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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.9.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gDRutils.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.9.4’
* 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 ‘gDRutils’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SE_metadata.Rd: SummarizedExperiment-class
  convert_mae_assay_to_dt.Rd: SummarizedExperiment-class,
    MultiAssayExperiment-class
  convert_se_assay_to_dt.Rd: SummarizedExperiment-class
  is_exp_empty.Rd: SummarizedExperiment-class
  split_SE_components.Rd: SummarizedExperiment-class
  validate_se_assay_name.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ‘gDRutils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_gDR_session_info
> ### Title: get gDR package and their version installed in the environment
> ### Aliases: get_gDR_session_info
> ### Keywords: package_utils
> 
> ### ** Examples
> 
> get_gDR_session_info()
Error in `[.data.table`(pkg_data, , `:=`(UsedVersion, Version[order(match(LibPath,  : 
  attempt access index 3/3 in VECTOR_ELT
Calls: get_gDR_session_info -> [ -> [.data.table
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.   └─data.table:::`[.data.table`(...)
  ── Error ('test-utils.R:1133:3'): get_gDR_session_info behaves correctly under various conditions ──
  Error in ``[.data.table`(pkg_data, , `:=`(UsedVersion, Version[order(match(LibPath, .libPaths()))[1]]), by = Package)`: attempt access index 3/3 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─checkmate::expect_data_table(get_gDR_session_info()) at test-utils.R:1133:3
   2. │ └─checkmate::checkDataTable(...)
   3. └─gDRutils::get_gDR_session_info()
   4.   ├─...[]
   5.   └─data.table:::`[.data.table`(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 832 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/gDRutils.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRutils
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘gDRutils’ ...
** this is package ‘gDRutils’ version ‘1.9.4’
** using staged installation
** R
** inst
** 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 (gDRutils)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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("gDRutils")
> library("testthat")
> 
> test_check("gDRutils")
Saving _problems/test-utils-296.R
Saving _problems/test-utils-1133.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 832 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-utils.R:293:3'): average_biological_replicates_dt works as expected ──
Error in ``[.data.table`(data, , `:=`((sd_fields), lapply(.SD, calc_sd)), .SDcols = average_fields, by = group_by)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
    ▆
 1. └─gDRutils::average_biological_replicates_dt(...) at test-utils.R:293:3
 2.   ├─...[]
 3.   └─data.table:::`[.data.table`(...)
── Error ('test-utils.R:1133:3'): get_gDR_session_info behaves correctly under various conditions ──
Error in ``[.data.table`(pkg_data, , `:=`(UsedVersion, Version[order(match(LibPath, .libPaths()))[1]]), by = Package)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
    ▆
 1. ├─checkmate::expect_data_table(get_gDR_session_info()) at test-utils.R:1133:3
 2. │ └─checkmate::checkDataTable(...)
 3. └─gDRutils::get_gDR_session_info()
 4.   ├─...[]
 5.   └─data.table:::`[.data.table`(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 832 ]
Error:
! Test failures.
Execution halted