##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges
###
##############################################################################
##############################################################################


* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* preparing ‘GenomicRanges’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package 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.)
2025-01-23 16:21:50.190 R[37957:980483391] XType: com.apple.fonts is not accessible.
2025-01-23 16:21:50.191 R[37957:980483391] XType: XTFontStaticRegistry is enabled.
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

Attaching package: ‘txdbmaker’

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

    UCSCFeatureDbTableSchema, browseUCSCtrack,
    getChromInfoFromBiomart, makeFDbPackageFromUCSC,
    makeFeatureDbFromUCSC, makePackageName, makeTxDb,
    makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF,
    makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage,
    makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC,
    supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables,
    supportedUCSCFeatureDbTracks, supportedUCSCtables

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(DESeq2) : there is no package called ‘DESeq2’

--- 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:BiocIO’:

    FileForFormat

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

    hubUrl

Error in x$.self$finalize() : attempt to apply non-function
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘Ten_things_slides.Rnw’

SUMMARY: processing the following file failed:
  ‘GenomicRangesHOWTOs.Rnw’

Error: Vignette re-building failed.
Execution halted