Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(karyotapR)
  Loading required package: SingleCellExperiment
  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
  
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      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'
  
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  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  > 
  > test_check("karyotapR")
  Failed with error:  'there is no package called 'GenomeInfoDb''
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ──
  Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
  Backtrace:
       ▆
    1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5
    2. │ └─base::withCallingHandlers(...)
    3. └─karyotapR:::newDummyTapestriExperiment()
    4.   └─karyotapR::getCytobands(tapestri.object)
    5.     └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE)
    6.       ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
    7.       └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges)
    8.         └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
    9.           └─GenomicRanges:::findOverlaps_GNCList(...)
   10.             ├─base::merge(seqinfo(query), seqinfo(subject))
   11.             └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
   12.               └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
   13.                 └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
   14.                   └─Seqinfo (local) FUN(X[[i]], ...)
   15.                     └─methods::is(arg, class(x))
   16.                       └─methods::getClassDef(class1)
   17.                         └─methods:::.requirePackage(package)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted