BBCAnalyzer 1.13.0
Sarah Sandmann
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BBCAnalyzer |
| Branch: master |
| Last Commit: 7a3b101 |
| Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### chmod a+r BBCAnalyzer -R && C:\Users\biocbuild\bbs-3.9-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 ... ERROR
--- re-building 'BBCAnalyzer.Rnw' using Sweave
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename,
cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get,
grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff,
sort, table, tapply, union, unique, unsplit, which, which.max, which.min
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
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
Error: processing vignette 'BBCAnalyzer.Rnw' failed with diagnostics:
chunk 7 (label = 8)
Error : scanVcf: missing value where TRUE/FALSE needed
path: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpYhEdqJ/Rinst14e413d0715e/BBCAnalyzer/extdata/dbsnp_138.part.vcf.gz
--- failed re-building 'BBCAnalyzer.Rnw'
SUMMARY: processing the following file failed:
'BBCAnalyzer.Rnw'
Error: Vignette re-building failed.
Execution halted