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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data VariantAnnotation
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, basename, cbind, colMeans, colSums,
colnames, dirname, do.call, duplicated, eval, evalq, get,
grep, grepl, intersect, is.unsorted, lapply, lengths,
mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit,
which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
type
The following object is masked from ‘package:base’:
strsplit
Attaching package: ‘VariantAnnotation’
The following object is masked from ‘package:base’:
tabulate
Please note that the SNPlocs.Hsapiens.dbSNP.20101109 package
contains outdated dbSNP data and will be deprecated in the near
future. We highly recommend that you use a SNPlocs package
based on a more recent dbSNP build for your analyses instead.
See available.SNPs() for the list of SNPlocs packages currently
available and make sure to pick up the most recent one.
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 2405 out-of-bound ranges located on
sequences 75253, 74357, 74359, 74360, 74361, 74362, 74363,
74358, 74364, 74365, 75254, 75259, 74368, 74369, 74366, 74367,
74370, 74372, 74373, 74374, 74375, 74378, 74377, 74380, 74381,
75262, 75263, 75265, 75266, 75268, 75269, 75271, 75273, 75276,
75281, 75282, 75283, 74389, 74383, 74384, 74385, 74386, 74387,
75287, 75288, 75286, 75289, 74390, 74391, 74392, 74393, 74394,
75291, 74395, 74396, 74397, 74398, 75302, 75304, 75305, and
75306. 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.
'select()' returned many:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 2405 out-of-bound ranges located on
sequences 75253, 74357, 74359, 74360, 74361, 74362, 74363,
74358, 74364, 74365, 75254, 75259, 74368, 74369, 74366, 74367,
74370, 74372, 74373, 74374, 74375, 74378, 74377, 74380, 74381,
75262, 75263, 75265, 75266, 75268, 75269, 75271, 75273, 75276,
75281, 75282, 75283, 74389, 74383, 74384, 74385, 74386, 74387,
75287, 75288, 75286, 75289, 74390, 74391, 74392, 74393, 74394,
75291, 74395, 74396, 74397, 74398, 75302, 75304, 75305, and
75306. 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.
Loading required package: RSQLite
Warning: 228 keys not found in PolyPhen database: rs114264124 rs149209714 ... rs146628983 rs138319189
Attaching package: ‘Matrix’
The following object is masked from ‘package:VariantAnnotation’:
expand
The following object is masked from ‘package:S4Vectors’:
expand
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
starting prefilter
prefiltering 3791 records
prefiltered to /tmp/RtmpotHKZZ/file720a423540a8
prefilter compressing and indexing ‘/tmp/RtmpotHKZZ/file720a423540a8’
starting filter
filtering 48 records
completed filtering
Attaching package: ‘AnnotationHub’
The following object is masked from ‘package:Biobase’:
cache
Error: processing vignette 'filterVcf.Rnw' failed with diagnostics:
chunk 6 (label = mcf7regulatoryRegions)
Error in value[[3L]](cond) : failed to connect
reason: Timeout was reached: Resolving timed out after 10000 milliseconds
Consider rerunning with 'localHub=TRUE'
Execution halted
