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

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
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"	4459
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 lconway

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: 2025-03-16 18:53:56 -0400 (Sun, 16 Mar 2025)

EndedAt: 2025-03-16 18:54:39 -0400 (Sun, 16 Mar 2025)

EllapsedTime: 42.3 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 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
2025-03-16 18:54:27.837716: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/Users/biocbuild/.virtualenvs/r-keras/lib/python3.9/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(
/Users/biocbuild/.virtualenvs/r-keras/lib/python3.9/site-packages/keras/src/layers/core/embedding.py:90: UserWarning: Argument `input_length` is deprecated. Just remove it.
  warnings.warn(

Quitting from ttgsea.Rmd:89-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'compile' applied to an object of class "c('keras.src.models.functional.Functional', 'keras.models.functional.Functional', 'keras.src.ops.function.Function', 'keras.ops.function.Function', 'keras.src.models.model.Model', 'keras.models.model.Model', 'keras.src.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.src.trainers.trainer.Trainer', 'keras.trainers.trainer.Trainer', 'keras.src.layers.layer.Layer', 'keras.layers.layer.Layer', 'keras.src.backend.tensorflow.layer.TFLayer', 'keras.backend.tensorflow.layer.TFLayer', 'keras.src.backend.tensorflow.trackable.KerasAutoTrackable', 'keras.backend.tensorflow.trackable.KerasAutoTrackable', 'tensorflow.python.trackable.autotrackable.AutoTrackable', 'tensorflow.python.trackable.base.Trackable', 'keras.src.ops.operation.Operation', 'keras.ops.operation.Operation', 'keras.src.saving.keras_saveable.KerasSaveable', 'keras.saving.keras_saveable.KerasSaveable', 'python.builtin.object')"
---
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. │ └─model %>% ...
 6. └─keras::compile(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ttgsea.Rmd' failed with diagnostics:
no applicable method for 'compile' applied to an object of class "c('keras.src.models.functional.Functional', 'keras.models.functional.Functional', 'keras.src.ops.function.Function', 'keras.ops.function.Function', 'keras.src.models.model.Model', 'keras.models.model.Model', 'keras.src.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.src.trainers.trainer.Trainer', 'keras.trainers.trainer.Trainer', 'keras.src.layers.layer.Layer', 'keras.layers.layer.Layer', 'keras.src.backend.tensorflow.layer.TFLayer', 'keras.backend.tensorflow.layer.TFLayer', 'keras.src.backend.tensorflow.trackable.KerasAutoTrackable', 'keras.backend.tensorflow.trackable.KerasAutoTrackable', 'tensorflow.python.trackable.autotrackable.AutoTrackable', 'tensorflow.python.trackable.base.Trackable', 'keras.src.ops.operation.Operation', 'keras.ops.operation.Operation', 'keras.src.saving.keras_saveable.KerasSaveable', 'keras.saving.keras_saveable.KerasSaveable', 'python.builtin.object')"
--- failed re-building ‘ttgsea.Rmd’

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

Error: Vignette re-building failed.
Execution halted