############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r sketchR -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data sketchR ### ############################################################################## ############################################################################## * checking for file 'sketchR/DESCRIPTION' ... OK * preparing 'sketchR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'sketchR.Rmd' using rmarkdown 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: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\sketchR\1.1.0\universal added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-h2466b09_7 ca-certificates conda-forge/win-64::ca-certificates-2024.7.4-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.46.0-h2466b09_0 libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1 openssl conda-forge/win-64::openssl-3.3.1-h2466b09_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython setuptools conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0 sqlite conda-forge/win-64::sqlite-3.46.0-h2466b09_0 tk conda-forge/win-64::tk-8.6.13-h5226925_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0 vc conda-forge/win-64::vc-14.3-h8a93ad2_20 vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/win-64::xz-5.2.6-h8d14728_0 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\sketchR\1.1.0\universal added / updated specs: - anndata=0.10.5.post1 - array-api-compat=1.4.1 - blosc=1.21.5 - bottleneck=1.3.7 - brotli-bin=1.1.0 - brotli=1.1.0 - bzip2=1.0.8 - ca-certificates=2023.11.17 - cached-property=1.5.2 - cached_property=1.5.2 - certifi=2023.11.17 - colorama=0.4.6 - contourpy=1.2.0 - cycler=0.12.1 - dunamai=1.19.0 - exceptiongroup=1.2.0 - fonttools=4.47.2 - freetype=2.12.1 - get_version=3.5.5 - git=2.43.0 - h5py=3.8.0 - hdf5=1.14.0 - importlib-metadata=7.0.1 - importlib_metadata=7.0.1 - intel-openmp=2024.0.0 - joblib=1.1.0 - jpeg=9e - kiwisolver=1.4.5 - krb5=1.21.2 - lcms2=2.12 - legacy-api-wrap=1.2 - lerc=3.0 - libaec=1.1.2 - libblas=3.9.0 - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 - libcurl=8.5.0 - libdeflate=1.10 - libffi=3.4.2 - libhwloc=2.9.3 - libiconv=1.17 - liblapack=3.9.0 - libpng=1.6.42 - libsqlite=3.44.2 - libssh2=1.11.0 - libtiff=4.3.0 - libwebp-base=1.3.2 - libwebp=1.3.2 - libxcb=1.13 - libxml2=2.12.4 - libzlib=1.2.13 - llvmlite=0.40.1 - lz4-c=1.9.4 - m2w64-gcc-libgfortran=5.3.0 - m2w64-gcc-libs-core=5.3.0 - m2w64-gcc-libs=5.3.0 - m2w64-gmp=6.1.0 - m2w64-libwinpthread-git=5.0.0.4634.697f757 - matplotlib-base=3.6.3 - mkl=2024.0.0 - msys2-conda-epoch=20160418 - munkres=1.0.7 - natsort=8.4.0 - networkx=3.2 - numba=0.57.1 - numexpr=2.7.3 - numpy=1.21.5 - openjpeg=2.5.0 - openssl=3.2.1 - packaging=23.2 - pandas=1.3.5 - patsy=0.5.6 - pillow=9.1.1 - pip=23.3.2 - pthread-stubs=0.4 - pthreads-win32=2.9.1 - pynndescent=0.5.11 - pyparsing=3.1.1 - pytables=3.7.0 - python-dateutil=2.8.2 - python[version='3.9.12.*,3.9.12.*'] - python_abi=3.9 - pytz=2023.4 - scanpy=1.7.2 - scikit-learn=1.0.2 - scipy=1.7.3 - seaborn-base=0.13.2 - seaborn=0.13.2 - setuptools-scm=8.0.4 - setuptools=69.0.3 - setuptools_scm=8.0.4 - sinfo=0.3.1 - six=1.16.0 - snappy=1.1.10 - sqlite=3.44.2 - statsmodels=0.13.5 - stdlib-list=0.10.0 - tbb=2021.11.0 - threadpoolctl=3.0.0 - tk=8.6.13 - tomli=2.0.1 - tqdm=4.66.1 - typing-extensions=4.9.0 - typing_extensions=4.9.0 - tzdata=2023d - ucrt=10.0.22621.0 - umap-learn=0.5.5 - unicodedata2=15.1.0 - vc14_runtime=14.38.33130 - vc=14.3 - vs2015_runtime=14.38.33130 - wheel=0.42.0 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xz=5.2.6 - zipp=3.17.0 - zlib=1.2.13 - zstd=1.5.5 The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.10.5.post1-pyhd8ed1ab_0 array-api-compat conda-forge/noarch::array-api-compat-1.4.1-pyhd8ed1ab_0 blosc conda-forge/win-64::blosc-1.21.5-hdccc3a2_0 bottleneck conda-forge/win-64::bottleneck-1.3.7-py39hc266a54_0 brotli conda-forge/win-64::brotli-1.1.0-hcfcfb64_1 brotli-bin conda-forge/win-64::brotli-bin-1.1.0-hcfcfb64_1 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 certifi conda-forge/noarch::certifi-2023.11.17-pyhd8ed1ab_2 colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 contourpy conda-forge/win-64::contourpy-1.2.0-py39h1f6ef14_0 cycler conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0 dunamai conda-forge/noarch::dunamai-1.19.0-pyhd8ed1ab_0 exceptiongroup conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2 fonttools conda-forge/win-64::fonttools-4.47.2-py39ha55989b_0 freetype conda-forge/win-64::freetype-2.12.1-hdaf720e_2 get_version conda-forge/noarch::get_version-3.5.5-pyhd8ed1ab_0 git conda-forge/win-64::git-2.43.0-h57928b3_1 h5py conda-forge/win-64::h5py-3.8.0-nompi_py39h8a0c37c_101 hdf5 conda-forge/win-64::hdf5-1.14.0-nompi_h918d9b7_103 importlib-metadata conda-forge/noarch::importlib-metadata-7.0.1-pyha770c72_0 importlib_metadata conda-forge/noarch::importlib_metadata-7.0.1-hd8ed1ab_0 intel-openmp conda-forge/win-64::intel-openmp-2024.0.0-h57928b3_49841 joblib conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0 jpeg conda-forge/win-64::jpeg-9e-hcfcfb64_3 kiwisolver conda-forge/win-64::kiwisolver-1.4.5-py39h1f6ef14_1 krb5 conda-forge/win-64::krb5-1.21.2-heb0366b_0 lcms2 conda-forge/win-64::lcms2-2.12-h2a16943_0 legacy-api-wrap conda-forge/noarch::legacy-api-wrap-1.2-py_0 lerc conda-forge/win-64::lerc-3.0-h0e60522_0 libaec conda-forge/win-64::libaec-1.1.2-h63175ca_1 libblas conda-forge/win-64::libblas-3.9.0-21_win64_mkl libbrotlicommon conda-forge/win-64::libbrotlicommon-1.1.0-hcfcfb64_1 libbrotlidec conda-forge/win-64::libbrotlidec-1.1.0-hcfcfb64_1 libbrotlienc conda-forge/win-64::libbrotlienc-1.1.0-hcfcfb64_1 libcblas conda-forge/win-64::libcblas-3.9.0-21_win64_mkl libcurl conda-forge/win-64::libcurl-8.5.0-hd5e4a3a_0 libdeflate conda-forge/win-64::libdeflate-1.10-h8ffe710_0 libhwloc conda-forge/win-64::libhwloc-2.9.3-default_haede6df_1009 libiconv conda-forge/win-64::libiconv-1.17-hcfcfb64_2 liblapack conda-forge/win-64::liblapack-3.9.0-21_win64_mkl libpng conda-forge/win-64::libpng-1.6.42-h19919ed_0 libssh2 conda-forge/win-64::libssh2-1.11.0-h7dfc565_0 libtiff conda-forge/win-64::libtiff-4.3.0-hc4061b1_4 libwebp conda-forge/win-64::libwebp-1.3.2-hcfcfb64_1 libwebp-base conda-forge/win-64::libwebp-base-1.3.2-hcfcfb64_1 libxcb conda-forge/win-64::libxcb-1.13-hcd874cb_1004 libxml2 conda-forge/win-64::libxml2-2.12.4-hc3477c8_1 llvmlite conda-forge/win-64::llvmlite-0.40.1-py39hd28a505_0 lz4-c conda-forge/win-64::lz4-c-1.9.4-hcfcfb64_0 m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6 m2w64-gcc-libs conda-forge/win-64::m2w64-gcc-libs-5.3.0-7 m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7 m2w64-gmp conda-forge/win-64::m2w64-gmp-6.1.0-2 m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2 matplotlib-base conda-forge/win-64::matplotlib-base-3.6.3-py39haf65ace_0 mkl conda-forge/win-64::mkl-2024.0.0-h66d3029_49657 msys2-conda-epoch conda-forge/win-64::msys2-conda-epoch-20160418-1 munkres bioconda/noarch::munkres-1.0.7-py_1 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 networkx conda-forge/noarch::networkx-3.2-pyhd8ed1ab_0 numba conda-forge/win-64::numba-0.57.1-py39hadaa1c4_0 numexpr conda-forge/win-64::numexpr-2.7.3-py39h2e25243_2 numpy conda-forge/win-64::numpy-1.21.5-py39h6331f09_1 openjpeg conda-forge/win-64::openjpeg-2.5.0-hb211442_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 pandas pkgs/main/win-64::pandas-1.3.5-py39h6214cd6_0 patsy conda-forge/noarch::patsy-0.5.6-pyhd8ed1ab_0 pillow conda-forge/win-64::pillow-9.1.1-py39ha53f419_0 pthread-stubs conda-forge/win-64::pthread-stubs-0.4-hcd874cb_1001 pthreads-win32 conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3 pynndescent conda-forge/noarch::pynndescent-0.5.11-pyhca7485f_0 pyparsing conda-forge/noarch::pyparsing-3.1.1-pyhd8ed1ab_0 pytables conda-forge/win-64::pytables-3.7.0-py39h33f4363_4 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/win-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2023.4-pyhd8ed1ab_0 scanpy bioconda/noarch::scanpy-1.7.2-pyhdfd78af_0 scikit-learn conda-forge/win-64::scikit-learn-1.0.2-py39he931e04_0 scipy conda-forge/win-64::scipy-1.7.3-py39hfbf2dce_1 seaborn conda-forge/noarch::seaborn-0.13.2-hd8ed1ab_2 seaborn-base conda-forge/noarch::seaborn-base-0.13.2-pyhd8ed1ab_2 setuptools-scm conda-forge/noarch::setuptools-scm-8.0.4-pyhd8ed1ab_1 setuptools_scm conda-forge/noarch::setuptools_scm-8.0.4-hd8ed1ab_1 sinfo conda-forge/noarch::sinfo-0.3.1-py_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 snappy conda-forge/win-64::snappy-1.1.10-hfb803bf_1 statsmodels conda-forge/win-64::statsmodels-0.13.5-py39hc266a54_2 stdlib-list conda-forge/noarch::stdlib-list-0.10.0-pyhd8ed1ab_0 tbb conda-forge/win-64::tbb-2021.11.0-h91493d7_1 threadpoolctl conda-forge/noarch::threadpoolctl-3.0.0-pyh8a188c0_0 tomli conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0 tqdm conda-forge/noarch::tqdm-4.66.1-pyhd8ed1ab_0 typing-extensions conda-forge/noarch::typing-extensions-4.9.0-hd8ed1ab_0 typing_extensions conda-forge/noarch::typing_extensions-4.9.0-pyha770c72_0 umap-learn conda-forge/win-64::umap-learn-0.5.5-py39hcbf5309_1 unicodedata2 conda-forge/win-64::unicodedata2-15.1.0-py39ha55989b_0 xorg-libxau conda-forge/win-64::xorg-libxau-1.0.11-hcd874cb_0 xorg-libxdmcp conda-forge/win-64::xorg-libxdmcp-1.1.3-hcd874cb_0 zipp conda-forge/noarch::zipp-3.17.0-pyhd8ed1ab_0 zlib conda-forge/win-64::zlib-1.2.13-h2466b09_6 zstd conda-forge/win-64::zstd-1.5.5-h12be248_0 The following packages will be DOWNGRADED: ca-certificates 2024.7.4-h56e8100_0 --> 2023.11.17-h56e8100_0 libsqlite 3.46.0-h2466b09_0 --> 3.44.2-hcfcfb64_0 libzlib 1.3.1-h2466b09_1 --> 1.2.13-h2466b09_6 openssl 3.3.1-h2466b09_1 --> 3.2.1-h2466b09_2 pip 24.0-pyhd8ed1ab_0 --> 23.3.2-pyhd8ed1ab_0 setuptools 70.3.0-pyhd8ed1ab_0 --> 69.0.3-pyhd8ed1ab_0 sqlite 3.46.0-h2466b09_0 --> 3.44.2-hcfcfb64_0 tzdata 2024a-h0c530f3_0 --> 2023d-h0c530f3_0 vc 14.3-h8a93ad2_20 --> 14.3-hcf57466_20 vc14_runtime 14.40.33810-ha82c5b3_20 --> 14.38.33130-h16ead72_20 vs2015_runtime 14.40.33810-h3bf8584_20 --> 14.38.33130-hcb4865c_20 wheel 0.43.0-pyhd8ed1ab_1 --> 0.42.0-pyhd8ed1ab_0 Preparing transaction: ...working... done Verifying transaction: ...working... failed CondaVerificationError: The package for scanpy located at C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\0\pkgs\scanpy-1.7.2-pyhdfd78af_0 appears to be corrupted. The path 'site-packages/scanpy/tests/_images/embedding-missing-values/test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_data-groups.all].png' specified in the package manifest cannot be found. CondaVerificationError: The package for scanpy located at C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\0\pkgs\scanpy-1.7.2-pyhdfd78af_0 appears to be corrupted. The path 'site-packages/scanpy/tests/_images/embedding-missing-values/test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.False-legend.on_right-groups.all].png' specified in the package manifest cannot be found. CondaVerificationError: The package for scanpy located at C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\0\pkgs\scanpy-1.7.2-pyhdfd78af_0 appears to be corrupted. The path 'site-packages/scanpy/tests/_images/embedding-missing-values/test_missing_values_categorical[spatial-na_color.black_tup-na_in_legend.True-legend.on_right-groups.all].png' specified in the package manifest cannot be found. ClobberError: This transaction has incompatible packages due to a shared path. packages: conda-forge/win-64::git-2.43.0-h57928b3_1, conda-forge/win-64::git-2.43.0-h57928b3_1 path: 'menu/menu-windows.json' Quitting from lines 134-138 [unnamed-chunk-4] (sketchR.Rmd) Error: processing vignette 'sketchR.Rmd' failed with diagnostics: one or more Python packages failed to install [error code 1] --- failed re-building 'sketchR.Rmd' SUMMARY: processing the following file failed: 'sketchR.Rmd' Error: Vignette re-building failed. Execution halted