Multiple platform build/check report for BioC 3.22 - BUILD results for orthos on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4596
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4538
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4536
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 orthos on nebbiolo2

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.

raw results

Summary

Package: orthos

Version: 1.7.2

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 orthos

StartedAt: 2025-08-18 18:40:17 -0400 (Mon, 18 Aug 2025)

EndedAt: 2025-08-18 18:41:57 -0400 (Mon, 18 Aug 2025)

EllapsedTime: 100.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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
2025-08-18 18:41:22.075413: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2025-08-18 18:41:22.149252: I external/local_tsl/tsl/cuda/cudart_stub.cc:31] Could not find cuda drivers on your machine, GPU will not be used.
2025-08-18 18:41:22.582425: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2025-08-18 18:41:22.582517: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2025-08-18 18:41:22.630788: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2025-08-18 18:41:22.726184: I external/local_tsl/tsl/cuda/cudart_stub.cc:31] Could not find cuda drivers on your machine, GPU will not be used.
2025-08-18 18:41:22.726866: I tensorflow/core/platform/cpu_feature_guard.cc:182] 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.
2025-08-18 18:41:24.248516: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT

Quitting from orthosIntro.Rmd:280-285 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: EH7869
  title: ContextEncoder_Human
  reason: 
---
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(...)
  8.           │ └─base::eval(call, callEnv)
  9.           │   └─base::eval(call, callEnv)
 10.           └─AnnotationHub (local) .nextMethod(...)
 11.             └─AnnotationHub (local) .local(x, i, j = j, ...)
 12.               └─AnnotationHub:::.Hub_get1(...)
 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: 
--- failed re-building ‘orthosIntro.Rmd’

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

Error: Vignette re-building failed.
Execution halted