SeqGSEA 1.23.4
Xi Wang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SeqGSEA |
| Branch: master |
| Last Commit: e8eba9b |
| Last Changed Date: 2018-12-13 14:48:46 -0400 (Thu, 13 Dec 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| 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 | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SeqGSEA
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* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* preparing ‘SeqGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SeqGSEA.Rnw’ using Sweave
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Warning: executing %dopar% sequentially: no parallel backend registered
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning: closing unused connection 6 (<-localhost:11245)
Warning: closing unused connection 5 (<-localhost:11245)
Warning in .local(object, ...) :
in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
chunk 34 (label = main_gsea)
Error in checkDataset(dataset = dataset, mart = mart) :
The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
--- failed re-building ‘SeqGSEA.Rnw’
SUMMARY: processing the following file failed:
‘SeqGSEA.Rnw’
Error: Vignette re-building failed.
Execution halted