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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ScreenR_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.12.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ScreenR’ 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 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 ... NOTE
checkRd: (-1) annotation_table.Rd:25: Lost braces
    25 |                  \url{https://cellecta.com/}{cellecta}}
       |                                             ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'compute_camera.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'select_number_barcode.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'unique_gene_symbols.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plot_barcode_trend       26.986  0.595  27.582
plot_zscore_distribution 26.014  0.425  26.439
compute_metrics          15.926  1.542  17.469
find_zscore_hit          12.818  0.230  13.048
find_robust_zscore_hit   12.459  0.516  12.979
* 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:
  Differences:
  `actual`:   "ggplot2::ggplot"
  `expected`: "gg"             
  
  ── Failure ('test-visualization.R:263:5'): Plot common Hit ─────────────────────
  Expected "gg" to equal `class(plot)[1]`.
  Differences:
  `actual`:   "gg"             
  `expected`: "ggplot2::ggplot"
  
  
  [ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ScreenR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ScreenR’ ...
** this is package ‘ScreenR’ version ‘1.12.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ScreenR)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(ScreenR)

Welcome to ScreenR
--------------------------

See ?ScreenR for a list of
available functions.

Enjoy!

> 
> test_check("ScreenR")
Saving _problems/test-MDS-52.R
Saving _problems/test-MDS-61.R
Saving _problems/test-MDS-70.R
Saving _problems/test-MDS-81.R
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
Saving _problems/test-visualization-57.R
Saving _problems/test-visualization-71.R
Saving _problems/test-visualization-85.R
Saving _problems/test-visualization-102.R
Saving _problems/test-visualization-108.R
Saving _problems/test-visualization-179.R
Using classic mode.
Saving _problems/test-visualization-263.R
[ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-MDS.R:52:5'): plot_mds NULL ──────────────────────────────────
Expected `class(plot)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:61:5'): plot_mds ───────────────────────────────────────
Expected `class(plot)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:70:5'): plot_explained_variance ────────────────────────
Expected `class(plot)[[1]]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:81:5'): plot_explained_variance CUM ────────────────────
Expected `class(plot)[[1]]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:57:5'): plot trend hit ───────────────────────
Expected `class(plot)[[1]]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:71:5'): Plot Boxplot violinplot ──────────────
Expected `class(p)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:85:5'): Plot Boxplot boxplot ─────────────────
Expected `class(p)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:102:5'): plot_barcode_lost_for_gene ──────────
Expected `class(p)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:108:5'): plot_barcode_lost_for_gene ──────────
Expected `class(p)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:179:5'): plot_zscore_distribution ────────────
Expected `class(p)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-visualization.R:263:5'): Plot common Hit ─────────────────────
Expected "gg" to equal `class(plot)[1]`.
Differences:
`actual`:   "gg"             
`expected`: "ggplot2::ggplot"


[ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]
Error:
! Test failures.
Execution halted