##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:singscore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singscore_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/singscore.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 ‘singscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singscore’ version ‘1.28.1’
* 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 ‘singscore’ 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 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 ... NOTE
plotDispersion: no visible binding for global variable ‘Score’
plotDispersion: no visible binding for global variable ‘Dispersion’
plotDispersion: no visible binding for global variable ‘Class’
plotDispersion: no visible binding for global variable ‘SampleText’
plotDispersion: no visible binding for global variable ‘SampleLabel’
plotNull: no visible binding for global variable ‘value’
plotNull: no visible binding for global variable ‘TotalScore’
plotNull: no visible binding for global variable ‘label’
plotRankDensity_intl: no visible binding for global variable ‘Ranks’
plotRankDensity_intl: no visible binding for global variable ‘upDown’
plotRankDensity_intl: no visible binding for global variable ‘hover’
plotScoreLandscape: no visible binding for global variable ‘sc1’
plotScoreLandscape: no visible binding for global variable ‘sc2’
plotScoreLandscape: no visible binding for global variable ‘count’
projectScoreLandscape: no visible binding for global variable ‘Class’
projectScoreLandscape: no visible binding for global variable
  ‘SampleLabel’
projectScoreLandscape: no visible binding for global variable
  ‘SampleText’
Undefined global functions or variables:
  Class Dispersion Ranks SampleLabel SampleText Score TotalScore count
  hover label sc1 sc2 upDown value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'rankGenes.Rd':
  ‘[Biobase:class.ExpressionSet]{"ExpressionSet"}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  multiScore.Rd: GeneSet-class
  plotRankDensity_intl.Rd: GeneSet-class
  simpleScore.Rd: GeneSet-class
  tgfb_gs_dn.Rd: GeneSet-class
  tgfb_gs_up.Rd: GeneSet-class
  toy_gs_dn.Rd: GeneSet-class
  toy_gs_up.Rd: GeneSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘singscore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDispersion
> ### Title: Plot the score v.s. despersion for all samples
> ### Aliases: plotDispersion
> 
> ### ** Examples
> 
> ranked <- rankGenes(toy_expr_se)
> scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn)
> plotDispersion(scoredf)
> plotDispersion(scoredf, isInteractive = TRUE)
Error in pm[[2]] : subscript out of bounds
Calls: plotDispersion -> <Anonymous> -> ggplotly.ggplot -> gg2list
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:
   3.   └─plotly:::ggplotly.ggplot(p1)
   4.     └─plotly::gg2list(...)
  ── Error ('test-projectScoreLandscape.R:70:2'): projectScoreLandscape works for interactive plots ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `pm[[2]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─singscore::projectScoreLandscape(...) at test-projectScoreLandscape.R:70:9
   2.   ├─plotly::ggplotly(p1, tooltip = c("label", "x", "y", "colour"))
   3.   └─plotly:::ggplotly.ggplot(p1, tooltip = c("label", "x", "y", "colour"))
   4.     └─plotly::gg2list(...)
  
  [ FAIL 3 | WARN 11 | SKIP 0 | PASS 128 ]
  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/singscore.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL singscore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘singscore’ ...
** this is package ‘singscore’ version ‘1.28.1’
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
*** moving datasets to lazyload DB
** 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 (singscore)

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.

> library(testthat)
> library(singscore)
> 
> test_check("singscore")
[ FAIL 3 | WARN 11 | SKIP 0 | PASS 128 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotDis.R:83:2'): plotDispersion interactive for single sigs ───
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─singscore::plotDispersion(scoredf, isInteractive = TRUE) at test-plotDis.R:83:9
 2.   ├─plotly::ggplotly(p1)
 3.   └─plotly:::ggplotly.ggplot(p1)
 4.     └─plotly::gg2list(...)
── Error ('test-plotDis.R:112:2'): plotDispersion interactive for up/dn sigs ───
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─singscore::plotDispersion(scoredf, isInteractive = TRUE) at test-plotDis.R:112:9
 2.   ├─plotly::ggplotly(p1)
 3.   └─plotly:::ggplotly.ggplot(p1)
 4.     └─plotly::gg2list(...)
── Error ('test-projectScoreLandscape.R:70:2'): projectScoreLandscape works for interactive plots ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─singscore::projectScoreLandscape(...) at test-projectScoreLandscape.R:70:9
 2.   ├─plotly::ggplotly(p1, tooltip = c("label", "x", "y", "colour"))
 3.   └─plotly:::ggplotly.ggplot(p1, tooltip = c("label", "x", "y", "colour"))
 4.     └─plotly::gg2list(...)

[ FAIL 3 | WARN 11 | SKIP 0 | PASS 128 ]
Error: Test failures
Execution halted