SplicingGraphs 1.11.0
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| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs | | 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 SplicingGraphs -R && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SplicingGraphs
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* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* preparing 'SplicingGraphs':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* 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: GenomicFeatures
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: AnnotationDbi
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: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:Biostrings':
complement
Loading required package: grid
- plotting genomic range: from=21671261.8, to=21743672.2
- nb of reads to plot (i.e. overlapping with that range): 87
Error: processing vignette 'SplicingGraphs.Rnw' failed with diagnostics:
chunk 44 (label = plotTranscripts_sg_3183_and_reads_as_pdf)
Error : Starting with BioC 3.2, the "grglist" method for GAlignmentPairs objects
*always* returns the ranges "ordered as in query". Therefore the
'order.as.in.query' argument is now ignored (and defunct).
Execution halted