[ Started: 2023-11-04 19:01:32 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 [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Contains 1 files. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-11-04 19:02:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-11-04 19:02:09] [TRACE] [OmnipathR] Cache locked: FALSE 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/1.13.4/liana/0.1.13/liana_cell2cell added / updated specs: - python=3.8.8 The following packages will be downloaded: package | build ---------------------------|----------------- libsqlite-3.44.0 | h2797004_0 826 KB conda-forge ncurses-6.4 | h59595ed_2 864 KB conda-forge sqlite-3.44.0 | h2c6b66d_0 817 KB conda-forge wheel-0.41.3 | pyhd8ed1ab_0 57 KB conda-forge ------------------------------------------------------------ Total: 2.5 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 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_2 libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_2 libsqlite conda-forge/linux-64::libsqlite-3.44.0-h2797004_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_2 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-h2797004_0 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: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell added / updated specs: - python=3.8.8 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-h06a4308_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl conda-forge::openssl-1.1.1w-hd590300_0 --> pkgs/main::openssl-1.1.1w-h7f8727e_0 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: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/omnipath/.cache/R/basilisk/1.13.4/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 ---------------------------|----------------- c-ares-1.21.0 | hd590300_0 119 KB conda-forge ------------------------------------------------------------ Total: 119 KB 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-h7f98852_4 c-ares conda-forge/linux-64::c-ares-1.21.0-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_2 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_2 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 SUPERSEDED by a higher-priority channel: ca-certificates pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.7.22-hbcca054_0 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 c-ares-1.21.0 | 119 KB | | 0% c-ares-1.21.0 | 119 KB | ########## | 100% c-ares-1.21.0 | 119 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting cell2cell==0.6.8 Downloading cell2cell-0.6.8-py3-none-any.whl (170 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.8/170.8 kB 6.9 MB/s eta 0:00:00 Collecting anndata2ri==1.0.6 Using cached anndata2ri-1.0.6-py3-none-any.whl (24 kB) Requirement already satisfied: numpy>=1.16 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from cell2cell==0.6.8) (1.24.4) Requirement already satisfied: pandas>=1.0.0 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from cell2cell==0.6.8) (1.4.2) Collecting xlrd>=1.1 (from cell2cell==0.6.8) Using cached xlrd-2.0.1-py2.py3-none-any.whl (96 kB) Collecting openpyxl>=2.6.2 (from cell2cell==0.6.8) Using cached openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) Collecting networkx>=2.3 (from cell2cell==0.6.8) Using cached networkx-3.1-py3-none-any.whl (2.1 MB) Collecting matplotlib<=3.5.1,>=3.2.0 (from cell2cell==0.6.8) Downloading matplotlib-3.5.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 61.1 MB/s eta 0:00:00 Collecting seaborn>=0.11.0 (from cell2cell==0.6.8) Using cached seaborn-0.13.0-py3-none-any.whl.metadata (5.3 kB) Collecting scikit-learn (from cell2cell==0.6.8) Using cached scikit_learn-1.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting umap-learn (from cell2cell==0.6.8) Using cached umap_learn-0.5.4-py3-none-any.whl Collecting tqdm (from cell2cell==0.6.8) Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) Collecting statsmodels (from cell2cell==0.6.8) Using cached statsmodels-0.14.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.2 MB) Collecting statannotations (from cell2cell==0.6.8) Using cached statannotations-0.6.0-py3-none-any.whl.metadata (8.0 kB) Collecting tensorly==0.8.1 (from cell2cell==0.6.8) Downloading tensorly-0.8.1-py3-none-any.whl (229 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 229.7/229.7 kB 17.3 MB/s eta 0:00:00 Collecting kneed (from cell2cell==0.6.8) Using cached kneed-0.8.5-py3-none-any.whl.metadata (5.5 kB) Collecting scanpy (from cell2cell==0.6.8) Downloading scanpy-1.9.6-py3-none-any.whl.metadata (6.0 kB) Collecting gseapy==1.0.3 (from cell2cell==0.6.8) Downloading gseapy-1.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 38.4 MB/s eta 0:00:00 Collecting get_version (from anndata2ri==1.0.6) Using cached get_version-3.5.4-py3-none-any.whl (18 kB) Requirement already satisfied: rpy2>=3.4 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from anndata2ri==1.0.6) (3.4.5) Requirement already satisfied: tzlocal in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from anndata2ri==1.0.6) (5.2) Collecting anndata (from anndata2ri==1.0.6) Using cached anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB) Collecting scipy (from gseapy==1.0.3->cell2cell==0.6.8) Using cached scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB) Collecting requests (from gseapy==1.0.3->cell2cell==0.6.8) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting cycler>=0.10 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Downloading fonttools-4.44.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (153 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.6/153.6 kB 15.0 MB/s eta 0:00:00 Collecting kiwisolver>=1.0.1 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Using cached kiwisolver-1.4.5-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (6.4 kB) Collecting packaging>=20.0 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting pillow>=6.2.0 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Using cached Pillow-10.1.0-cp38-cp38-manylinux_2_28_x86_64.whl.metadata (9.5 kB) Collecting pyparsing>=2.2.1 (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) Using cached pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB) Requirement already satisfied: python-dateutil>=2.7 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from matplotlib<=3.5.1,>=3.2.0->cell2cell==0.6.8) (2.8.2) Collecting et-xmlfile (from openpyxl>=2.6.2->cell2cell==0.6.8) Using cached et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) Requirement already satisfied: pytz>=2020.1 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from pandas>=1.0.0->cell2cell==0.6.8) (2023.3.post1) Requirement already satisfied: cffi>=1.10.0 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from rpy2>=3.4->anndata2ri==1.0.6) (1.14.6) Requirement already satisfied: jinja2 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from rpy2>=3.4->anndata2ri==1.0.6) (3.1.2) Collecting h5py>=3 (from anndata->anndata2ri==1.0.6) Using cached h5py-3.10.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting natsort (from anndata->anndata2ri==1.0.6) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting dunamai (from get_version->anndata2ri==1.0.6) Using cached dunamai-1.19.0-py3-none-any.whl.metadata (10.0 kB) Collecting get-annotations (from scanpy->cell2cell==0.6.8) Downloading get_annotations-0.1.2-py3-none-any.whl (4.5 kB) Collecting joblib (from scanpy->cell2cell==0.6.8) Using cached joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB) Collecting numba>=0.41.0 (from scanpy->cell2cell==0.6.8) Using cached numba-0.58.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB) Collecting patsy (from scanpy->cell2cell==0.6.8) Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB) Collecting seaborn>=0.11.0 (from cell2cell==0.6.8) Downloading seaborn-0.12.2-py3-none-any.whl (293 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 31.0 MB/s eta 0:00:00 Collecting session-info (from scanpy->cell2cell==0.6.8) Using cached session_info-1.0.0-py3-none-any.whl Collecting threadpoolctl>=2.0.0 (from scikit-learn->cell2cell==0.6.8) Using cached threadpoolctl-3.2.0-py3-none-any.whl.metadata (10.0 kB) Collecting pynndescent>=0.5 (from umap-learn->cell2cell==0.6.8) Using cached pynndescent-0.5.10-py3-none-any.whl Collecting tbb>=2019.0 (from umap-learn->cell2cell==0.6.8) Using cached tbb-2021.10.0-py2.py3-none-manylinux1_x86_64.whl.metadata (1.0 kB) Collecting seaborn>=0.11.0 (from cell2cell==0.6.8) Using cached seaborn-0.11.2-py3-none-any.whl (292 kB) Requirement already satisfied: backports.zoneinfo in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from tzlocal->anndata2ri==1.0.6) (0.2.1) Requirement already satisfied: pycparser in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from cffi>=1.10.0->rpy2>=3.4->anndata2ri==1.0.6) (2.21) Collecting llvmlite<0.42,>=0.41.0dev0 (from numba>=0.41.0->scanpy->cell2cell==0.6.8) Using cached llvmlite-0.41.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB) Collecting importlib-metadata (from numba>=0.41.0->scanpy->cell2cell==0.6.8) Using cached importlib_metadata-6.8.0-py3-none-any.whl.metadata (5.1 kB) Requirement already satisfied: six in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from patsy->scanpy->cell2cell==0.6.8) (1.16.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/lib/python3.8/site-packages (from jinja2->rpy2>=3.4->anndata2ri==1.0.6) (2.1.3) Collecting charset-normalizer<4,>=2 (from requests->gseapy==1.0.3->cell2cell==0.6.8) Downloading charset_normalizer-3.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests->gseapy==1.0.3->cell2cell==0.6.8) Downloading idna-3.4-py3-none-any.whl (61 kB) 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statannotations-0.6.0-py3-none-any.whl (32 kB) Using cached tqdm-4.66.1-py3-none-any.whl (78 kB) Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB) Downloading fonttools-4.44.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 57.3 MB/s eta 0:00:00 Using cached h5py-3.10.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB) Using cached joblib-1.3.2-py3-none-any.whl (302 kB) Using cached kiwisolver-1.4.5-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB) Using cached numba-0.58.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB) Using cached packaging-23.2-py3-none-any.whl (53 kB) Using cached Pillow-10.1.0-cp38-cp38-manylinux_2_28_x86_64.whl (3.6 MB) Using cached pyparsing-3.1.1-py3-none-any.whl (103 kB) Using cached tbb-2021.10.0-py2.py3-none-manylinux1_x86_64.whl (4.4 MB) Using cached threadpoolctl-3.2.0-py3-none-any.whl (15 kB) Using cached dunamai-1.19.0-py3-none-any.whl (25 kB) Using cached natsort-8.4.0-py3-none-any.whl (38 kB) Downloading requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 6.2 MB/s eta 0:00:00 Downloading certifi-2023.7.22-py3-none-any.whl (158 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.3/158.3 kB 15.5 MB/s eta 0:00:00 Downloading charset_normalizer-3.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (141 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 141.1/141.1 kB 14.1 MB/s eta 0:00:00 Using cached llvmlite-0.41.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.6 MB) Downloading urllib3-2.0.7-py3-none-any.whl (124 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 124.2/124.2 kB 6.4 MB/s eta 0:00:00 Using cached importlib_metadata-6.8.0-py3-none-any.whl (22 kB) Using cached stdlib_list-0.9.0-py3-none-any.whl (75 kB) Using cached zipp-3.17.0-py3-none-any.whl (7.4 kB) Installing collected packages: tbb, 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-2023.7.22 charset-normalizer-3.3.2 cycler-0.12.1 dunamai-1.19.0 et-xmlfile-1.1.0 fonttools-4.44.0 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-0.9.0 tbb-2021.10.0 tensorly-0.8.1 threadpoolctl-3.2.0 tqdm-4.66.1 umap-learn-0.5.4 urllib3-2.0.7 xlrd-2.0.1 zipp-3.17.0 sh: 5: /home/omnipath/.cache/R/basilisk/1.13.4/liana/0.1.13/liana_cell2cell/etc/conda/activate.d/activate-r-base.sh: [[: not found 0%| | 0/16 [00:00