VariantFiltering 1.7.1
Robert Castelo
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantFiltering | | Last Changed Rev: 109730 / Revision: 109826 | | Last Changed Date: 2015-10-19 06:47:17 -0400 (Mon, 19 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 VariantFiltering
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* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* preparing ‘VariantFiltering’:
* 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, 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: VariantAnnotation
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 BSgenome annotation package BSgenome.Hsapiens.UCSC.hg19
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Loading SNPlocs annotation package SNPlocs.Hsapiens.dbSNP.20120608
Loading annotation package MafDb.ESP6500SI.V2.SSA137
Loading annotation package MafDb.ALL.wgs.phase1.release.v3.20101123
Loading annotation package MafDb.ExAC.r0.3.sites
Loading annotation package PolyPhen.Hsapiens.dbSNP131
Loading annotation package SIFT.Hsapiens.dbSNP137
Loading annotation package phastCons100way.UCSC.hg19
Fetching annotation object humanGenesPhylostrata
Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics:
chunk 5
Error : The "ifelse" methods for Rle objects are defunct. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
Execution halted