This page was generated on 2023-02-06 11:06:28 -0500 (Mon, 06 Feb 2023).
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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 BSgenome
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* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* preparing ‘BSgenome’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BSgenomeForge.Rnw’ using Sweave
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, aperm, 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
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: GenomicRanges
Loading required package: rtracklayer
--- finished re-building ‘BSgenomeForge.Rnw’
--- re-building ‘GenomeSearching.Rnw’ using Sweave
Loading required package: AnnotationDbi
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")'.
Loading required package: BSgenome.Hsapiens.UCSC.hg38
Error: processing vignette 'GenomeSearching.Rnw' failed with diagnostics:
chunk 24 (label = f1)
Error : package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg38.masked’:
.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38.masked', details:
call: validObject(.Object)
error: invalid class “RdaCollection” object:
files
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273333v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273334v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273335v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273336v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273341v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273342v1_fix.masks.rda',
'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273343v1_fix.masks.rda',
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'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_KQ759759v2_fix.masks.rda',
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'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr20_MU273388v1_fix.masks.rda',
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'/Library
--- failed re-building ‘GenomeSearching.Rnw’
SUMMARY: processing the following file failed:
‘GenomeSearching.Rnw’
Error: Vignette re-building failed.
Execution halted