| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-18 11:45 -0400 (Tue, 18 Mar 2025).
| 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" | 4537 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
| 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 | ||||
| Package 1428/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NeuCA 1.13.0 (landing page) Hao Feng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the NeuCA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NeuCA.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. |
| Package: NeuCA |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NeuCA |
| StartedAt: 2025-03-17 17:48:24 -0400 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 17:49:52 -0400 (Mon, 17 Mar 2025) |
| EllapsedTime: 87.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 NeuCA
###
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* checking for file ‘NeuCA/DESCRIPTION’ ... OK
* preparing ‘NeuCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NeuCA.Rmd’ using rmarkdown
2025-03-17 17:49:19.307118: 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/dense.py:87: UserWarning: Do not pass an `input_shape`/`input_dim` argument to a layer. When using Sequential models, prefer using an `Input(shape)` object as the first layer in the model instead.
super().__init__(activity_regularizer=activity_regularizer, **kwargs)
Quitting from NeuCA.Rmd:75-80 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ValueError: Only input tensors may be passed as positional arguments. The following argument value should be passed as a keyword argument: <Sequential name=sequential, built=False> (of type <class 'keras.src.models.sequential.Sequential'>)
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. ├─NeuCA::NeuCA(...)
2. │ └─NeuCA:::BigNN(...)
3. │ └─... %>% ...
4. ├─generics::compile(...)
5. ├─keras::layer_dense(., units = nClass, activation = last_act)
6. │ └─keras::create_layer(...)
7. ├─keras::layer_dense(., units = 64, activation = "relu")
8. │ └─keras::create_layer(...)
9. ├─keras::layer_dense(., units = 128, activation = "relu")
10. │ └─keras::create_layer(...)
11. └─keras::layer_dense(., units = 256, activation = "relu", input_shape = ncol(train_count))
12. └─keras::create_layer(...)
13. ├─keras:::compose_layer(object, layer)
14. └─keras:::compose_layer.default(object, layer)
15. └─reticulate (local) layer(object, ...)
16. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'NeuCA.Rmd' failed with diagnostics:
ValueError: Only input tensors may be passed as positional arguments. The following argument value should be passed as a keyword argument: <Sequential name=sequential, built=False> (of type <class 'keras.src.models.sequential.Sequential'>)
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘NeuCA.Rmd’
SUMMARY: processing the following file failed:
‘NeuCA.Rmd’
Error: Vignette re-building failed.
Execution halted