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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 gmapR
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* 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 <div>:<number>..<number>)
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