Multiple platform build/check report for BioC 3.21 - BUILD results for ttgsea on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4547
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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 ttgsea on kjohnson3

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

Version: 1.15.0

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

StartedAt: 2025-03-21 17:57:54 -0400 (Fri, 21 Mar 2025)

EndedAt: 2025-03-21 17:58:12 -0400 (Fri, 21 Mar 2025)

EllapsedTime: 17.2 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 ttgsea
###
##############################################################################
##############################################################################


* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* preparing ‘ttgsea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ttgsea.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 ttgsea.Rmd:89-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ValueError: Unrecognized keyword arguments passed to Embedding: {'input_length': 30}
Run `reticulate::py_last_error()` for details.
---
Backtrace:
     ▆
  1. ├─ttgsea::fit_model(...)
  2. │ └─model %>% ...
  3. ├─keras::fit(., x_train, y_train, batch_size, epochs, ...)
  4. ├─ttgsea::bi_lstm(num_tokens, embedding_dim, length_seq, num_units)
  5. │ └─... %>% keras::layer_dense(1)
  6. ├─keras::layer_dense(., 1)
  7. │ └─keras::create_layer(...)
  8. ├─keras::bidirectional(...)
  9. │ └─keras::create_layer(keras$layers$Bidirectional, object, args)
 10. └─keras::layer_embedding(...)
 11.   └─keras::create_layer(keras$layers$Embedding, object, args)
 12.     ├─base::do.call(layer_class, args)
 13.     └─reticulate (local) `<python.builtin.type>`(...)
 14.       └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ttgsea.Rmd' failed with diagnostics:
ValueError: Unrecognized keyword arguments passed to Embedding: {'input_length': 30}
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘ttgsea.Rmd’

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

Error: Vignette re-building failed.
Execution halted