174b7_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: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/omnipath/.cache/R/basilisk/1.15.1/liana/0.1.13/liana_cell2cell

  added / updated specs:
    - python=3.8.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    ca-certificates-2023.11.17 |       hbcca054_0         151 KB  conda-forge
    ld_impl_linux-64-2.40      |       h41732ed_0         688 KB  conda-forge
    libffi-3.3                 |       h58526e2_2          51 KB  conda-forge
    libgcc-ng-13.2.0           |       h807b86a_3         755 KB  conda-forge
    libgomp-13.2.0             |       h807b86a_3         412 KB  conda-forge
    libsqlite-3.44.0           |       h2797004_0         826 KB  conda-forge
    libstdcxx-ng-13.2.0        |       h7e041cc_3         3.7 MB  conda-forge
    libzlib-1.2.13             |       hd590300_5          60 KB  conda-forge
    ncurses-6.4                |       h59595ed_2         864 KB  conda-forge
    openssl-1.1.1w             |       hd590300_0         1.9 MB  conda-forge
    pip-23.3.1                 |     pyhd8ed1ab_0         1.3 MB  conda-forge
    python-3.8.8               |hffdb5ce_0_cpython        26.1 MB  conda-forge
    readline-8.2               |       h8228510_1         275 KB  conda-forge
    setuptools-68.2.2          |     pyhd8ed1ab_0         454 KB  conda-forge
    sqlite-3.44.0              |       h2c6b66d_0         817 KB  conda-forge
    tk-8.6.13                  |noxft_h4845f30_101         3.2 MB  conda-forge
    wheel-0.41.3               |     pyhd8ed1ab_0          57 KB  conda-forge
    xz-5.2.6                   |       h166bdaf_0         409 KB  conda-forge
    zlib-1.2.13                |       hd590300_5          91 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        41.9 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-2023.11.17-hbcca054_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_3
  libsqlite          conda-forge/linux-64::libsqlite-3.44.0-h2797004_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
  ncurses            conda-forge/linux-64::ncurses-6.4-h59595ed_2
  openssl            conda-forge/linux-64::openssl-1.1.1w-hd590300_0
  pip                conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.8.8-hffdb5ce_0_cpython
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  setuptools         conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
  sqlite             conda-forge/linux-64::sqlite-3.44.0-h2c6b66d_0
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
  wheel              conda-forge/noarch::wheel-0.41.3-pyhd8ed1ab_0
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0
  zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.10.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/omnipath/.cache/R/basilisk/1.15.1/liana/0.1.13/liana_cell2cell

  added / updated specs:
    - python=3.8.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2023.08.22 |       h06a4308_0         123 KB
    openssl-1.1.1w             |       h7f8727e_0         3.7 MB
    ------------------------------------------------------------
                                           Total:         3.9 MB

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.11.~ --> pkgs/main::ca-certificates-2023.08.22-h06a4308_0
  openssl            conda-forge::openssl-1.1.1w-hd590300_0 --> pkgs/main::openssl-1.1.1w-h7f8727e_0



Downloading and Extracting Packages

ca-certificates-2023 | 123 KB    |            |   0% 
ca-certificates-2023 | 123 KB    | ########## | 100% 
ca-certificates-2023 | 123 KB    | ########## | 100% 

openssl-1.1.1w       | 3.7 MB    |            |   0% 
openssl-1.1.1w       | 3.7 MB    | ########## | 100% 
openssl-1.1.1w       | 3.7 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.10.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/omnipath/.cache/R/basilisk/1.15.1/liana/0.1.13/liana_cell2cell

  added / updated specs:
    - pandas=1.4.2
    - python[version='3.8.8.*,3.8.8.*']
    - rpy2=3.4.5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _r-mutex-1.0.1             |      anacondar_1           3 KB  conda-forge
    backports-1.0              |     pyhd8ed1ab_3           6 KB  conda-forge
    backports.zoneinfo-0.2.1   |   py38h01eb140_8          50 KB  conda-forge
    binutils_impl_linux-64-2.39|       he00db2b_1         4.7 MB  conda-forge
    binutils_linux-64-2.39     |      h5fc0e48_13          27 KB  conda-forge
    bwidget-1.9.14             |       ha770c72_1         120 KB  conda-forge
    bzip2-1.0.8                |       hd590300_5         248 KB  conda-forge
    c-ares-1.22.1              |       hd590300_0         146 KB  conda-forge
    cairo-1.16.0               |    h6cf1ce9_1008         1.5 MB  conda-forge
    cffi-1.14.6                |   py38ha65f79e_0         226 KB  conda-forge
    curl-7.86.0                |       h7bff187_1          91 KB  conda-forge
    expat-2.5.0                |       hcb278e6_1         134 KB  conda-forge
    font-ttf-dejavu-sans-mono-2.37|       hab24e00_0         388 KB  conda-forge
    font-ttf-inconsolata-3.000 |       h77eed37_0          94 KB  conda-forge
    font-ttf-source-code-pro-2.038|       h77eed37_0         684 KB  conda-forge
    font-ttf-ubuntu-0.83       |       hab24e00_0         1.9 MB  conda-forge
    fontconfig-2.14.2          |       h14ed4e7_0         266 KB  conda-forge
    fonts-conda-ecosystem-1    |                0           4 KB  conda-forge
    fonts-conda-forge-1        |                0           4 KB  conda-forge
    freetype-2.12.1            |       h267a509_2         620 KB  conda-forge
    fribidi-1.0.10             |       h36c2ea0_0         112 KB  conda-forge
    gcc_impl_linux-64-9.5.0    |      h99780fb_19        43.5 MB  conda-forge
    gcc_linux-64-9.5.0         |      h4258300_13          29 KB  conda-forge
    gettext-0.21.1             |       h27087fc_0         4.1 MB  conda-forge
    gfortran_impl_linux-64-9.5.0|      hf1096a2_19        14.6 MB  conda-forge
    gfortran_linux-64-9.5.0    |      hdb51d14_13          28 KB  conda-forge
    graphite2-1.3.13           |    h58526e2_1001         102 KB  conda-forge
    gsl-2.7                    |       he838d99_0         3.2 MB  conda-forge
    gxx_impl_linux-64-9.5.0    |      h99780fb_19        10.6 MB  conda-forge
    gxx_linux-64-9.5.0         |      h43f449f_13          28 KB  conda-forge
    harfbuzz-3.0.0             |       h83ec7ef_1         2.0 MB  conda-forge
    icu-68.2                   |       h9c3ff4c_0        13.1 MB  conda-forge
    jinja2-3.1.2               |     pyhd8ed1ab_1          99 KB  conda-forge
    jpeg-9e                    |       h0b41bf4_3         235 KB  conda-forge
    kernel-headers_linux-64-2.6.32|      he073ed8_16         692 KB  conda-forge
    keyutils-1.6.1             |       h166bdaf_0         115 KB  conda-forge
    krb5-1.19.3                |       h3790be6_0         1.4 MB  conda-forge
    ld_impl_linux-64-2.39      |       hcc3a1bd_1         675 KB  conda-forge
    lerc-4.0.0                 |       h27087fc_0         275 KB  conda-forge
    libblas-3.9.0              |19_linux64_openblas          14 KB  conda-forge
    libcblas-3.9.0             |19_linux64_openblas          14 KB  conda-forge
    libcurl-7.86.0             |       h7bff187_1         348 KB  conda-forge
    libdeflate-1.14            |       h166bdaf_0          81 KB  conda-forge
    libedit-3.1.20191231       |       he28a2e2_2         121 KB  conda-forge
    libev-4.33                 |       h516909a_1         104 KB  conda-forge
    libexpat-2.5.0             |       hcb278e6_1          76 KB  conda-forge
    libgcc-devel_linux-64-9.5.0|      h0a57e50_19         4.0 MB  conda-forge
    libgfortran-ng-13.2.0      |       h69a702a_3          23 KB  conda-forge
    libgfortran5-13.2.0        |       ha4646dd_3         1.4 MB  conda-forge
    libglib-2.68.4             |       h3e27bee_0         3.0 MB  conda-forge
    libiconv-1.17              |       h166bdaf_0         1.4 MB  conda-forge
    liblapack-3.9.0            |19_linux64_openblas          14 KB  conda-forge
    libnghttp2-1.51.0          |       hdcd2b5c_0         608 KB  conda-forge
    libopenblas-0.3.24         |pthreads_h413a1c8_0         5.2 MB  conda-forge
    libpng-1.6.39              |       h753d276_0         276 KB  conda-forge
    libsanitizer-9.5.0         |      h2f262e1_19         6.9 MB  conda-forge
    libssh2-1.10.0             |       haa6b8db_3         234 KB  conda-forge
    libstdcxx-devel_linux-64-9.5.0|      h0a57e50_19         9.9 MB  conda-forge
    libtiff-4.4.0              |       h82bc61c_5         473 KB  conda-forge
    libuuid-2.38.1             |       h0b41bf4_0          33 KB  conda-forge
    libwebp-base-1.3.2         |       hd590300_0         392 KB  conda-forge
    libxcb-1.15                |       h0b41bf4_0         375 KB  conda-forge
    libxml2-2.9.12             |       h72842e0_0         772 KB  conda-forge
    make-4.3                   |       hd18ef5c_1         507 KB  conda-forge
    markupsafe-2.1.3           |   py38h01eb140_1          23 KB  conda-forge
    numpy-1.24.4               |   py38h59b608b_0         6.4 MB  conda-forge
    pandas-1.4.2               |   py38h47df419_2        12.6 MB  conda-forge
    pango-1.48.10              |       h54213e6_2         403 KB  conda-forge
    pcre-8.45                  |       h9c3ff4c_0         253 KB  conda-forge
    pcre2-10.37                |       hc3806b6_1         1.1 MB  conda-forge
    pixman-0.42.2              |       h59595ed_0         376 KB  conda-forge
    pthread-stubs-0.4          |    h36c2ea0_1001           5 KB  conda-forge
    pycparser-2.21             |     pyhd8ed1ab_0         100 KB  conda-forge
    python-dateutil-2.8.2      |     pyhd8ed1ab_0         240 KB  conda-forge
    python_abi-3.8             |           4_cp38           6 KB  conda-forge
    pytz-2023.3.post1          |     pyhd8ed1ab_0         183 KB  conda-forge
    r-base-4.1.1               |       hb93adac_1        24.8 MB  conda-forge
    rpy2-3.4.5                 |py38r41h6c62de6_3         377 KB  conda-forge
    sed-4.8                    |       he412f7d_0         264 KB  conda-forge
    simplegeneric-0.8.1        |             py_1           7 KB  conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    sysroot_linux-64-2.12      |      he073ed8_16        14.6 MB  conda-forge
    tktable-2.10               |       h0c5db8f_5          88 KB  conda-forge
    tzdata-2023c               |       h71feb2d_0         115 KB  conda-forge
    tzlocal-5.2                |   py38h578d9bd_0          32 KB  conda-forge
    xorg-kbproto-1.0.7         |    h7f98852_1002          27 KB  conda-forge
    xorg-libice-1.1.1          |       hd590300_0          57 KB  conda-forge
    xorg-libsm-1.2.4           |       h7391055_0          27 KB  conda-forge
    xorg-libx11-1.8.7          |       h8ee46fc_0         809 KB  conda-forge
    xorg-libxau-1.0.11         |       hd590300_0          14 KB  conda-forge
    xorg-libxdmcp-1.1.3        |       h7f98852_0          19 KB  conda-forge
    xorg-libxext-1.3.4         |       h0b41bf4_2          49 KB  conda-forge
    xorg-libxrender-0.9.11     |       hd590300_0          37 KB  conda-forge
    xorg-libxt-1.3.0           |       hd590300_1         370 KB  conda-forge
    xorg-renderproto-0.11.1    |    h7f98852_1002           9 KB  conda-forge
    xorg-xextproto-7.3.0       |    h0b41bf4_1003          30 KB  conda-forge
    xorg-xproto-7.0.31         |    h7f98852_1007          73 KB  conda-forge
    zstd-1.5.5                 |       hfc55251_0         532 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       206.1 MB

The following NEW packages will be INSTALLED:

  _r-mutex           conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
  backports          conda-forge/noarch::backports-1.0-pyhd8ed1ab_3
  backports.zoneinfo conda-forge/linux-64::backports.zoneinfo-0.2.1-py38h01eb140_8
  binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.39-he00db2b_1
  binutils_linux-64  conda-forge/linux-64::binutils_linux-64-2.39-h5fc0e48_13
  bwidget            conda-forge/linux-64::bwidget-1.9.14-ha770c72_1
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  c-ares             conda-forge/linux-64::c-ares-1.22.1-hd590300_0
  cairo              conda-forge/linux-64::cairo-1.16.0-h6cf1ce9_1008
  cffi               conda-forge/linux-64::cffi-1.14.6-py38ha65f79e_0
  curl               conda-forge/linux-64::curl-7.86.0-h7bff187_1
  expat              conda-forge/linux-64::expat-2.5.0-hcb278e6_1
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig         conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0
  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0
  freetype           conda-forge/linux-64::freetype-2.12.1-h267a509_2
  fribidi            conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0
  gcc_impl_linux-64  conda-forge/linux-64::gcc_impl_linux-64-9.5.0-h99780fb_19
  gcc_linux-64       conda-forge/linux-64::gcc_linux-64-9.5.0-h4258300_13
  gettext            conda-forge/linux-64::gettext-0.21.1-h27087fc_0
  gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.5.0-hf1096a2_19
  gfortran_linux-64  conda-forge/linux-64::gfortran_linux-64-9.5.0-hdb51d14_13
  graphite2          conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0
  gxx_impl_linux-64  conda-forge/linux-64::gxx_impl_linux-64-9.5.0-h99780fb_19
  gxx_linux-64       conda-forge/linux-64::gxx_linux-64-9.5.0-h43f449f_13
  harfbuzz           conda-forge/linux-64::harfbuzz-3.0.0-h83ec7ef_1
  icu                conda-forge/linux-64::icu-68.2-h9c3ff4c_0
  jinja2             conda-forge/noarch::jinja2-3.1.2-pyhd8ed1ab_1
  jpeg               conda-forge/linux-64::jpeg-9e-h0b41bf4_3
  kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_16
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.19.3-h3790be6_0
  lerc               conda-forge/linux-64::lerc-4.0.0-h27087fc_0
  libblas            conda-forge/linux-64::libblas-3.9.0-19_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-19_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-7.86.0-h7bff187_1
  libdeflate         conda-forge/linux-64::libdeflate-1.14-h166bdaf_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libexpat           conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1
  libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.5.0-h0a57e50_19
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_3
  libgfortran5       conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_3
  libglib            conda-forge/linux-64::libglib-2.68.4-h3e27bee_0
  libiconv           conda-forge/linux-64::libiconv-1.17-h166bdaf_0
  liblapack          conda-forge/linux-64::liblapack-3.9.0-19_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.51.0-hdcd2b5c_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.24-pthreads_h413a1c8_0
  libpng             conda-forge/linux-64::libpng-1.6.39-h753d276_0
  libsanitizer       conda-forge/linux-64::libsanitizer-9.5.0-h2f262e1_19
  libssh2            conda-forge/linux-64::libssh2-1.10.0-haa6b8db_3
  libstdcxx-devel_l~ conda-forge/linux-64::libstdcxx-devel_linux-64-9.5.0-h0a57e50_19
  libtiff            conda-forge/linux-64::libtiff-4.4.0-h82bc61c_5
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libwebp-base       conda-forge/linux-64::libwebp-base-1.3.2-hd590300_0
  libxcb             conda-forge/linux-64::libxcb-1.15-h0b41bf4_0
  libxml2            conda-forge/linux-64::libxml2-2.9.12-h72842e0_0
  make               conda-forge/linux-64::make-4.3-hd18ef5c_1
  markupsafe         conda-forge/linux-64::markupsafe-2.1.3-py38h01eb140_1
  numpy              conda-forge/linux-64::numpy-1.24.4-py38h59b608b_0
  pandas             conda-forge/linux-64::pandas-1.4.2-py38h47df419_2
  pango              conda-forge/linux-64::pango-1.48.10-h54213e6_2
  pcre               conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
  pcre2              conda-forge/linux-64::pcre2-10.37-hc3806b6_1
  pixman             conda-forge/linux-64::pixman-0.42.2-h59595ed_0
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/linux-64::python_abi-3.8-4_cp38
  pytz               conda-forge/noarch::pytz-2023.3.post1-pyhd8ed1ab_0
  r-base             conda-forge/linux-64::r-base-4.1.1-hb93adac_1
  rpy2               conda-forge/linux-64::rpy2-3.4.5-py38r41h6c62de6_3
  sed                conda-forge/linux-64::sed-4.8-he412f7d_0
  simplegeneric      conda-forge/noarch::simplegeneric-0.8.1-py_1
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  sysroot_linux-64   conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_16
  tktable            conda-forge/linux-64::tktable-2.10-h0c5db8f_5
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0
  tzlocal            conda-forge/linux-64::tzlocal-5.2-py38h578d9bd_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.1.1-hd590300_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.4-h7391055_0
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.7-h8ee46fc_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.3.0-hd590300_1
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
  zstd               conda-forge/linux-64::zstd-1.5.5-hfc55251_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.11.17-hbcca054_0

The following packages will be SUPERSEDED by a higher-priority channel:

  openssl              pkgs/main::openssl-1.1.1w-h7f8727e_0 --> conda-forge::openssl-1.1.1w-hd590300_0

The following packages will be DOWNGRADED:

  ld_impl_linux-64                          2.40-h41732ed_0 --> 2.39-hcc3a1bd_1



Downloading and Extracting Packages

libuuid-2.38.1       | 33 KB     |            |   0% 
libuuid-2.38.1       | 33 KB     | ########## | 100% 
libuuid-2.38.1       | 33 KB     | ########## | 100% 

xorg-xextproto-7.3.0 | 30 KB     |            |   0% 
xorg-xextproto-7.3.0 | 30 KB     | ########## | 100% 
xorg-xextproto-7.3.0 | 30 KB     | ########## | 100% 

make-4.3             | 507 KB    |            |   0% 
make-4.3             | 507 KB    | ########## | 100% 
make-4.3             | 507 KB    | ########## | 100% 

xorg-kbproto-1.0.7   | 27 KB     |            |   0% 
xorg-kbproto-1.0.7   | 27 KB     | ########## | 100% 

libgfortran-ng-13.2. | 23 KB     |            |   0% 
libgfortran-ng-13.2. | 23 KB     | ########## | 100% 
libgfortran-ng-13.2. | 23 KB     | ########## | 100% 

liblapack-3.9.0      | 14 KB     |            |   0% 
liblapack-3.9.0      | 14 KB     | ########## | 100% 
liblapack-3.9.0      | 14 KB     | ########## | 100% 

pycparser-2.21       | 100 KB    |            |   0% 
pycparser-2.21       | 100 KB    | ########## | 100% 

xorg-libsm-1.2.4     | 27 KB     |            |   0% 
xorg-libsm-1.2.4     | 27 KB     | ########## | 100% 
xorg-libsm-1.2.4     | 27 KB     | ########## | 100% 

libedit-3.1.20191231 | 121 KB    |            |   0% 
libedit-3.1.20191231 | 121 KB    | ########## | 100% 

tzlocal-5.2          | 32 KB     |            |   0% 
tzlocal-5.2          | 32 KB     | ########## | 100% 
tzlocal-5.2          | 32 KB     | ########## | 100% 

libglib-2.68.4       | 3.0 MB    |            |   0% 
libglib-2.68.4       | 3.0 MB    | ########## | 100% 
libglib-2.68.4       | 3.0 MB    | ########## | 100% 

_r-mutex-1.0.1       | 3 KB      |            |   0% 
_r-mutex-1.0.1       | 3 KB      | ########## | 100% 

freetype-2.12.1      | 620 KB    |            |   0% 
freetype-2.12.1      | 620 KB    | ########## | 100% 
freetype-2.12.1      | 620 KB    | ########## | 100% 

cffi-1.14.6          | 226 KB    |            |   0% 
cffi-1.14.6          | 226 KB    | 7          |   7% 
cffi-1.14.6          | 226 KB    | ########## | 100% 

font-ttf-ubuntu-0.83 | 1.9 MB    |            |   0% 
font-ttf-ubuntu-0.83 | 1.9 MB    | ########## | 100% 
font-ttf-ubuntu-0.83 | 1.9 MB    | ########## | 100% 

pcre-8.45            | 253 KB    |            |   0% 
pcre-8.45            | 253 KB    | ########## | 100% 

jinja2-3.1.2         | 99 KB     |            |   0% 
jinja2-3.1.2         | 99 KB     | ########## | 100% 

gfortran_impl_linux- | 14.6 MB   |            |   0% 
gfortran_impl_linux- | 14.6 MB   | ####2      |  42% 
gfortran_impl_linux- | 14.6 MB   | ########## | 100% 
gfortran_impl_linux- | 14.6 MB   | ########## | 100% 

pthread-stubs-0.4    | 5 KB      |            |   0% 
pthread-stubs-0.4    | 5 KB      | ########## | 100% 

jpeg-9e              | 235 KB    |            |   0% 
jpeg-9e              | 235 KB    | ########## | 100% 
jpeg-9e              | 235 KB    | ########## | 100% 

sed-4.8              | 264 KB    |            |   0% 
sed-4.8              | 264 KB    | ########## | 100% 

xorg-libxrender-0.9. | 37 KB     |            |   0% 
xorg-libxrender-0.9. | 37 KB     | ########## | 100% 
xorg-libxrender-0.9. | 37 KB     | ########## | 100% 

fonts-conda-ecosyste | 4 KB      |            |   0% 
fonts-conda-ecosyste | 4 KB      | ########## | 100% 

pixman-0.42.2        | 376 KB    |            |   0% 
pixman-0.42.2        | 376 KB    | ########## | 100% 
pixman-0.42.2        | 376 KB    | ########## | 100% 

xorg-libxext-1.3.4   | 49 KB     |            |   0% 
xorg-libxext-1.3.4   | 49 KB     | ########## | 100% 
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Building wheels for collected packages: umap-learn
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  Created wheel for umap-learn: filename=umap_learn-0.5.5-py3-none-any.whl size=86831 sha256=d6fe5184484272ba86011a3264f382ce3a5431e08556a8b805605b5c77b5e741
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Successfully built umap-learn
Installing collected packages: zipp, xlrd, urllib3, tqdm, threadpoolctl, stdlib-list, scipy, pyparsing, pillow, patsy, packaging, networkx, natsort, llvmlite, kiwisolver, joblib, idna, h5py, get-annotations, fonttools, et-xmlfile, cycler, charset-normalizer, certifi, tensorly, session-info, scikit-learn, requests, openpyxl, matplotlib, kneed, importlib-metadata, dunamai, statsmodels, seaborn, numba, gseapy, get_version, anndata, statannotations, pynndescent, anndata2ri, umap-learn, scanpy, cell2cell
Successfully installed anndata-0.9.2 anndata2ri-1.0.6 cell2cell-0.6.8 certifi-2023.11.17 charset-normalizer-3.3.2 cycler-0.12.1 dunamai-1.19.0 et-xmlfile-1.1.0 fonttools-4.44.3 get-annotations-0.1.2 get_version-3.5.4 gseapy-1.0.3 h5py-3.10.0 idna-3.4 importlib-metadata-6.8.0 joblib-1.3.2 kiwisolver-1.4.5 kneed-0.8.5 llvmlite-0.41.1 matplotlib-3.5.1 natsort-8.4.0 networkx-3.1 numba-0.58.1 openpyxl-3.1.2 packaging-23.2 patsy-0.5.3 pillow-10.1.0 pynndescent-0.5.10 pyparsing-3.1.1 requests-2.31.0 scanpy-1.9.6 scikit-learn-1.3.2 scipy-1.10.1 seaborn-0.11.2 session-info-1.0.0 statannotations-0.6.0 statsmodels-0.14.0 stdlib-list-0.10.0 tensorly-0.8.1 threadpoolctl-3.2.0 tqdm-4.66.1 umap-learn-0.5.5 urllib3-2.1.0 xlrd-2.0.1 zipp-3.17.0

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[2023-11-20 14:00:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
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[2023-11-20 14:00:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
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[2023-11-20 14:00:33] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-11-20 14:00:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
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[2023-11-20 14:00:33] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
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[2023-11-20 14:00:33] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
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[2023-11-20 14:00:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2023-11-20 14:00:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
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[2023-11-20 14:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
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[2023-11-20 14:00:47] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
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[2023-11-20 14:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
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[2023-11-20 14:00:47] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2023-11-20 14:00:48] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2023-11-20 14:00:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
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[2023-11-20 14:00:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
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[2023-11-20 14:00:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
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[2023-11-20 14:00:51] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
--- finished re-building ‘liana_cc2tensor.Rmd’

--- re-building ‘liana_custom_op.Rmd’ using rmarkdown
[2023-11-20 14:01:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
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[2023-11-20 14:01:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:06] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2023-11-20 14:01:06] [INFO]    [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1]
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:06] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:06] [SUCCESS] [OmnipathR] Downloaded 4568 interactions.
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1]
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:07] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:07] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2023-11-20 14:01:07] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1]
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:08] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:08] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2023-11-20 14:01:09] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:09] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2023-11-20 14:01:10] [INFO]    [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1]
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:10] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2023-11-20 14:01:10] [SUCCESS] [OmnipathR] Downloaded 2484 interactions.
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1]
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2023-11-20 14:01:11] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1]
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:12] [SUCCESS] [OmnipathR] Downloaded 1796 interactions.
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:13] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`.
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2023-11-20 14:01:13] [INFO]    [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1]
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-11-20 14:01:13] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`.
[2023-11-20 14:01:13] [SUCCESS] [OmnipathR] Downloaded 2001 annotation records.
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] Bypassing call: `OmnipathR::filter_intercell_network(., simplify = FALSE, ...)`.
[2023-11-20 14:01:13] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.

Quitting from lines 159-196 [pm_omni] (liana_custom_op.Rmd)
Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics:
no applicable method for 'tbl_vars' applied to an object of class "NULL"
--- failed re-building ‘liana_custom_op.Rmd’

--- re-building ‘liana_devel.Rmd’ using rmarkdown
--- finished re-building ‘liana_devel.Rmd’

--- re-building ‘liana_nichenet.Rmd’ using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Quitting from lines 92-99 [unnamed-chunk-5] (liana_nichenet.Rmd)
Error: processing vignette 'liana_nichenet.Rmd' failed with diagnostics:
cannot replicate NULL to a non-zero length
--- failed re-building ‘liana_nichenet.Rmd’

--- re-building ‘liana_ortho.Rmd’ using rmarkdown
[2023-11-20 14:03:12] [TRACE]   [OmnipathR] Bypassing call: `homologene_raw()`.
[2023-11-20 14:03:12] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.

Quitting from lines 73-74 [show_taxid] (liana_ortho.Rmd)
Error: processing vignette 'liana_ortho.Rmd' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 'na.omit': no applicable method for 'pull' applied to an object of class "list"
--- failed re-building ‘liana_ortho.Rmd’

--- re-building ‘liana_tutorial.Rmd’ using rmarkdown
--- finished re-building ‘liana_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘liana_custom_op.Rmd’ ‘liana_nichenet.Rmd’ ‘liana_ortho.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-11-20 14:04:57 CET ]