############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenoGAM ### ############################################################################## ############################################################################## * checking for file ‘GenoGAM/DESCRIPTION’ ... OK * preparing ‘GenoGAM’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘GenoGAM.Rmd’ using rmarkdown Warning: The closing backticks on line 331 ("````") in GenoGAM.Rmd do not match the opening backticks "```" on line 326. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). Warning: The closing backticks on line 347 ("````") in GenoGAM.Rmd do not match the opening backticks "```" on line 338. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). 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 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, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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: HDF5Array Loading required package: DelayedArray Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'DelayedArray' The following objects are masked from 'package:base': aperm, apply, rowsum, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 17 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 14 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 8 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. as(, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead as(, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 17 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 14 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 8 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: : ... may be used in an incorrect context: 'readData(config, settings = settings, ...)' INFO [2022-10-18 18:46:38] Reading in data INFO [2022-10-18 18:46:38] Reading in wt_1 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. INFO [2022-10-18 18:46:44] Reading in wt_2 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. INFO [2022-10-18 18:46:46] Reading in mutant_1 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 17 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 14 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. INFO [2022-10-18 18:46:48] Reading in mutant_2 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 8 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. INFO [2022-10-18 18:46:50] Finished reading in data Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 INFO [2022-10-18 18:46:52] Writing chrI to HDF5 INFO [2022-10-18 18:46:52] chrI written Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 17 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 14 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 9 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 10 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 Warning in GenomicRanges:::valid.GenomicRanges.seqinfo(x) : GAlignments object contains 8 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 5 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence chrI. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning: Package 'GenoGAM' is deprecated and will be removed from Bioconductor version 3.16 as(, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead Quitting from lines 409-415 (GenoGAM.Rmd) Error: processing vignette 'GenoGAM.Rmd' failed with diagnostics: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in `[.data.frame`(x, i): undefined columns selected --- failed re-building ‘GenoGAM.Rmd’ SUMMARY: processing the following file failed: ‘GenoGAM.Rmd’ Error: Vignette re-building failed. Execution halted