* using log directory 'd:/Rcompile/CRANpkg/local/4.6/karyotapR.Rcheck'
* using R Under development (unstable) (2025-10-10 r88914 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'karyotapR/DESCRIPTION' ... OK
* this is package 'karyotapR' version '1.0.1'
* 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 whether package 'karyotapR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'GaussianMixtureCalls.R'
* 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 ... [10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s] OK
* checking whether the package can be unloaded cleanly ... [9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s] OK
* checking loading without being on the library search path ... [10s] OK
* checking use of S3 registration ... 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 ... [22s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 R/sysdata.rda ... OK
* checking examples ... [34s] ERROR
Running examples in 'karyotapR-Ex.R' failed
The error most likely occurred in:

> ### Name: getCytobands
> ### Title: Add chromosome cytobands and chromosome arms to
> ###   'TapestriExperiment'
> ### Aliases: getCytobands
> 
> ### ** Examples
> 
> tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
ℹ Moving gRNA probe  to `altExp` slot "grnaCounts".
ℹ Moving barcode probe  to `altExp` slot "barcodeCounts".
ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts".
> tap.object <- getCytobands(tap.object, genome = "hg19")
ℹ Adding cytobands from hg19.
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Error in .requirePackage(package) : 
  unable to load required package 'GenomeInfoDb'
Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [11s] ERROR
  Running 'testthat.R' [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
  
  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
  
  Attaching package: 'IRanges'
  
  The following object is masked from 'package:grDevices':
  
      windows
  
  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
  
  > 
  > 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
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [4s] OK
* DONE
Status: 2 ERRORs, 1 NOTE