recount 1.6.3
Leonardo Collado-Torres
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/recount |
| Branch: RELEASE_3_7 |
| Last Commit: 9b98081 |
| Last Changed Date: 2018-07-28 02:20:41 -0400 (Sat, 28 Jul 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | 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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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recount
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* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning in citation("EnsDb.Hsapiens.v79") :
no date field in DESCRIPTION file of package 'EnsDb.Hsapiens.v79'
Warning in citation("org.Hs.eg.db") :
no date field in DESCRIPTION file of package 'org.Hs.eg.db'
Writing 30 Bibtex entries ... OK
Results written to file 'quickstartRef.bib'
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, lengths, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'application/octet-stream' length 3130229 bytes (3.0 MB)
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downloaded 3.0 MB
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Quitting from lines 594-610 (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
cannot open URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Execution halted