Multiple platform build/check report for BioC 3.22 - BUILD results for DeepPINCS on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 DeepPINCS on lconway

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

Version: 1.17.0

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

StartedAt: 2025-10-23 16:40:13 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 16:41:22 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 68.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DeepPINCS
###
##############################################################################
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* checking for file ‘DeepPINCS/DESCRIPTION’ ... OK
* preparing ‘DeepPINCS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DeepPINCS.Rmd’ using rmarkdown
2025-10-23 16:40:50.588117: 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(

Quitting from DeepPINCS.Rmd:81-108 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ValueError: For a `build()` method with more than one argument, all arguments should have a `_shape` suffix and match an argument from `call()`. E.g. `build(self, foo_shape, bar_shape)`  For layer 'MultiLinear', Received `build()` argument `self`, which does not end in `_shape`.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
     ▆
  1. ├─DeepPINCS::fit_cpi(...)
  2. │ ├─base::do.call(net_args$compound, net_args$compound_args)
  3. │ └─DeepPINCS::gcn_in_out(...)
  4. │   └─x %>% layer_multi_linear(units = temp_units) %>% ...
  5. ├─keras::layer_activation(., activation = gcn_activation[i])
  6. │ └─keras::create_layer(...)
  7. └─keras (local) layer_multi_linear(., units = temp_units)
  8.   └─keras::create_layer(Layer, object, args)
  9.     ├─keras:::compose_layer(object, layer)
 10.     └─keras:::compose_layer.default(object, layer)
 11.       └─reticulate (local) layer(object, ...)
 12.         └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DeepPINCS.Rmd' failed with diagnostics:
ValueError: For a `build()` method with more than one argument, all arguments should have a `_shape` suffix and match an argument from `call()`. E.g. `build(self, foo_shape, bar_shape)`  For layer 'MultiLinear', Received `build()` argument `self`, which does not end in `_shape`.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘DeepPINCS.Rmd’

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

Error: Vignette re-building failed.
Execution halted