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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:singscore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings singscore_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singscore.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘singscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singscore’ version ‘1.30.0’
* 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 ‘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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/singscore.Rcheck/00check.log’
for details.