Multiple platform build/check report for BioC 3.20 - BUILD results for velociraptor on palomino6

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4677
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4416
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4444
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4393
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4373
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 velociraptor on palomino6

To the developers/maintainers of the velociraptor package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/velociraptor.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: velociraptor
Version: 1.15.4
Command: chmod a+r velociraptor -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data velociraptor
StartedAt: 2024-07-15 21:23:59 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 21:34:33 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 633.9 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r velociraptor -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data velociraptor
###
##############################################################################
##############################################################################


* checking for file 'velociraptor/DESCRIPTION' ... OK
* preparing 'velociraptor':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'velociraptor.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\velociraptor\1.15.4\env

  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\velociraptor\1.15.4\env

  added / updated specs:
    - anndata=0.10.5.post1
    - array-api-compat=1.6
    - blosc=1.21.5
    - brotli-bin=1.1.0
    - brotli=1.1.0
    - bzip2=1.0.8
    - ca-certificates=2024.2.2
    - cached-property=1.5.2
    - cached_property=1.5.2
    - certifi=2024.2.2
    - colorama=0.4.6
    - contourpy=1.2.1
    - cycler=0.12.1
    - exceptiongroup=1.2.0
    - fonttools=4.51.0
    - freetype=2.12.1
    - glib-tools=2.80.2
    - glib=2.80.2
    - gst-plugins-base=1.24.3
    - gstreamer=1.24.3
    - h5py=3.8.0
    - hdf5=1.14.0
    - icu=73.2
    - importlib-metadata=7.1.0
    - importlib_metadata=7.1.0
    - intel-openmp=2024.1.0
    - joblib=1.4.2
    - kiwisolver=1.4.5
    - krb5=1.21.2
    - lcms2=2.16
    - legacy-api-wrap=1.4
    - lerc=4.0.0
    - libaec=1.1.3
    - libblas=3.9.0
    - libbrotlicommon=1.1.0
    - libbrotlidec=1.1.0
    - libbrotlienc=1.1.0
    - libcblas=3.9.0
    - libclang13=18.1.5
    - libcurl=8.8.0
    - libdeflate=1.20
    - libffi=3.4.2
    - libglib=2.80.2
    - libhwloc=2.10.0
    - libiconv=1.17
    - libintl-devel=0.22.5
    - libintl=0.22.5
    - libjpeg-turbo=3.0.0
    - liblapack=3.9.0
    - libogg=1.3.4
    - libpng=1.6.43
    - libsqlite=3.45.3
    - libssh2=1.11.0
    - libtiff=4.6.0
    - libvorbis=1.3.7
    - libwebp-base=1.4.0
    - libxcb=1.15
    - libxml2=2.12.7
    - libzlib=1.2.13
    - llvmlite=0.40.1
    - loompy=2.0.16
    - 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
    - matplotlib=3.6.3
    - mkl=2024.1.0
    - msys2-conda-epoch=20160418
    - munkres=1.0.7
    - natsort=8.4.0
    - networkx=3.2
    - numba=0.57.1
    - numexpr=2.7.3
    - numpy=1.21.1
    - openjpeg=2.5.2
    - openssl=3.3.0
    - packaging=24.0
    - pandas=1.5.2
    - patsy=0.5.6
    - pcre2=10.43
    - pillow=10.3.0
    - pip=24.0
    - ply=3.11
    - pthread-stubs=0.4
    - pthreads-win32=2.9.1
    - pynndescent=0.5.12
    - pyparsing=3.1.2
    - pyqt5-sip=12.12.2
    - pyqt=5.15.9
    - pytables=3.7.0
    - python-dateutil=2.9.0
    - python[version='3.9.12.*,3.9.12.*']
    - python_abi=3.9
    - pytz=2024.1
    - qt-main=5.15.8
    - scanpy=1.7.2
    - scikit-learn=1.5.0
    - scipy=1.13.1
    - scvelo=0.2.5
    - seaborn-base=0.13.2
    - seaborn=0.13.2
    - setuptools-scm=8.1.0
    - setuptools=70.0.0
    - setuptools_scm=8.1.0
    - sinfo=0.3.1
    - sip=6.7.12
    - six=1.16.0
    - snappy=1.2.0
    - sqlite=3.45.3
    - statsmodels=0.14.2
    - stdlib-list=0.10.0
    - tbb=2021.12.0
    - threadpoolctl=3.5.0
    - tk=8.6.13
    - toml=0.10.2
    - tomli=2.0.1
    - tornado=6.4
    - tqdm=4.66.4
    - typing-extensions=4.11.0
    - typing=3.10.0.0
    - typing_extensions=4.11.0
    - tzdata=2024a
    - ucrt=10.0.22621.0
    - umap-learn=0.5.5
    - unicodedata2=15.1.0
    - vc14_runtime=14.38.33135
    - vc=14.3
    - vs2015_runtime=14.38.33135
    - wheel=0.43.0
    - xorg-libxau=1.0.11
    - xorg-libxdmcp=1.1.3
    - xz=5.2.6
    - zipp=3.17.0
    - zstd=1.5.6


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-1.6-pyhd8ed1ab_0
  blosc              conda-forge/win-64::blosc-1.21.5-hbd69f2e_1
  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-2024.2.2-pyhd8ed1ab_0
  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
  contourpy          conda-forge/win-64::contourpy-1.2.1-py39h1f6ef14_0
  cycler             conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0
  exceptiongroup     conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2
  fonttools          conda-forge/win-64::fonttools-4.51.0-py39ha55989b_0
  freetype           conda-forge/win-64::freetype-2.12.1-hdaf720e_2
  glib               conda-forge/win-64::glib-2.80.2-h0df6a38_0
  glib-tools         conda-forge/win-64::glib-tools-2.80.2-h2f9d560_0
  gst-plugins-base   conda-forge/win-64::gst-plugins-base-1.24.3-hba88be7_0
  gstreamer          conda-forge/win-64::gstreamer-1.24.3-h5006eae_0
  h5py               conda-forge/win-64::h5py-3.8.0-nompi_py39h8a0c37c_101
  hdf5               conda-forge/win-64::hdf5-1.14.0-nompi_h918d9b7_103
  icu                conda-forge/win-64::icu-73.2-h63175ca_0
  importlib-metadata conda-forge/noarch::importlib-metadata-7.1.0-pyha770c72_0
  importlib_metadata conda-forge/noarch::importlib_metadata-7.1.0-hd8ed1ab_0
  intel-openmp       conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966
  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
  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::lcms2-2.16-h67d730c_0
  legacy-api-wrap    conda-forge/noarch::legacy-api-wrap-1.4-pyhd8ed1ab_1
  lerc               conda-forge/win-64::lerc-4.0.0-h63175ca_0
  libaec             conda-forge/win-64::libaec-1.1.3-h63175ca_0
  libblas            conda-forge/win-64::libblas-3.9.0-22_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-3.9.0-22_win64_mkl
  libclang13         conda-forge/win-64::libclang13-18.1.5-default_hf64faad_0
  libcurl            conda-forge/win-64::libcurl-8.8.0-hd5e4a3a_0
  libdeflate         conda-forge/win-64::libdeflate-1.20-hcfcfb64_0
  libglib            conda-forge/win-64::libglib-2.80.2-h0df6a38_0
  libhwloc           conda-forge/win-64::libhwloc-2.10.0-default_h8125262_1001
  libiconv           conda-forge/win-64::libiconv-1.17-hcfcfb64_2
  libintl            conda-forge/win-64::libintl-0.22.5-h5728263_2
  libintl-devel      conda-forge/win-64::libintl-devel-0.22.5-h5728263_2
  libjpeg-turbo      conda-forge/win-64::libjpeg-turbo-3.0.0-hcfcfb64_1
  liblapack          conda-forge/win-64::liblapack-3.9.0-22_win64_mkl
  libogg             conda-forge/win-64::libogg-1.3.4-h8ffe710_1
  libpng             conda-forge/win-64::libpng-1.6.43-h19919ed_0
  libssh2            conda-forge/win-64::libssh2-1.11.0-h7dfc565_0
  libtiff            conda-forge/win-64::libtiff-4.6.0-hddb2be6_3
  libvorbis          conda-forge/win-64::libvorbis-1.3.7-h0e60522_0
  libwebp-base       conda-forge/win-64::libwebp-base-1.4.0-hcfcfb64_0
  libxcb             conda-forge/win-64::libxcb-1.15-hcd874cb_0
  libxml2            conda-forge/win-64::libxml2-2.12.7-h283a6d9_1
  llvmlite           conda-forge/win-64::llvmlite-0.40.1-py39hd28a505_0
  loompy             bioconda/noarch::loompy-2.0.16-py_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         conda-forge/win-64::matplotlib-3.6.3-py39hcbf5309_0
  matplotlib-base    conda-forge/win-64::matplotlib-base-3.6.3-py39haf65ace_0
  mkl                conda-forge/win-64::mkl-2024.1.0-h66d3029_692
  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-1.21.1-py39h6635163_0
  openjpeg           conda-forge/win-64::openjpeg-2.5.2-h3d672ee_0
  packaging          conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0
  pandas             conda-forge/win-64::pandas-1.5.2-py39h2ba5b7c_2
  patsy              conda-forge/noarch::patsy-0.5.6-pyhd8ed1ab_0
  pcre2              conda-forge/win-64::pcre2-10.43-h17e33f8_0
  pillow             conda-forge/win-64::pillow-10.3.0-py39h9ee4981_0
  ply                conda-forge/noarch::ply-3.11-pyhd8ed1ab_2
  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-0.5.12-pyhca7485f_0
  pyparsing          conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0
  pyqt               conda-forge/win-64::pyqt-5.15.9-py39hb77abff_5
  pyqt5-sip          conda-forge/win-64::pyqt5-sip-12.12.2-py39h99910a6_5
  pytables           conda-forge/win-64::pytables-3.7.0-py39h33f4363_4
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
  python_abi         conda-forge/win-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  qt-main            conda-forge/win-64::qt-main-5.15.8-hcef0176_21
  scanpy             bioconda/noarch::scanpy-1.7.2-pyhdfd78af_0
  scikit-learn       conda-forge/win-64::scikit-learn-1.5.0-py39hdd013cc_1
  scipy              conda-forge/win-64::scipy-1.13.1-py39h1a10956_0
  scvelo             bioconda/noarch::scvelo-0.2.5-pyhdfd78af_0
  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-8.1.0-pyhd8ed1ab_0
  setuptools_scm     conda-forge/noarch::setuptools_scm-8.1.0-hd8ed1ab_0
  sinfo              conda-forge/noarch::sinfo-0.3.1-py_0
  sip                conda-forge/win-64::sip-6.7.12-py39h99910a6_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  snappy             conda-forge/win-64::snappy-1.2.0-hfb803bf_1
  statsmodels        conda-forge/win-64::statsmodels-0.14.2-py39h4b0a98a_0
  stdlib-list        conda-forge/noarch::stdlib-list-0.10.0-pyhd8ed1ab_0
  tbb                conda-forge/win-64::tbb-2021.12.0-hc790b64_1
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0
  toml               conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
  tomli              conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0
  tornado            conda-forge/win-64::tornado-6.4.1-py39ha55e580_0
  tqdm               conda-forge/noarch::tqdm-4.66.4-pyhd8ed1ab_0
  typing             conda-forge/noarch::typing-3.10.0.0-pyhd8ed1ab_1
  typing-extensions  conda-forge/noarch::typing-extensions-4.11.0-hd8ed1ab_0
  typing_extensions  conda-forge/noarch::typing_extensions-4.11.0-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
  zstd               conda-forge/win-64::zstd-1.5.6-h0ea2cb4_0

The following packages will be DOWNGRADED:

  ca-certificates                       2024.7.4-h56e8100_0 --> 2024.2.2-h56e8100_0
  libsqlite                               3.46.0-h2466b09_0 --> 3.45.3-hcfcfb64_0
  libzlib                                  1.3.1-h2466b09_1 --> 1.2.13-h2466b09_6
  openssl                                  3.3.1-h2466b09_1 --> 3.3.0-h2466b09_3
  setuptools                            70.3.0-pyhd8ed1ab_0 --> 70.0.0-pyhd8ed1ab_0
  sqlite                                  3.46.0-h2466b09_0 --> 3.45.3-hcfcfb64_0
  vc                                       14.3-h8a93ad2_20 --> 14.3-ha32ba9b_20
  vc14_runtime                      14.40.33810-ha82c5b3_20 --> 14.38.33135-h835141b_20
  vs2015_runtime                    14.40.33810-h3bf8584_20 --> 14.38.33135-h22015db_20


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.



Quitting from lines 76-82 [unnamed-chunk-5] (velociraptor.Rmd)
Error: processing vignette 'velociraptor.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building 'velociraptor.Rmd'

SUMMARY: processing the following file failed:
  'velociraptor.Rmd'

Error: Vignette re-building failed.
Execution halted