##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings iSEEu_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/iSEEu.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-05 04:38:30 UTC
* checking for file ‘iSEEu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iSEEu’ version ‘1.25.0’
* 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 ‘iSEEu’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘iSEEhex’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘iSEE:::.dataParamBoxOpen’ ‘iSEE:::.multiSelectHistory’
  ‘iSEE:::.noSelection’ ‘iSEE:::.organizationHeight’
  ‘iSEE:::.organizationWidth’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AggregatedDotPlot.Rd: SummarizedExperiment-class, colData,
    ExperimentColorMap, Panel-class, .cacheCommonInfo,
    .refineParameters, .defineInterface, .defineDataInterface,
    .defineOutput, .panelColor, .fullName, .hideInterface,
    .createObservers, .generateOutput, ggplot, .renderOutput,
    .exportOutput, .definePanelTour, ComplexHeatmapPlot-class
  DynamicMarkerTable-class.Rd: rowData, RowTable-class, Table-class,
    Panel-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .fullName, .hideInterface,
    .createObservers, .generateTable, .definePanelTour
  DynamicReducedDimensionPlot-class.Rd: ColumnDotPlot-class,
    DotPlot-class, Panel-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .fullName, .createObservers,
    .generateDotPlotData, .multiSelectionInvalidated, .definePanelTour
  FeatureSetTable-class.Rd: SummarizedExperiment-class, Panel-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .fullName, .hideInterface, .defineOutput, datatable,
    .createObservers, .generateOutput, .renderOutput,
    .multiSelectionDimension, .multiSelectionCommands,
    .multiSelectionActive, .multiSelectionClear,
    .multiSelectionAvailable, .definePanelTour
  GeneSetTable-class.Rd: Panel-class, .defineDataInterface,
    .panelColor, .fullName, .hideInterface, .defineOutput, datatable,
    .createObservers, .generateOutput, .renderOutput,
    .multiSelectionDimension, .multiSelectionCommands,
    .multiSelectionActive, .multiSelectionClear,
    .multiSelectionAvailable
  LogFCLogFCPlot-class.Rd: RowDataPlot-class, rowData,
    RowDotPlot-class, DotPlot-class, Panel-class,
    SummarizedExperiment-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .allowableXAxisChoices,
    .allowableYAxisChoices, .hideInterface, .fullName,
    .createObservers, .generateDotPlotData, .prioritizeDotPlotData,
    .colorByNoneDotPlotField, .colorByNoneDotPlotScale,
    .generateDotPlot, ColumnDataPlot-class, ggplot, .definePanelTour,
    .getDotPlotColorHelp, RowDataPlot
  MAPlot-class.Rd: RowDataPlot-class, rowData, RowDotPlot-class,
    DotPlot-class, Panel-class, SummarizedExperiment-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .allowableXAxisChoices, .allowableYAxisChoices,
    .hideInterface, .fullName, .createObservers, .generateDotPlotData,
    .prioritizeDotPlotData, .colorByNoneDotPlotField,
    .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class,
    ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot
  MarkdownBoard-class.Rd: Panel-class, RowDataPlot-class,
    .defineDataInterface, .panelColor, .hideInterface, .fullName,
    .createObservers, .defineOutput, .renderOutput, .generateOutput,
    .exportOutput, .definePanelTour
  VolcanoPlot-class.Rd: RowDataPlot-class, RowDotPlot-class,
    DotPlot-class, Panel-class, rowData, SummarizedExperiment-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .allowableXAxisChoices, .allowableYAxisChoices,
    .hideInterface, .fullName, .createObservers, .generateDotPlotData,
    .prioritizeDotPlotData, .colorByNoneDotPlotField,
    .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class,
    ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot
  global-TableExtraFields.Rd: iSEE
  globals-PValuePattern.Rd: rowData, iSEE
  modeEmpty.Rd: iSEE
  modeGating.Rd: SummarizedExperiment, iSEE
  modeReducedDim.Rd: SingleCellExperiment, SingleCellExperiment-class,
    iSEE
  registerDEFields.Rd: Panel-class, SummarizedExperiment-class,
    rowData, iSEE
  registerFeatureSetCollections.Rd: SummarizedExperiment-class, iSEE,
    CharacterList-class, metadata, mcols
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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in GeneSetTable(PanelId = 1L) : 'GeneSetTable' is deprecated.
  Warning in setPValuePattern(old) : 'setPValuePattern' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
AggregatedDotPlot                 13.675  0.968  14.643
modeReducedDim                    12.273  0.458  12.731
DynamicMarkerTable-class           5.825  0.439   6.264
DynamicReducedDimensionPlot-class  5.482  0.353   5.836
* 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:
   22.                               │ └─methods::initialize(value, ...)
   23.                               └─RSQLite:::result_create(conn@ptr, statement)
  
  [ FAIL 3 | WARN 45 | SKIP 0 | PASS 250 ]
  Error:
  ! Test failures.
  Warning messages:
  1: In .library_size_factors(assay(x, assay.type), ...) :
    'librarySizeFactors' is deprecated.
  Use 'scrapper::centerSizeFactors' instead.
  See help("Deprecated")
  2: In .local(x, ...) : 'normalizeCounts' is deprecated.
  Use 'scrapper::normalizeCounts' instead.
  See help("Deprecated")
  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, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/iSEEu.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL iSEEu
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘iSEEu’ ...
** this is package ‘iSEEu’ version ‘1.25.0’
** using staged installation
** R
** 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 (iSEEu)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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(iSEEu)
Loading required package: iSEE
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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

Loading required package: S4Vectors

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: Seqinfo
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")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: iSEEhex
> 
> test_check("iSEEu")
Loading required package: scuttle
Loading required package: ggplot2
Saving _problems/test-FeatureSetTable-15.R
Saving _problems/test-FeatureSetTable-135.R
Saving _problems/test-FeatureSetTable-150.R
[ FAIL 3 | WARN 45 | SKIP 0 | PASS 250 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-FeatureSetTable.R:15:5'): createGeneSetCommands works as expected ──
Error: database or disk is full
Backtrace:
     ▆
  1. └─base::eval(parse(text = cmds$collections[1]), envir = env) at test-FeatureSetTable.R:15:5
  2.   └─base::eval(parse(text = cmds$collections[1]), envir = env)
  3.     ├─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  4.     └─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  5.       └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
  6.         └─AnnotationDbi:::.keys(x, keytype)
  7.           └─AnnotationDbi:::.legacyKeys(x, keytype)
  8.             └─AnnotationDbi:::.queryForKeys(x, keytype)
  9.               └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 10.                 ├─DBI::dbGetQuery(conn, SQL)
 11.                 └─DBI::dbGetQuery(conn, SQL)
 12.                   └─DBI (local) .local(conn, statement, ...)
 13.                     ├─DBI::dbSendQuery(conn, statement, ...)
 14.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 15.                       └─RSQLite (local) .local(conn, statement, ...)
 16.                         ├─methods::new(...)
 17.                         │ ├─methods::initialize(value, ...)
 18.                         │ └─methods::initialize(value, ...)
 19.                         └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test-FeatureSetTable.R:135:5'): FeatureSetTable responds to registration of commands ──
Error: database or disk is full
Backtrace:
     ▆
  1. ├─iSEE::.cacheCommonInfo(out, se) at test-FeatureSetTable.R:135:5
  2. └─iSEEu::.cacheCommonInfo(out, se)
  3.   └─base::lapply(...)
  4.     └─iSEEu (local) FUN(X[[i]], ...)
  5.       └─base::eval(parse(text = code), envir = env)
  6.         └─base::eval(parse(text = code), envir = env)
  7.           ├─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  8.           └─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  9.             └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 10.               └─AnnotationDbi:::.keys(x, keytype)
 11.                 └─AnnotationDbi:::.legacyKeys(x, keytype)
 12.                   └─AnnotationDbi:::.queryForKeys(x, keytype)
 13.                     └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 14.                       ├─DBI::dbGetQuery(conn, SQL)
 15.                       └─DBI::dbGetQuery(conn, SQL)
 16.                         └─DBI (local) .local(conn, statement, ...)
 17.                           ├─DBI::dbSendQuery(conn, statement, ...)
 18.                           └─RSQLite::dbSendQuery(conn, statement, ...)
 19.                             └─RSQLite (local) .local(conn, statement, ...)
 20.                               ├─methods::new(...)
 21.                               │ ├─methods::initialize(value, ...)
 22.                               │ └─methods::initialize(value, ...)
 23.                               └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test-FeatureSetTable.R:150:5'): FeatureSetCommands constructor falls back to the defaults ──
Error: database or disk is full
Backtrace:
     ▆
  1. ├─iSEE::.cacheCommonInfo(out, se) at test-FeatureSetTable.R:150:5
  2. └─iSEEu::.cacheCommonInfo(out, se)
  3.   └─base::lapply(...)
  4.     └─iSEEu (local) FUN(X[[i]], ...)
  5.       └─base::eval(parse(text = code), envir = env)
  6.         └─base::eval(parse(text = code), envir = env)
  7.           ├─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  8.           └─AnnotationDbi::keys(org.Hs.eg.db::org.Hs.eg.db, keytype = "GOALL")
  9.             └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 10.               └─AnnotationDbi:::.keys(x, keytype)
 11.                 └─AnnotationDbi:::.legacyKeys(x, keytype)
 12.                   └─AnnotationDbi:::.queryForKeys(x, keytype)
 13.                     └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 14.                       ├─DBI::dbGetQuery(conn, SQL)
 15.                       └─DBI::dbGetQuery(conn, SQL)
 16.                         └─DBI (local) .local(conn, statement, ...)
 17.                           ├─DBI::dbSendQuery(conn, statement, ...)
 18.                           └─RSQLite::dbSendQuery(conn, statement, ...)
 19.                             └─RSQLite (local) .local(conn, statement, ...)
 20.                               ├─methods::new(...)
 21.                               │ ├─methods::initialize(value, ...)
 22.                               │ └─methods::initialize(value, ...)
 23.                               └─RSQLite:::result_create(conn@ptr, statement)

[ FAIL 3 | WARN 45 | SKIP 0 | PASS 250 ]
Error:
! Test failures.
Warning messages:
1: In .library_size_factors(assay(x, assay.type), ...) :
  'librarySizeFactors' is deprecated.
Use 'scrapper::centerSizeFactors' instead.
See help("Deprecated")
2: In .local(x, ...) : 'normalizeCounts' is deprecated.
Use 'scrapper::normalizeCounts' instead.
See help("Deprecated")
Execution halted