R453Plus1Toolbox 1.20.0
Hans-Ulrich Klein
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/R453Plus1Toolbox | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| oaxaca | 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’:
anyDuplicated, append, as.data.frame, as.vector,
cbind, colnames, do.call, duplicated, eval,
evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
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
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
Attaching package: ‘ShortRead’
The following object is masked from ‘package:VariantAnnotation’:
readInfo
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 : 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2
Execution halted