##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SingleCellAlleleExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SingleCellAlleleExperiment_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SingleCellAlleleExperiment.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SingleCellAlleleExperiment/DESCRIPTION’ ... OK
* this is package ‘SingleCellAlleleExperiment’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleCellAlleleExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
SingleCellAlleleExperiment 51.053  6.626  58.514
scae_subset                38.563  5.812  45.162
read_allele_counts         31.413  5.616  37.746
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘scae_intro.Rmd’ using rmarkdown

Quitting from scae_intro.Rmd:154-156 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: EH9456
  title: pbmc_10k_barcodes.txt
  reason: 1 resources failed to download
---
Backtrace:
     ▆
  1. └─scaeData::scaeDataGet(dataset = "pbmc_10k")
  2.   ├─scaeData:::ehub_out(get_barcodes_10k(), get_features_10k(), get_counts_10k())
  3.   │ └─scaeData:::demo_dir_file(bc_dir, dir = TRUE)
  4.   │   └─base::sub(".*/", "", ehub_dir)
  5.   │     └─base::is.factor(x)
  6.   └─scaeData:::get_barcodes_10k()
  7.     ├─base::suppressMessages(eh[["EH9456"]])
  8.     │ └─base::withCallingHandlers(...)
  9.     ├─eh[["EH9456"]]
 10.     └─eh[["EH9456"]]
 11.       └─ExperimentHub (local) .local(x, i, j = j, ...)
 12.         ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
 13.         │ └─base::eval(call, callEnv)
 14.         │   └─base::eval(call, callEnv)
 15.         └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
 16.           └─AnnotationHub (local) .local(x, i, j = j, ...)
 17.             └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 18.               └─base::tryCatch(...)
 19.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 20.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21.                     └─value[[3L]](cond)
 22.                       └─base::tryCatch(...)
 23.                         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 24.                           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 25.                             └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scae_intro.Rmd' failed with diagnostics:
failed to load resource
  name: EH9456
  title: pbmc_10k_barcodes.txt
  reason: 1 resources failed to download
--- failed re-building ‘scae_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SingleCellAlleleExperiment.Rcheck/00check.log’
for details.