##############################################################################
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###
### Running command:
###
###   /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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.38.0’
* 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
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: Lolliplot-class
> ### Title: Class Lolliplot
> ### Aliases: Lolliplot-class Lolliplot
> 
> ### ** Examples
> 
> # Load a pre-existing data set
> dataset <- PIK3CA
> 
> # mode 1, amino acid changes are not present
> 
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.

> library(BSgenome.Hsapiens.UCSC.hg38)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

The following object is masked from ‘package:BiocIO’:

    FileForFormat

> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> BSgenome <- BSgenome.Hsapiens.UCSC.hg38
> 
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+           "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification")
> dataset.mode1 <- dataset[,keep]
> colnames(dataset.mode1) <- c("chromosome", "start", "stop", "reference", "variant",
+                              "sample", "gene", "consequence")
> 
> 
> # mode 2, amino acid changes are present
> 
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+           "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification",
+           "Transcript_ID", "HGVSp")
> dataset.mode2 <- dataset[,keep]
> colnames(dataset.mode2) <- c("chromosome", "start", "stop", "reference", "variant",
+                              "sample", "gene", "consequence", "transcript", "proteinCoord")
> 
> # run Lolliplot
> 
> object <- Lolliplot(dataset.mode1, transcript="ENST00000263967",
+                     species="hsapiens", txdb=txdb, BSgenome=BSgenome)
This function is part of the new S4 feature and is under active development, did you mean to use lolliplot() with a lowercase l?
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
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-3.20-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GenVisR’ ...
** 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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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")
Error : Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
[ FAIL 7 | WARN 7 | SKIP 100 | PASS 437 ]

══ Skipped tests (100) ═════════════════════════════════════════════════════════
• On Bioconductor (44): 'test-MutSpectra-class.R:285:5',
  'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:303:5',
  'test-MutSpectra-class.R:336:5', 'test-MutSpectra-class.R:345:5',
  'test-MutSpectra-class.R:354:5', 'test-MutSpectra-class.R:405:5',
  'test-MutSpectra-class.R:413:5', 'test-MutSpectra-class.R:440:5',
  'test-MutSpectra-class.R:450:5', 'test-Rainfall-class.R:247:5',
  'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:263:5',
  'test-Rainfall-class.R:297:5', 'test-Rainfall-class.R:305:5',
  'test-Rainfall-class.R:348:5', 'test-Rainfall-class.R:355:5',
  'test-Rainfall-class.R:389:5', 'test-Waterfall-class.R:662:5',
  'test-Waterfall-class.R:670:5', 'test-Waterfall-class.R:678:5',
  'test-Waterfall-class.R:686:5', 'test-Waterfall-class.R:722:5',
  'test-Waterfall-class.R:733:5', 'test-Waterfall-class.R:741:5',
  'test-Waterfall-class.R:750:5', 'test-Waterfall-class.R:758:5',
  'test-Waterfall-class.R:794:5', 'test-Waterfall-class.R:808:5',
  'test-Waterfall-class.R:819:5', 'test-Waterfall-class.R:830:5',
  'test-Waterfall-class.R:841:5', 'test-Waterfall-class.R:852:5',
  'test-Waterfall-class.R:868:5', 'test-Waterfall-class.R:906:5',
  'test-Waterfall-class.R:991:5', 'test-Waterfall-class.R:1005:5',
  'test-Waterfall-class.R:1019:5', 'test-Waterfall-class.R:1033:5',
  'test-Waterfall-class.R:1048:5', 'test-Waterfall-class.R:1062:5',
  'test-Waterfall-class.R:1076:5', 'test-Waterfall-class.R:1105:5',
  'test-Waterfall-class.R:1122:5'
• mart recieved try-error (55): 'test-Lolliplot-class.R:68:5',
  'test-Lolliplot-class.R:74:5', 'test-Lolliplot-class.R:97:5',
  'test-Lolliplot-class.R:151:5', 'test-Lolliplot-class.R:160:5',
  'test-Lolliplot-class.R:181:5', 'test-Lolliplot-class.R:189:5',
  'test-Lolliplot-class.R:201:5', 'test-Lolliplot-class.R:207:5',
  'test-Lolliplot-class.R:213:5', 'test-Lolliplot-class.R:237:5',
  'test-Lolliplot-class.R:254:5', 'test-Lolliplot-class.R:265:5',
  'test-Lolliplot-class.R:290:5', 'test-Lolliplot-class.R:296:5',
  'test-Lolliplot-class.R:308:5', 'test-Lolliplot-class.R:315:5',
  'test-Lolliplot-class.R:322:5', 'test-Lolliplot-class.R:329:5',
  'test-Lolliplot-class.R:349:5', 'test-Lolliplot-class.R:368:5',
  'test-Lolliplot-class.R:386:5', 'test-Lolliplot-class.R:395:5',
  'test-Lolliplot-class.R:404:5', 'test-Lolliplot-class.R:412:5',
  'test-Lolliplot-class.R:428:5', 'test-Lolliplot-class.R:434:5',
  'test-Lolliplot-class.R:443:5', 'test-Lolliplot-class.R:452:5',
  'test-Lolliplot-class.R:465:5', 'test-Lolliplot-class.R:477:5',
  'test-Lolliplot-class.R:490:5', 'test-Lolliplot-class.R:498:5',
  'test-Lolliplot-class.R:509:5', 'test-Lolliplot-class.R:522:5',
  'test-Lolliplot-class.R:545:5', 'test-Lolliplot-class.R:561:5',
  'test-Lolliplot-class.R:570:6', 'test-Lolliplot-class.R:580:5',
  'test-Lolliplot-class.R:587:5', 'test-Lolliplot-class.R:597:5',
  'test-Lolliplot-class.R:608:5', 'test-Lolliplot-class.R:621:5',
  'test-Lolliplot-class.R:632:5', 'test-Lolliplot-class.R:647:5',
  'test-Lolliplot-class.R:660:5', 'test-Lolliplot-class.R:669:5',
  'test-Lolliplot-class.R:681:5', 'test-Lolliplot-class.R:693:5',
  'test-Lolliplot-class.R:712:5', 'test-Lolliplot-class.R:729:5',
  'test-Lolliplot-class.R:737:5', 'test-Lolliplot-class.R:746:5',
  'test-Lolliplot-class.R:752:5', 'test-Lolliplot-class.R:777:5'
• mart recieved try-error, biomart is possibly down or there is no internet
  connection. (1): 'test-Lolliplot-class.R:62:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Lolliplot-class.R:80:5'): retreiveMart works in verbose mode ───
Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-Lolliplot-class.R:80:5
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::retrieveMart(...)
  7. └─GenVisR:::retrieveMart(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = host)
 10.       └─biomaRt:::.useMart(...)
 11.         └─biomaRt:::.listMarts(...)
── Error ('test-Lolliplot-class.R:113:5'): annotateGene warns if transcript is not a character ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-Lolliplot-class.R:113:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:121:5'): annotateGene warns if more than 1 element is supplied to transcript ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-Lolliplot-class.R:121:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:137:5'): annotateGene works in verbose mode ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-Lolliplot-class.R:137:5
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:768:5'): Lolliplot constructor outputs a S4 class object ──
Error in `eval(code, test_env)`: object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. └─testthat::expect_s4_class(Lolliplot.out, "Lolliplot") at test-Lolliplot-class.R:768:5
 2.   └─testthat::quasi_label(enquo(object), arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-Lolliplot-class.R:791:5'): getGrob successfully retrieves grob objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'getGrob': object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-Lolliplot-class.R:791:5
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─GenVisR::getGrob(Lolliplot.out, index = 1)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))
── Error ('test-Lolliplot-class.R:818:5'): getData retrieves specified slot data correctly ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'getData': object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-Lolliplot-class.R:818:5
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─GenVisR::getData(Lolliplot.out, index = 1)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))

[ FAIL 7 | WARN 7 | SKIP 100 | PASS 437 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
• Waterfall-class/addgene-waterfall.svg
• Waterfall-class/drawplot-waterfall.svg
• Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
• Waterfall-class/final-waterfall-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg
• Waterfall-class/final-waterfall-and-top-sub-plot.svg
• Waterfall-class/final-waterfall-base.svg
• Waterfall-class/gene-plot-add-layers.svg
• Waterfall-class/gene-plot-frequency-complex.svg
• Waterfall-class/gene-plot-frequency-simple.svg
• Waterfall-class/gene-plot-proportion-complex.svg
• 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