##############################################################################
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###
### 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
###
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##############################################################################


* 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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SingleCellAlleleExperiment
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SingleCellAlleleExperiment’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleCellAlleleExperiment)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SingleCellAlleleExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> library(scaeData)
> 
> test_check("SingleCellAlleleExperiment")

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Retrieving barcode identifiers for **pbmc 5k** dataset...DONE
Retrieving feature identifiers for **pbmc 5k** dataset...DONE
Retrieving quantification matrix for **pbmc 5k** dataset...DONE

Data Read_in completed
Using org.Hs to retrieve NCBI gene identifiers.
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 0 UMI counts.
  Generating SCAE object: Aggregating alleles corresponding to the same gene
  Generating SCAE object: Aggregating genes corresponding to the same functional groups
SingleCellAlleleExperiment object completed
class: SingleCellAlleleExperiment 
dim: 62764 884452 
metadata(0):
assays(1): counts
rownames(62764): ENSG00000279928.2 ENSG00000228037.1 ... HLA_class_I
  HLA_class_II
rowData names(4): Ensembl_ID NI_I Quant_type Symbol
colnames(884452): AAACCCAAGAAACACT AAACCCAAGAAACCCA ...
  TTTGTTGTCTTTCTAG TTTGTTGTCTTTGGAG
colData names(2): Sample Barcode
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
---------------
Including a total of 21 immune related features:
Allele-level information (12): A*02:01:01:01 A*29:02:01:01 ...
  DPB1*04:01:01:01 DPB1*15:01:01:01
Immune genes (7): HLA-A HLA-B ... HLA-DPA1 HLA-DPB1
Functional level information (2): HLA_class_I HLA_class_II
Filtering performed on default value at 0 UMI counts.
Data Read_in completed
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 0 UMI counts.
  Generating SCAE object: Compute Library Factors before adding new layers
  Generating SCAE object: Aggregating alleles corresponding to the same gene
  Generating SCAE object: Aggregating genes corresponding to the same functional groups
SingleCellAlleleExperiment object completed
Filtering performed on default value at 0 UMI counts.
Data Read_in completed
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 0 UMI counts.
  Generating SCAE object: Aggregating alleles corresponding to the same gene
  Generating SCAE object: Aggregating genes corresponding to the same functional groups
SingleCellAlleleExperiment object completed
Retrieving barcode identifiers for **pbmc 5k** dataset...DONE
Retrieving feature identifiers for **pbmc 5k** dataset...DONE
Retrieving quantification matrix for **pbmc 5k** dataset...DONE
Filtering performed based on the inflection point at: 911 UMI counts.
Data Read_in completed
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 911 UMI counts.
  Generating SCAE object: Aggregating alleles corresponding to the same gene
  Generating SCAE object: Aggregating genes corresponding to the same functional groups
SingleCellAlleleExperiment object completed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
> 
> proc.time()
   user  system elapsed 
218.327  33.075 252.957