Panagiotis Papasaikas
| Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 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 2025-09-29 11:41 -0400 (Mon, 29 Sep 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" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
| 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: 2025-09-26 04:38:21 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 04:47:20 -0000 (Fri, 26 Sep 2025) |
| EllapsedTime: 538.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos
###
##############################################################################
##############################################################################
* 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
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos
added / updated specs:
- python=3.12
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h4777abc_8
ca-certificates conda-forge/noarch::ca-certificates-2025.8.3-hbd8a1cb_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.44-h9df1782_2
libexpat conda-forge/linux-aarch64::libexpat-2.7.1-hfae3067_0
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1
libgcc conda-forge/linux-aarch64::libgcc-15.1.0-he277a41_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_5
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_5
liblzma conda-forge/linux-aarch64::liblzma-5.8.1-h86ecc28_2
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h86ecc28_1
libsqlite conda-forge/linux-aarch64::libsqlite-3.50.4-h022381a_0
libuuid conda-forge/linux-aarch64::libuuid-2.41.2-h3e4203c_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.5.3-h8e36d6e_1
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
python conda-forge/linux-aarch64::python-3.12.11-h1683364_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8382b9d_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/linux-aarch64::tk-8.6.13-noxft_h5688188_102
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.7.0
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.7.0
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
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Requirement already satisfied: pip==25.2 in /home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos/lib/python3.12/site-packages (25.2)
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Requirement already satisfied: setuptools==80.9.0 in /home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos/lib/python3.12/site-packages (80.9.0)
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Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
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Collecting tensorflow==2.19.0
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Using cached werkzeug-3.1.3-py3-none-any.whl.metadata (3.7 kB)
Requirement already satisfied: wheel==0.45.1 in /home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos/lib/python3.12/site-packages (0.45.1)
Collecting wrapt==1.17.3
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Installing collected packages: pytz, namex, libclang, flatbuffers, wrapt, urllib3, tzdata, typing_extensions, termcolor, tensorboard-data-server, six, Pygments, protobuf, pillow, packaging, opt_einsum, numpy, mdurl, MarkupSafe, Markdown, idna, grpcio, gast, charset-normalizer, certifi, absl-py, Werkzeug, requests, python-dateutil, optree, ml_dtypes, markdown-it-py, h5py, google-pasta, astunparse, tensorboard, rich, pandas, keras, tensorflow, tf-keras
Successfully installed Markdown-3.8.2 MarkupSafe-3.0.2 Pygments-2.19.2 Werkzeug-3.1.3 absl-py-2.3.1 astunparse-1.6.3 certifi-2025.8.3 charset-normalizer-3.4.3 flatbuffers-25.2.10 gast-0.6.0 google-pasta-0.2.0 grpcio-1.74.0 h5py-3.14.0 idna-3.10 keras-3.11.3 libclang-18.1.1 markdown-it-py-4.0.0 mdurl-0.1.2 ml_dtypes-0.5.3 namex-0.1.0 numpy-1.26.4 opt_einsum-3.4.0 optree-0.17.0 packaging-25.0 pandas-2.3.2 pillow-11.3.0 protobuf-5.29.5 python-dateutil-2.9.0.post0 pytz-2025.2 requests-2.32.5 rich-14.1.0 six-1.17.0 tensorboard-2.19.0 tensorboard-data-server-0.7.2 tensorflow-2.19.0 termcolor-3.1.0 tf-keras-2.19.0 typing_extensions-4.15.0 tzdata-2025.2 urllib3-2.5.0 wrapt-1.17.3
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