############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gmapR ### ############################################################################## ############################################################################## * checking for file ‘gmapR/DESCRIPTION’ ... OK * preparing ‘gmapR’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘gmapR.Rnw’ using Sweave Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min 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: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GenomicFeatures Loading required package: Seqinfo Loading required package: GenomicRanges Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: BiocIO Loading required package: rtracklayer Loading required package: Rsamtools NOTE: genome 'TP53_demo_3.22.1' already exists, not overwriting Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 18 out-of-bound ranges located on sequence chr17. 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 18 out-of-bound ranges located on sequence chr17. 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 20 out-of-bound ranges located on sequence TP53. 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 18 out-of-bound ranges located on sequence TP53. 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 14 out-of-bound ranges located on sequence TP53. 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 18 out-of-bound ranges located on sequence TP53. 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 14 out-of-bound ranges located on sequence TP53. 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 32 out-of-bound ranges located on sequence TP53. 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. Error parsing TP53:-9550..-9549. Expecting coords (as
:..) Problematic line was: >701792 TP53:-9550..-9549 donor 2 Error: processing vignette 'gmapR.Rnw' failed with diagnostics: chunk 4 (label = set_TP53_splicesites) Error in writeLines(lines, p) : ignoring SIGPIPE signal --- failed re-building ‘gmapR.Rnw’ SUMMARY: processing the following file failed: ‘gmapR.Rnw’ Error: Vignette re-building failed. Execution halted