##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CRISPRball.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CRISPRball_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRball.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRball/DESCRIPTION’ ... OK
* this is package ‘CRISPRball’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CRISPRball’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CRISPRball-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_bar
> ### Title: Create interactive bar plot
> ### Aliases: plot_bar
> 
> ### ** Examples
> 
> library(CRISPRball)
> count.summ <- read.delim(system.file("extdata", "escneg.countsummary.txt",
+     package = "CRISPRball"
+ ), check.names = FALSE)
> # Gini Index plot
> plot_bar(count.summ)
Error in pm[[2]] : subscript out of bounds
Calls: plot_bar ... %||% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list
Execution halted
<pool> Checked-out object deleted before being returned.
<pool> Make sure to `poolReturn()` all objects retrieved with `poolCheckout().`
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
get_depmap_essentiality 2.94  0.554   7.576
* 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:
    1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "Zerocounts") at test-plotting_qc.R:10:5
    2. │ ├─... %>% ...
    3. │ ├─plotly::ggplotly(gg, tooltip = c("y"))
    4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y"))
    5. │   └─plotly::gg2list(...)
    6. ├─plotly::config(...)
    7. │ └─plotly:::modify_list(p$x$config, args)
    8. │   ├─utils::modifyList(x %||% list(), y %||% list(), ...)
    9. │   │ └─base::stopifnot(is.list(x), is.list(val))
   10. │   └─x %||% list()
   11. └─plotly::layout(...)
  
  [ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ]
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRball.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CRISPRball
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘CRISPRball’ ...
** this is package ‘CRISPRball’ version ‘1.4.0’
** using staged installation
** R
** data
** 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 (CRISPRball)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(CRISPRball)
Loading required package: shinyBS
> 
> test_check("CRISPRball")
Loading required package: pool
Loading required package: RSQLite
-- removing the lower 10% of variables based on variance
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

[ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotting_depmap.R:143:5'): plot_depmap_dependency returns a plotly object ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df)) at test-plotting_depmap.R:143:5
 2. │ └─base::withCallingHandlers(...)
 3. ├─CRISPRball::plot_depmap_dependency(df)
 4. │ ├─ggplotly(gg, tooltip = "text") %>% ...
 5. │ ├─plotly::ggplotly(gg, tooltip = "text")
 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 7. │   └─plotly::gg2list(...)
 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density"))
── Error ('test-plotting_depmap.R:156:5'): plot_depmap_dependency contains correct traces ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df)) at test-plotting_depmap.R:156:5
 2. │ └─base::withCallingHandlers(...)
 3. ├─CRISPRball::plot_depmap_dependency(df)
 4. │ ├─ggplotly(gg, tooltip = "text") %>% ...
 5. │ ├─plotly::ggplotly(gg, tooltip = "text")
 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 7. │   └─plotly::gg2list(...)
 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density"))
── Error ('test-plotting_depmap.R:164:5'): plot_depmap_dependency assigns correct colors ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test-plotting_depmap.R:164:5
 2. │ └─base::withCallingHandlers(...)
 3. ├─CRISPRball::plot_depmap_dependency(...)
 4. │ ├─ggplotly(gg, tooltip = "text") %>% ...
 5. │ ├─plotly::ggplotly(gg, tooltip = "text")
 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 7. │   └─plotly::gg2list(...)
 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density"))
── Error ('test-plotting_depmap.R:174:5'): plot_depmap_dependency shows dependency threshold line when depline = TRUE ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df, depline = TRUE)) at test-plotting_depmap.R:174:5
 2. │ └─base::withCallingHandlers(...)
 3. ├─CRISPRball::plot_depmap_dependency(df, depline = TRUE)
 4. │ ├─ggplotly(gg, tooltip = "text") %>% ...
 5. │ ├─plotly::ggplotly(gg, tooltip = "text")
 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 7. │   └─plotly::gg2list(...)
 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density"))
── Error ('test-plotting_depmap.R:181:5'): plot_depmap_dependency does not show dependency threshold line when depline = FALSE ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df, depline = FALSE)) at test-plotting_depmap.R:181:5
 2. │ └─base::withCallingHandlers(...)
 3. ├─CRISPRball::plot_depmap_dependency(df, depline = FALSE)
 4. │ ├─ggplotly(gg, tooltip = "text") %>% ...
 5. │ ├─plotly::ggplotly(gg, tooltip = "text")
 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 7. │   └─plotly::gg2list(...)
 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density"))
── Error ('test-plotting_depmap.R:197:5'): plot_depmap_expression returns a plotly object ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_expression(df.expression)) at test-plotting_depmap.R:197:5
 2. │ └─base::withCallingHandlers(...)
 3. └─CRISPRball::plot_depmap_expression(df.expression)
 4.   ├─plotly::ggplotly(gg, tooltip = "text")
 5.   └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 6.     └─plotly::gg2list(...)
── Error ('test-plotting_depmap.R:209:5'): plot_depmap_expression assigns correct colors ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test-plotting_depmap.R:209:5
 2. │ └─base::withCallingHandlers(...)
 3. └─CRISPRball::plot_depmap_expression(df.expression, color = "#FF0000")
 4.   ├─plotly::ggplotly(gg, tooltip = "text")
 5.   └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 6.     └─plotly::gg2list(...)
── Error ('test-plotting_depmap.R:224:5'): plot_depmap_cn returns a plotly object ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_cn(df.cn)) at test-plotting_depmap.R:224:5
 2. │ └─base::withCallingHandlers(...)
 3. └─CRISPRball::plot_depmap_cn(df.cn)
 4.   ├─plotly::ggplotly(gg, tooltip = "text")
 5.   └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 6.     └─plotly::gg2list(...)
── Error ('test-plotting_depmap.R:238:5'): plot_depmap_cn assigns correct colors ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─base::suppressWarnings(plot <- plot_depmap_cn(df.cn, color = "#FF0000")) at test-plotting_depmap.R:238:5
 2. │ └─base::withCallingHandlers(...)
 3. └─CRISPRball::plot_depmap_cn(df.cn, color = "#FF0000")
 4.   ├─plotly::ggplotly(gg, tooltip = "text")
 5.   └─plotly:::ggplotly.ggplot(gg, tooltip = "text")
 6.     └─plotly::gg2list(...)
── Error ('test-plotting_qc.R:4:5'): plot_bar returns a plotly object ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "GiniIndex") at test-plotting_qc.R:4:5
  2. │ ├─... %>% ...
  3. │ ├─plotly::ggplotly(gg, tooltip = c("y"))
  4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y"))
  5. │   └─plotly::gg2list(...)
  6. ├─plotly::config(...)
  7. │ └─plotly:::modify_list(p$x$config, args)
  8. │   ├─utils::modifyList(x %||% list(), y %||% list(), ...)
  9. │   │ └─base::stopifnot(is.list(x), is.list(val))
 10. │   └─x %||% list()
 11. └─plotly::layout(...)
── Error ('test-plotting_qc.R:10:5'): plot_bar handles different y parameters ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "Zerocounts") at test-plotting_qc.R:10:5
  2. │ ├─... %>% ...
  3. │ ├─plotly::ggplotly(gg, tooltip = c("y"))
  4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y"))
  5. │   └─plotly::gg2list(...)
  6. ├─plotly::config(...)
  7. │ └─plotly:::modify_list(p$x$config, args)
  8. │   ├─utils::modifyList(x %||% list(), y %||% list(), ...)
  9. │   │ └─base::stopifnot(is.list(x), is.list(val))
 10. │   └─x %||% list()
 11. └─plotly::layout(...)

[ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ]
Error: Test failures
Execution halted