Multiple platform build/check report for BioC 3.19 - BUILD results for velociraptor on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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 kjohnson3

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: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data velociraptor

StartedAt: 2024-06-10 06:29:27 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 06:34:21 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 293.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R 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... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/velociraptor/1.14.0/env

  added / updated specs:
    - python=3.8


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.6.2-hf0a4a13_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.45.3-h091b4b1_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.8.19-h2469fbe_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_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... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - kiwisolver=1.2.0
  - umap-learn=0.4.6
  - numexpr=2.7.1
  - statsmodels=0.12.0
  - matplotlib=3.3.1
  - llvmlite=0.34.0
  - numpy=1.19.1
  - stdlib-list=0.6.0
  - numba=0.51.2
  - anndata=0.7.4
  - cffi=1.14.1
  - tornado=6.0.4
  - pillow=7.2.0
  - pandas=1.1.2

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



Quitting from lines 70-73 [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