Panagiotis Papasaikas
| Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/orthos |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7a7da9f |
| git_last_commit_date: 2025-09-25 04:58:23 -0400 (Thu, 25 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-06 11:42 -0400 (Mon, 06 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
| 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 1507/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| orthos 1.6.1 (landing page) Panagiotis Papasaikas
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the orthos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/orthos.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: orthos |
| Version: 1.6.1 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos |
| StartedAt: 2025-10-03 03:16:53 -0000 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 03:21:26 -0000 (Fri, 03 Oct 2025) |
| EllapsedTime: 272.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos
###
##############################################################################
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* checking for file ‘orthos/DESCRIPTION’ ... OK
* preparing ‘orthos’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘orthosIntro.Rmd’ using rmarkdown
Quitting from orthosIntro.Rmd:280-285 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
name: EH7869
title: ContextEncoder_Human
reason: ValueError: File format not supported: filepath=/home/biocbuild/.cache/R/ExperimentHub/105fa62ab56edc_7919. Keras 3 only supports V3 `.keras` files and legacy H5 format files (`.h5` extension). Note that the legacy SavedModel format is not supported by `load_model()` in Keras 3. In order to reload a TensorFlow SavedModel as an inference-only layer in Keras 3, use `keras.layers.TFSMLayer(/home/biocbuild/.cache/R/ExperimentHub/105fa62ab56edc_7919, call_endpoint='serving_default')` (note that your `call_endpoint` might have a different name).
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. └─orthos::decomposeVar(...)
2. └─basilisk::basiliskRun(...)
3. └─orthos (local) fun(...)
4. ├─AnnotationHub::query(hub, query_keys)[[1]]
5. └─AnnotationHub::query(hub, query_keys)[[1]]
6. └─ExperimentHub (local) .local(x, i, j = j, ...)
7. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
8. │ └─base::eval(call, callEnv)
9. │ └─base::eval(call, callEnv)
10. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
11. └─AnnotationHub (local) .local(x, i, j = j, ...)
12. └─AnnotationHub:::.Hub_get1(x[i], force = force, verbose = verbose)
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─value[[3L]](cond)
17. └─base::tryCatch(...)
18. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
19. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'orthosIntro.Rmd' failed with diagnostics:
failed to load resource
name: EH7869
title: ContextEncoder_Human
reason: ValueError: File format not supported: filepath=/home/biocbuild/.cache/R/ExperimentHub/105fa62ab56edc_7919. Keras 3 only supports V3 `.keras` files and legacy H5 format files (`.h5` extension). Note that the legacy SavedModel format is not supported by `load_model()` in Keras 3. In order to reload a TensorFlow SavedModel as an inference-only layer in Keras 3, use `keras.layers.TFSMLayer(/home/biocbuild/.cache/R/ExperimentHub/105fa62ab56edc_7919, call_endpoint='serving_default')` (note that your `call_endpoint` might have a different name).
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘orthosIntro.Rmd’
SUMMARY: processing the following file failed:
‘orthosIntro.Rmd’
Error: Vignette re-building failed.
Execution halted