R453Plus1Toolbox 1.21.2
Hans-Ulrich Klein
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/R453Plus1Toolbox | | Last Changed Rev: 113044 / Revision: 116626 | | Last Changed Date: 2016-01-28 17:22:03 -0800 (Thu, 28 Jan 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | [ 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 R453Plus1Toolbox
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* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* preparing ‘R453Plus1Toolbox’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* 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, 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, unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
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: Biostrings
Loading required package: XVector
Attaching package: ‘VariantAnnotation’
The following object is masked from ‘package:base’:
tabulate
Warning: 'AVASet(dirname)' is deprecated.
Use 'AVASet(dirname, avaBin)' instead.
See help("Deprecated")
Reading sample data ... done
Reading reference sequences ... done
Reading variant data ... done
Reading amplicon data ... done
Variants:
Amplicons:
assayDataAmp:4 features, 6 samples
element names:forwCountrevCount
featureDataAmp:
Reference sequences:
Loading required package: BiocParallel
Loading required package: GenomicAlignments
combined forward & reverse filter set to 0.05
forward filter set to 0.1
reverse filter set to 0.05
combined forward & reverse filter set to 0
combined forward & reverse filter set to 0
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
chunk 31 (label = plotVariants)
Error in useMart("ensembl", dataset = "hsapiens_gene_ensembl") :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
Execution halted