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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenVisR_1.43.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GenVisR.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 ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.43.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘GenVisR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildWaterfallPlot,WaterfallData: no visible global function definition
  for ‘tail’
setTierTwo,data.table: no visible global function definition for ‘tail’
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenVisR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Waterfall-class
> ### Title: Class Waterfall
> ### Aliases: Waterfall-class Waterfall
> 
> ### ** Examples
> 
> set.seed(426)
> 
> # create a data frame with required column names
> mutationDF <- data.frame("sample"=sample(c("sample_1", "sample_2", "sample_3"), 10, replace=TRUE),
+                          "gene"=sample(c("egfr", "tp53", "rb1", "apc"), 10, replace=TRUE),
+                          "mutation"=sample(c("missense", "frame_shift", "splice_site"), 10, replace=TRUE))
> 
> # set the mutation hierarchy (required for DF)
> hierarchyDF <- data.frame("mutation"=c("missense", "frame_shift", "slice_site"),
+                           "color"=c("#3B3B98", "#BDC581", "#6A006A"))
>                           
> # Run the Waterfall Plot and draw the output
> Waterfall.out <- Waterfall(mutationDF, mutationHierarchy=hierarchyDF)
Warning in setMutationHierarchy(object, mutationHierarchy = mutationHierarchy,  :
  The following mutations were found in the input however were not specified in the mutationHierarchy! splice_site adding these in as least important and assigning random colors!
Error in `[.data.table`(primaryData, , `:=`(count, .N), by = list(gene,  : 
  attempt access index 4/4 in VECTOR_ELT
Calls: Waterfall ... constructGeneData -> constructGeneData -> [ -> [.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:
   6.         ├─x[, `:=`(tmp, .GRP), by = list(key)]
   7.         └─data.table:::`[.data.table`(x, , `:=`(tmp, .GRP), by = list(key))
  ── Error ('test-Waterfall-class.R:379:1'): (code run outside of `test_that()`) ──
  Error in ``[.data.table`(primaryData, , `:=`(count, .N), by = list(gene))`: attempt access index 4/4 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─GenVisR:::recurrenceSubset(...) at test-Waterfall-class.R:379:1
   2. └─GenVisR:::recurrenceSubset(...)
   3.   ├─primaryData[, `:=`(count, .N), by = list(gene)]
   4.   └─data.table:::`[.data.table`(primaryData, , `:=`(count, .N), by = list(gene))
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 395 ]
  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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘GenVisR’ ...
** this is package ‘GenVisR’ version ‘1.43.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (GenVisR)

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(testthat)
> library(GenVisR)
> 
> test_check("GenVisR")
Saving _problems/test-Lolliplot-class-422.R
Saving _problems/test-Waterfall-class-379.R
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 395 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Lolliplot-class.R:421:5'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(x, , `:=`(tmp, .GRP), by = list(key))`: attempt access index 21/21 in VECTOR_ELT
Backtrace:
    ▆
 1. ├─GenVisR:::setTierTwo(...) at test-Lolliplot-class.R:421:5
 2. └─GenVisR:::setTierTwo(...)
 3.   └─GenVisR (local) .local(object, ...)
 4.     └─base::lapply(object, a)
 5.       └─GenVisR (local) FUN(X[[i]], ...)
 6.         ├─x[, `:=`(tmp, .GRP), by = list(key)]
 7.         └─data.table:::`[.data.table`(x, , `:=`(tmp, .GRP), by = list(key))
── Error ('test-Waterfall-class.R:379:1'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(primaryData, , `:=`(count, .N), by = list(gene))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
    ▆
 1. ├─GenVisR:::recurrenceSubset(...) at test-Waterfall-class.R:379:1
 2. └─GenVisR:::recurrenceSubset(...)
 3.   ├─primaryData[, `:=`(count, .N), by = list(gene)]
 4.   └─data.table:::`[.data.table`(primaryData, , `:=`(count, .N), by = list(gene))

[ FAIL 2 | WARN 4 | SKIP 0 | PASS 395 ]
Error:
! Test failures.
Execution halted