simpleSingleCell 1.4.1
Aaron Lun
| Snapshot Date: 2019-04-16 16:31:01 -0400 (Tue, 16 Apr 2019) |
| URL: https://git.bioconductor.org/packages/simpleSingleCell |
| Branch: RELEASE_3_8 |
| Last Commit: 63253aa |
| Last Changed Date: 2019-01-08 11:01:14 -0400 (Tue, 08 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | [ ERROR ] | |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data simpleSingleCell
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* checking for file ‘simpleSingleCell/DESCRIPTION’ ... OK
* preparing ‘simpleSingleCell’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: dbplyr
adding rname 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip'
adding rname 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.sdrf.txt'
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
Loading required package: AnnotationDbi
'select()' returned 1:many mapping between keys and columns
Loading required package: GenomicFeatures
'select()' returned 1:1 mapping between keys and columns
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
Attaching package: 'limma'
The following object is masked from 'package:scater':
plotMDS
The following object is masked from 'package:BiocGenerics':
plotMA
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
adding rname 'https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_mRNA_17-Aug-2014.txt'
adding rname 'https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_mito_17-Aug-2014.txt'
adding rname 'https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_spikes_17-Aug-2014.txt'
'select()' returned 1:many mapping between keys and columns
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
adding rname 'http://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k/pbmc4k_raw_gene_bc_matrices.tar.gz'
Loading required package: ensembldb
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:scater':
filter
The following object is masked from 'package:stats':
filter
Warning in xy.coords(x, y, xlabel, ylabel, log) :
1 y value <= 0 omitted from logarithmic plot
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
Warning: 'add_ticks' is deprecated.
Use '+ geom_rug(...)' instead.
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz'
Warning: download failed
web resource path: 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz'
local file path: 'raw_data/8a75845c57c_GSE81076%255FD2%255F3%255F7%255F10%255F17%252Etxt%252Egz'
reason: Server denied you to change to the given directory
Warning: bfcadd() failed; resource removed
rid: BFC7
fpath: 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz'
reason: download failed
Warning in value[[3L]](cond) :
trying to add rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz' produced error:
bfcadd() failed; see warnings()
Quitting from lines 50-54 (work-5-mnn.Rmd)
Error: processing vignette 'work-5-mnn.Rmd' failed with diagnostics:
not all 'rnames' found or unique.
Execution halted