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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* preparing ‘GenomicRanges’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GenomicRangesIntroduction.Rmd’ using rmarkdown

Quitting from GenomicRangesIntroduction.Rmd:663-673 [subjectx_declaration]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package 'GenomicFeatures' could not be loaded
---
Backtrace:
    ▆
 1. └─base::library(TxDb.Hsapiens.UCSC.hg38.knownGene)
 2.   └─base::.getRequiredPackages2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GenomicRangesIntroduction.Rmd' failed with diagnostics:
package 'GenomicFeatures' could not be loaded
--- failed re-building ‘GenomicRangesIntroduction.Rmd’

--- re-building ‘ExtendingGenomicRanges.Rnw’ using Sweave

Error: processing vignette 'ExtendingGenomicRanges.Rnw' failed with diagnostics:
 chunk 6 (label = vranges) 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'extraColumnSlotNames': class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

--- failed re-building ‘ExtendingGenomicRanges.Rnw’

--- re-building ‘GRanges_and_GRangesList_slides.Rnw’ using Sweave
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


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

The following object is masked from ‘package:Biobase’:

    rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: Rsamtools
Error: package or namespace load failed for ‘Rsamtools’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

Error: processing vignette 'GRanges_and_GRangesList_slides.Rnw' failed with diagnostics:
 chunk 28 (label = findOverlaps1) 
Error : package ‘Rsamtools’ could not be loaded

--- failed re-building ‘GRanges_and_GRangesList_slides.Rnw’

--- re-building ‘GenomicRangesHOWTOs.Rnw’ using Sweave
Loading required package: Rsamtools
Error: package or namespace load failed for ‘Rsamtools’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 6 (label = readGAlignments_2) 
Error : package ‘Rsamtools’ could not be loaded

--- failed re-building ‘GenomicRangesHOWTOs.Rnw’

--- re-building ‘Ten_things_slides.Rnw’ using Sweave

Error: processing vignette 'Ten_things_slides.Rnw' failed with diagnostics:
 chunk 1 (label = setup) 
Error : package or namespace load failed for ‘Rsamtools’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

--- failed re-building ‘Ten_things_slides.Rnw’

SUMMARY: processing the following files failed:
  ‘GenomicRangesIntroduction.Rmd’ ‘ExtendingGenomicRanges.Rnw’
  ‘GRanges_and_GRangesList_slides.Rnw’ ‘GenomicRangesHOWTOs.Rnw’
  ‘Ten_things_slides.Rnw’

Error: Vignette re-building failed.
Execution halted