BBCAnalyzer 1.1.0
Sarah Sandmann
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BBCAnalyzer | | Last Changed Rev: 109592 / Revision: 109948 | | 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 | NotNeeded | ERROR | skipped | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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### Running command:
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### chmod a+r BBCAnalyzer -R && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BBCAnalyzer
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* checking for file 'BBCAnalyzer/DESCRIPTION' ... OK
* preparing 'BBCAnalyzer':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ...Warning: running command '"c:/biocbld/bbs-3.3-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: BSgenome
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: 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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Determine Target
Analyze Reads
Sample 1 out of 2
Position 1 out of 7
Position 2 out of 7
Position 3 out of 7
Position 4 out of 7
Position 5 out of 7
Position 6 out of 7
Position 7 out of 7
Sample 2 out of 2
Position 1 out of 7
Position 2 out of 7
Position 3 out of 7
Position 4 out of 7
Position 5 out of 7
Position 6 out of 7
Position 7 out of 7
Analyze Frequency
Sample 1
Sample 2
Report Variants
Sample 1
Sample 2
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in plot.window(xlim, ylim, log = log, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, :
`mgp[1:3]' are of differing sign
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 1 else 2, cex.axis = cex.axis, ...) :
`mgp[1:3]' are of differing sign
Warning in plot.window(xlim, ylim, log = log, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, :
`mgp[1:3]' are of differing sign
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 1 else 2, cex.axis = cex.axis, ...) :
`mgp[1:3]' are of differing sign
Determine Target
Analyze Reads
Sample 1 out of 2
Position 1 out of 3
Position 2 out of 3
Position 3 out of 3
Sample 2 out of 2
Position 1 out of 3
Position 2 out of 3
Position 3 out of 3
Analyze Frequency
Sample 1
Sample 2
Error: processing vignette 'BBCAnalyzer.Rnw' failed with diagnostics:
chunk 2 (label = Example2)
Error in if (nchar(as.character(vcf[k, 5])) > 1 && vcountPattern(",", :
missing value where TRUE/FALSE needed
Execution halted