Multiple platform build/check report for BioC 3.19 - BUILD results for sketchR on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4741
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4483
merida1	macOS 12.7.4 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4512
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD results for sketchR on palomino7

To the developers/maintainers of the sketchR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sketchR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: sketchR
Version: 1.0.0
Command: chmod a+r sketchR -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data sketchR
StartedAt: 2024-07-11 20:58:52 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 21:09:37 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 645.2 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r sketchR -R && E:\biocbuild\bbs-3.19-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\1.16.0\sketchR\1.0.0\universal

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
  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-70.2.0-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\1.16.0\sketchR\1.0.0\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                            70.2.0-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\116~1.0\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\116~1.0\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\116~1.0\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