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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:standR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings standR_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/standR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-22 02:58:40 UTC
* using option ‘--no-vignettes’
* checking for file ‘standR/DESCRIPTION’ ... OK
* this is package ‘standR’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.23/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.23/data/annotation/src/contrib/PACKAGES'
 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 ‘standR’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Connection timed out after 10003 milliseconds
    Consider rerunning with 'localHub=TRUE'
  Backtrace:
      ▆
   1. └─ExperimentHub::ExperimentHub() at test-prepareDecon.R:3:3
   2.   └─AnnotationHub::.Hub(...)
   3.     └─base::tryCatch(...)
   4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/standR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL standR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘standR’ ...
** this is package ‘standR’ version ‘1.17.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘drawPCA’ with signature ‘"DGEList"’: no definition for class “DGEList”
in method for ‘drawPCA’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotDR’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment”
in method for ‘plotMDS’ with signature ‘"DGEList","ANY","ANY","ANY"’: no definition for class “DGEList”
in method for ‘plotMDS’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotRLExpr’ with signature ‘"DGEList","ANY"’: no definition for class “DGEList”
** help
*** installing help indices
*** copying figures
** 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 (standR)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> library(testthat)
> library(standR)
> 
> test_check("standR")
Loading required namespace: SpatialExperiment
New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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

Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
Loading required namespace: scater
Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'scater'

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

    plotMDS

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

Saving _problems/test-prepareDecon-3.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-prepareDecon.R:3:3'): Testing the function of preparation of spatialDecon ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10003 milliseconds
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub() at test-prepareDecon.R:3:3
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
Error:
! Test failures.
Execution halted