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### Running command:
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### /Library/Frameworks/R.framework/Resources/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
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GenomicRangesIntroduction.Rmd’ using rmarkdown
--- finished re-building ‘GenomicRangesIntroduction.Rmd’
--- re-building ‘ExtendingGenomicRanges.Rnw’ using Sweave
--- finished 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.)
2025-11-12 16:20:36.910 R[97318:2222485] XType: Using static font registry.
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
--- finished re-building ‘GRanges_and_GRangesList_slides.Rnw’
--- re-building ‘GenomicRangesHOWTOs.Rnw’ using Sweave
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of
type exon. This information was ignored.
Warning in .makeTxDb_normarg_chrominfo(chrominfo) :
genome version information is not available for this TxDb object
OK
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: ‘AnnotationHub’
The following object is masked from ‘package:Biobase’:
cache
loading from cache
Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
chunk 40 (label = count_table)
Error in library(edgeR) : there is no package called ‘edgeR’
--- failed re-building ‘GenomicRangesHOWTOs.Rnw’
--- re-building ‘Ten_things_slides.Rnw’ using Sweave
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: ‘rtracklayer’
The following object is masked from ‘package:AnnotationHub’:
hubUrl
--- finished re-building ‘Ten_things_slides.Rnw’
SUMMARY: processing the following file failed:
‘GenomicRangesHOWTOs.Rnw’
Error: Vignette re-building failed.
Execution halted