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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RFGeneRank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RFGeneRank_0.99.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/RFGeneRank.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* 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: 2026-04-09 01:46:26 UTC
* using option ‘--no-vignettes’
* checking for file ‘RFGeneRank/DESCRIPTION’ ... OK
* this is package ‘RFGeneRank’ version ‘0.99.4’
* 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 ‘RFGeneRank’ 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 whether startup messages can be suppressed ... 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 ‘RFGeneRank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: validate_genes
> ### Title: Validate a ranked gene set with alternate learners via k-fold CV
> ### Aliases: validate_genes
> 
> ### ** Examples
> 
> # Toy expression matrix: 10 genes x 12 samples
> expr <- matrix(
+   stats::rnorm(10 * 12),
+   nrow = 10,
+   dimnames = list(
+     paste0("gene", 1:10),
+     paste0("sample", 1:12)
+   )
+ )
> 
> # Binary labels as a factor (balanced)
> label <- factor(rep(c("A", "B"), each = 6))
> 
> se <- SummarizedExperiment::SummarizedExperiment(
+   assays  = list(expr = expr),
+   colData = S4Vectors::DataFrame(label = label)
+ )
> 
> # Use the first 5 genes as a toy signature
> genes <- rownames(expr)[1:5]
> 
> # Validate using ranger only (fast and robust for examples)
> res <- validate_genes(
+   se        = se,
+   genes     = genes,
+   methods   = "ranger",
+   k         = 3,
+   seed      = 1,
+   label_col = "label"
+ )
Error in choose_threshold(p_use, y, thr_metric, cost) : 
  'list' object cannot be coerced to type 'double'
Calls: validate_genes -> lapply -> FUN -> choose_threshold
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:
   3.     └─RFGeneRank (local) FUN(X[[i]], ...)
   4.       └─RFGeneRank (local) choose_threshold(p_use, y, thr_metric, cost)
  ── Error ('test-validate_genes.R:301:3'): validate_genes runs ranger path and returns expected components ──
  Error in `choose_threshold(p_use, y, thr_metric, cost)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      ▆
   1. └─RFGeneRank::validate_genes(...) at test-validate_genes.R:301:3
   2.   └─base::lapply(methods, run_one_method)
   3.     └─RFGeneRank (local) FUN(X[[i]], ...)
   4.       └─RFGeneRank (local) choose_threshold(p_use, y, thr_metric, cost)
  
  [ FAIL 2 | WARN 9 | SKIP 5 | PASS 486 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/RFGeneRank.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RFGeneRank
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘RFGeneRank’ ...
** this is package ‘RFGeneRank’ version ‘0.99.4’
** 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 (RFGeneRank)

R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"
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(RFGeneRank)
RFGeneRank: Cross-validated, stable predictive gene ranking for transcriptomics
> 
> test_check("RFGeneRank")
Found2batches
Adjusting for0covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data

Setting levels: control = Case, case = Control
Setting direction: controls < cases
Setting levels: control = Case, case = Control
Setting direction: controls < cases
Setting levels: control = Case, case = Control
Setting direction: controls > cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Setting levels: control = A, case = B
Setting direction: controls < cases
Batch~label: p=1, Cramer's V=0.000
Found2batches
Adjusting for1covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data


'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
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:RFGeneRank':

    params

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

Batch~label: p=1, Cramer's V=0.000
Saving _problems/test-validate_genes-112.R
Saving _problems/test-validate_genes-310.R
Batch~label: p=1, Cramer's V=0.000
[ FAIL 2 | WARN 9 | SKIP 5 | PASS 486 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test.R:2:3'
• This branch is only hit when org.Hs.eg.db is absent (2):
  'test-plots.R:745:3', 'test-plots.R:764:3'
• empty test (1): 'test-plots.R:1352:1'
• length(candidates) == 0 is TRUE (1): 'test-check_utils.R:66:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-validate_genes.R:103:3'): validate_genes runs with ranger and returns summary plus method entry ──
Error in `choose_threshold(p_use, y, thr_metric, cost)`: 'list' object cannot be coerced to type 'double'
Backtrace:
    ▆
 1. └─RFGeneRank::validate_genes(...) at test-validate_genes.R:103:3
 2.   └─base::lapply(methods, run_one_method)
 3.     └─RFGeneRank (local) FUN(X[[i]], ...)
 4.       └─RFGeneRank (local) choose_threshold(p_use, y, thr_metric, cost)
── Error ('test-validate_genes.R:301:3'): validate_genes runs ranger path and returns expected components ──
Error in `choose_threshold(p_use, y, thr_metric, cost)`: 'list' object cannot be coerced to type 'double'
Backtrace:
    ▆
 1. └─RFGeneRank::validate_genes(...) at test-validate_genes.R:301:3
 2.   └─base::lapply(methods, run_one_method)
 3.     └─RFGeneRank (local) FUN(X[[i]], ...)
 4.       └─RFGeneRank (local) choose_threshold(p_use, y, thr_metric, cost)

[ FAIL 2 | WARN 9 | SKIP 5 | PASS 486 ]
Error:
! Test failures.
Execution halted