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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_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenVisR.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.35.0’
* 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 ... NOTE
Found the following non-portable file paths:
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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
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 tmp
* 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
> ### Title: Construct a waterfall plot
> ### Aliases: waterfall
> 
> ### ** Examples
> 
> # Plot the data
> waterfall(brcaMAF, plotGenes=c("PIK3CA", "TP53", "USH2A", "MLL3", "BRCA1"))
Checking if input is properly formatted...
Calculating frequency of mutations...
Warning: The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(mutation_counts). In the next version, this warning will become an error.
Removing genes not in: PIK3CA, TP53, USH2A, MLL3, BRCA1
setting mutation hierarchy...
Warning: The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.
Error in heatmap_grob[["grobs"]][[ind_legend]] : no such index at level 2
Calls: waterfall -> waterfall_align
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:
  • Waterfall-class/gene-plot-proportion-simple.svg
  • Waterfall-class/main-waterfall-add-layers.svg
  • Waterfall-class/main-waterfall-plot-base.svg
  • Waterfall-class/main-waterfall-plot-drop-true.svg
  • Waterfall-class/main-waterfall-plot-grid-true.svg
  • Waterfall-class/main-waterfall-plot-label.svg
  • Waterfall-class/main-waterfall-plot-samplenames-false.svg
  • Waterfall-class/main-waterfall-plot-xtitle-false.svg
  • Waterfall-class/mutation-plot-add-layers.svg
  • Waterfall-class/mutation-plot-burden-complex.svg
  • Waterfall-class/mutation-plot-burden-simple.svg
  • Waterfall-class/mutation-plot-frequency-complex.svg
  • Waterfall-class/mutation-plot-frequency-simple.svg
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenVisR.Rcheck/00check.log’
for details.