Multiple platform build/check report for BioC 3.20 - BUILD results for DeProViR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 DeProViR on kjohnson3

To the developers/maintainers of the DeProViR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeProViR.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: DeProViR

Version: 1.2.0

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

StartedAt: 2024-11-08 16:51:16 -0500 (Fri, 08 Nov 2024)

EndedAt: 2024-11-08 16:59:55 -0500 (Fri, 08 Nov 2024)

EllapsedTime: 518.3 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 DeProViR
###
##############################################################################
##############################################################################


* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* preparing ‘DeProViR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DeProViR_tutorial.Rmd’ using rmarkdown
/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/urllib3/__init__.py:35: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
  warnings.warn(

Quitting from lines 218-246 [unnamed-chunk-2] (DeProViR_tutorial.Rmd)
Error: processing vignette 'DeProViR_tutorial.Rmd' failed with diagnostics:
ValueError: Unrecognized keyword arguments passed to Embedding: {'input_length': 1000, 'weights': [array([[ 0.      ,  0.      ,  0.      , ...,  0.      ,  0.      ,
         0.      ],
       [-0.45433 ,  1.0234  ,  0.024278, ..., -0.43769 ,  1.0169  ,
        -0.26706 ],
       [-0.27086 ,  0.044006, -0.02026 , ..., -0.4923  ,  0.63687 ,
         0.23642 ],
       ...,
       [-0.20314 ,  0.50467 , -0.25223 , ..., -0.34618 , -0.18627 ,
        -0.31606 ],
       [ 0.29492 ,  0.56874 , -0.20245 , ..., -0.16875 ,  0.51895 ,
        -0.50086 ],
       [-0.11752 ,  0.97272 , -0.29021 , ..., -0.50598 , -0.28476 ,
        -0.70045 ]])]}
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘DeProViR_tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘DeProViR_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted