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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:recount3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings recount3_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/recount3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘recount3/DESCRIPTION’ ... OK
* this is package ‘recount3’ version ‘1.20.0’
* 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 ‘recount3’ 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 ... ERROR
Running examples in ‘recount3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: available_projects
> ### Title: List available projects in recount3
> ### Aliases: available_projects
> 
> ### ** Examples
> 
> 
> ## Find all the human projects
> human_projects <- available_projects()
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Execution halted
* 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:
  ── Error ('test-transform_counts.R:10:5'): transforming counts works ───────────
  Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
  Backtrace:
      ▆
   1. └─recount3::create_rse(...) at test-transform_counts.R:10:5
   2.   └─recount3::create_rse_manual(...)
   3.     ├─base::match.arg(project_home)
   4.     │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
   5.     │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
   6.     └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
  
  [ FAIL 12 | WARN 5 | SKIP 0 | PASS 14 ]
  Error:
  ! Test failures.
  Execution halted
* 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 ‘recount3-quickstart.Rmd’ using rmarkdown

Quitting from recount3-quickstart.Rmd:159-175 [quick_example]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
---
Backtrace:
    ▆
 1. └─recount3::available_projects()
 2.   ├─recount3::available_samples(...)
 3.   │ └─base::file.path(...)
 4.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'recount3-quickstart.Rmd' failed with diagnostics:
'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
--- failed re-building ‘recount3-quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘recount3-quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/recount3.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL recount3
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘recount3’ ...
** this is package ‘recount3’ version ‘1.20.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (recount3)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.

> library(testthat)
> library(recount3)
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

> 
> test_check("recount3")
Saving _problems/test-available_projects-2.R
Saving _problems/test-create_hub-4.R
Saving _problems/test-create_rse-19.R
Saving _problems/test-create_rse_manual-16.R
Saving _problems/test-file_retrieve-15.R
Saving _problems/test-file_retrieve-21.R
Saving _problems/test-locate_url-6.R
Saving _problems/test-project_homes-9.R
Saving _problems/test-read_counts-18.R
Saving _problems/test-read_metadata-12.R
Saving _problems/test-recount3_cache_rm-7.R
Saving _problems/test-transform_counts-19.R
[ FAIL 12 | WARN 5 | SKIP 0 | PASS 14 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-available_projects.R:2:5'): number of available projects by organism works ──
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-available_projects.R:2:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─recount3::available_projects("human")
 5.   ├─recount3::available_samples(...)
 6.   │ └─base::file.path(...)
 7.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-create_hub.R:4:5'): creating a UCSC hub ────────────────────────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::available_samples("mouse") at test-create_hub.R:4:5
 2.   ├─base::file.path(...)
 3.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-create_rse.R:10:5'): Creating an RSE works (ercc) - user friendly function ──
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::create_rse(...) at test-create_rse.R:10:5
 2.   └─recount3::create_rse_manual(...)
 3.     ├─base::match.arg(project_home)
 4.     │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.     │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 6.     └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-create_rse_manual.R:11:5'): Creating an RSE works (ercc) ───────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::create_rse_manual(...) at test-create_rse_manual.R:11:5
 2.   ├─base::match.arg(project_home)
 3.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 4.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Failure ('test-file_retrieve.R:12:5'): caching recount3 files ───────────────
Expected `file_retrieve(test_url, test_bfc)` to be equivalent to `BiocFileCache::bfcrpath(test_bfc, test_url)`.
1/1 mismatches
x[1]: NA
y[1]: "/home/biocbuild/bbs-3.22-bioc/R/site-library/recount3/test_files/9f51506e
y[1]: f1f_sra.recount_project.DRP002835.MD.gz"
── Failure ('test-file_retrieve.R:18:5'): caching recount3 files ───────────────
Expected `file_retrieve(test_url, bfc = tempdir())` to throw a error.
── Error ('test-locate_url.R:2:5'): Locating URLs works ────────────────────────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::locate_url("SRP009615", "data_sources/sra", "jxn") at test-locate_url.R:2:5
 2.   ├─base::match.arg(project_home)
 3.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 4.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-project_homes.R:2:5'): Default project homes by organism ───────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-project_homes.R:2:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─recount3::project_homes("human")
── Error ('test-read_counts.R:10:5'): Reading counts works ─────────────────────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. ├─recount3::file_retrieve(...) at test-read_counts.R:10:5
 2. └─recount3::locate_url(...)
 3.   ├─base::match.arg(project_home)
 4.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 6.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-read_metadata.R:9:1'): (code run outside of `test_that()`) ─────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::locate_url("DRP002835", "data_sources/sra") at test-read_metadata.R:9:1
 2.   ├─base::match.arg(project_home)
 3.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 4.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-recount3_cache_rm.R:4:1'): (code run outside of `test_that()`) ──
Error in `BiocFileCache::bfcrpath(temp_bfc_rm, test_url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(temp_bfc_rm, test_url) at test-recount3_cache_rm.R:4:1
 2. └─BiocFileCache::bfcrpath(temp_bfc_rm, test_url)
── Error ('test-transform_counts.R:10:5'): transforming counts works ───────────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. └─recount3::create_rse(...) at test-transform_counts.R:10:5
 2.   └─recount3::create_rse_manual(...)
 3.     ├─base::match.arg(project_home)
 4.     │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 5.     │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 6.     └─recount3::project_homes(organism = organism, recount3_url = recount3_url)

[ FAIL 12 | WARN 5 | SKIP 0 | PASS 14 ]
Error:
! Test failures.
Execution halted