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This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1507/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
orthos 1.6.0  (landing page)
Panagiotis Papasaikas
Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/orthos
git_branch: RELEASE_3_21
git_last_commit: 9656fce
git_last_commit_date: 2025-04-15 13:18:18 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped

BUILD results for orthos on nebbiolo1

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: 1.6.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos
StartedAt: 2025-08-31 18:32:43 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 18:34:41 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 118.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/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
2025-08-31 18:33:53.824445: 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`.
2025-08-31 18:33:54.170085: 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: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.

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(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: 
--- failed re-building ‘orthosIntro.Rmd’

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

Error: Vignette re-building failed.
Execution halted