SomaticSignatures 2.7.0
Julian Gehring
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SomaticSignatures | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SomaticSignatures
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* checking for file ‘SomaticSignatures/DESCRIPTION’ ... OK
* preparing ‘SomaticSignatures’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: VariantAnnotation
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated,
append, as.data.frame, as.vector, cbind, colnames,
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, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
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: Rsamtools
Loading required package: XVector
Loading required package: Biostrings
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Loading required package: BSgenome
Loading required package: rtracklayer
Quitting from lines 374-391 (SomaticSignatures-vignette.Rhtml)
Error: processing vignette 'SomaticSignatures-vignette.Rhtml' failed with diagnostics:
The "ifelse" methods for Rle objects are defunct. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
Execution halted