recount 1.4.6
Leonardo Collado-Torres
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/recount |
| Branch: RELEASE_3_6 |
| Last Commit: b84043f |
| Last Changed Date: 2018-03-05 23:54:09 -0400 (Mon, 05 Mar 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r recount -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data recount
###
##############################################################################
##############################################################################
* checking for file 'recount/DESCRIPTION' ... OK
* preparing 'recount':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Warning in citation("BiocParallel") :
no date field in DESCRIPTION file of package 'BiocParallel'
Warning in citation("BiocParallel") :
could not determine year for 'BiocParallel' from package DESCRIPTION file
Warning in citation("BiocStyle") :
no date field in DESCRIPTION file of package 'BiocStyle'
Warning in citation("BiocStyle") :
could not determine year for 'BiocStyle' from package DESCRIPTION file
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, cbind, colMeans, colSums, 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, 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
Content type 'application/octet-stream' length 3120155 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "recount-quickstart_files/figure-html/maplot-1.png" -trim "recount-quickstart_files/figure-html/maplot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "recount-quickstart_files/figure-html/maplot-1.png" -trim "recount-quickstart_files/figure-html/maplot-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
Invalid Parameter - /figure-html
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata.
Falling back to 'SRP009615-results.utf8'
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_exon.Rdata'
Content type 'application/octet-stream' length 9002606 bytes (8.6 MB)
==================================================
downloaded 8.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_jx.Rdata'
Content type 'application/octet-stream' length 8515523 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 901-903 (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
argument is of length zero
Execution halted