RnaSeqTutorial 0.8.0
Nicolas Delhomme
| Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/RnaSeqTutorial | | Last Changed Rev: 3460 / Revision: 3730 | | Last Changed Date: 2015-10-13 13:14:23 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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### Running command:
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### chmod a+r RnaSeqTutorial -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RnaSeqTutorial
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* checking for file 'RnaSeqTutorial/DESCRIPTION' ... OK
* preparing 'RnaSeqTutorial':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.2-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: easyRNASeq
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: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
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: BSgenome
Loading required package: rtracklayer
Error: processing vignette 'RnaSeqTutorial.Rnw' failed with diagnostics:
chunk 15 (label = Exon Transcript Annotation)
Error : 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
Execution halted