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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings iSEE_2.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/iSEE.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘iSEE’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  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:
  ColumnDataPlot-class.Rd: colData, SummarizedExperiment-class
  ColumnDataTable-class.Rd: colData, SummarizedExperiment-class
  ColumnDotPlot-class.Rd: SummarizedExperiment-class, ggplot, colData
  ColumnTable-class.Rd: SummarizedExperiment-class, datatable
  ComplexHeatmapPlot-class.Rd: SummarizedExperiment-class, Heatmap,
    colData, columnAnnotation, rowData, rowAnnotation
  DotPlot-class.Rd: SummarizedExperiment-class, ggplot, rowData,
    colData, brushedPoints
  FeatureAssayPlot-class.Rd: assay, SummarizedExperiment-class, colData
  Panel-class.Rd: updateObject
  ReducedDimensionPlot-class.Rd: reducedDims,
    SingleCellExperiment-class
  RowDataPlot-class.Rd: rowData, SummarizedExperiment-class
  RowDataTable-class.Rd: rowData, SummarizedExperiment-class
  RowDotPlot-class.Rd: SummarizedExperiment-class, ggplot, rowData
  RowTable-class.Rd: SummarizedExperiment-class, datatable
  SampleAssayPlot-class.Rd: assay, SummarizedExperiment-class, colData
  Table-class.Rd: datatable, SummarizedExperiment-class
  addCustomLabelsCommands.Rd: ggplot
  addLabelCentersCommands.Rd: ggplot
  addMultiSelectionCommands.Rd: ggplot
  aes-utils.Rd: ggplot
  cache-utils.Rd: SummarizedExperiment-class, DataFrame-class, rowData,
    colData, ggplot, datatable
  checkColormapCompatibility.Rd: SingleCellExperiment-class
  cleanDataset.Rd: SummarizedExperiment-class, assay, rowData, colData,
    selectInput, SingleCellExperiment-class, reducedDims
  conditional-utils.Rd: conditionalPanel
  createCustomDimnamesModalObservers.Rd: SummarizedExperiment-class
  createCustomPanels.Rd: ggplot, SummarizedExperiment-class,
    selectInput, textInput, numericInput, checkboxInput
  createLandingPage.Rd: SummarizedExperiment,
    SummarizedExperiment-class, renderUI
  createProtectedParameterObservers.Rd: observeEvent
  extractAssaySubmatrix.Rd: SummarizedExperiment-class
  filterDTColumn.Rd: datatable
  hidden-inputs.Rd: selectInput
  iSEE.Rd: SummarizedExperiment-class, shinyApp, runApp
  interface-generics.Rd: SummarizedExperiment-class
  interface-wrappers.Rd: selectInput, hidden
  jitterPoints.Rd: offsetX
  labs-utils.Rd: ggplot
  lassoPoints.Rd: brushedPoints, in.out
  metadata-plot-generics.Rd: SummarizedExperiment-class, colData,
    rowData
  multi-select-generics.Rd: SummarizedExperiment-class
  observer-generics.Rd: SummarizedExperiment-class
  output-generics.Rd: plotOutput, dataTableOutput, tagList,
    SummarizedExperiment-class, renderPlot, ggplot
  plot-generics.Rd: SummarizedExperiment-class, ggplot,
    scale_color_manual
  processMultiSelections.Rd: SummarizedExperiment-class
  registerAppOptions.Rd: SummarizedExperiment-class
  retrieveOutput.Rd: SummarizedExperiment-class
  setCachedCommonInfo.Rd: SummarizedExperiment-class, int_metadata
  setup-generics.Rd: SummarizedExperiment-class, int_metadata,
    SingleCellExperiment-class
  single-select-generics.Rd: selectInput, checkboxInput
  synchronizeAssays.Rd: SingleCellExperiment-class
  table-generics.Rd: datatable, SummarizedExperiment-class
  visual-parameters-generics.Rd: SummarizedExperiment-class, colData
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
checkColormapCompatibility 9.576  0.620  10.200
iSEE                       6.247  0.492   6.739
synchronizeAssays          6.263  0.434   6.697
* 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-3.21-bioc/meat/iSEE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL iSEE
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘iSEE’ ...
** 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 (iSEE)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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(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: GenomeInfoDb
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
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.
Class: ExperimentColorMap
assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm
colData(1): passes_qc_checks_s
rowData(0):
all_discrete(0):
all_continuous(0):
global_discrete(1)
global_continuous(1)
[ FAIL 0 | WARN 6 | SKIP 2 | PASS 1481 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:3:1'
• waiting for a fix to the SCE itself (1): 'test_clean.R:100:5'

[ FAIL 0 | WARN 6 | SKIP 2 | PASS 1481 ]
> 
> proc.time()
   user  system elapsed 
 53.418   2.849  56.716