simpleSingleCell 1.8.0
Aaron Lun
| Snapshot Date: 2019-10-16 11:00:01 -0400 (Wed, 16 Oct 2019) |
| URL: https://git.bioconductor.org/packages/simpleSingleCell |
| Branch: RELEASE_3_9 |
| Last Commit: 0a95c65 |
| Last Changed Date: 2019-05-02 11:34:41 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | [ ERROR ] | |
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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 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
--- re-building ‘batch.Rmd’ using rmarkdown
Loading required package: dbplyr
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz'
Loading required package: AnnotationDbi
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, 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, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
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: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
'select()' returned 1:many mapping between keys and columns
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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, rowsum
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
Warning in isOutlier(QC$feature_control_ERCC$pct_counts, type = "higher", :
missing values ignored during outlier detection
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85241/suppl/GSE85241%5Fcellsystems%5Fdataset%5F4donors%5Fupdated%2Ecsv%2Egz'
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Warning in (function (jobs, data, centers, info, distance, k, query, get.index, :
tied distances detected in nearest-neighbor calculation
Warning in (function (jobs, data, centers, info, distance, k, query, get.index, :
tied distances detected in nearest-neighbor calculation
Warning in .test_block_internal(x, subset.row, clusters, block = block, :
no d.f. for blocked comparison between 13 and 2
--- finished re-building ‘batch.Rmd’
--- re-building ‘bigdata.Rmd’ using rmarkdown
Loading required package: HDF5Array
Loading required package: rhdf5
snapshotDate(): 2019-04-29
see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
downloading 0 resources
loading from cache
'EH1692 : 1692'
--- finished re-building ‘bigdata.Rmd’
--- re-building ‘de.Rmd’ using rmarkdown
Warning in .test_block_internal(x, subset.row, clusters, block = block, :
no d.f. for blocked comparison between 13 and 2
Attaching package: 'limma'
The following object is masked from 'package:scater':
plotMDS
The following object is masked from 'package:BiocGenerics':
plotMA
Attaching package: 'edgeR'
The following object is masked from 'package:SingleCellExperiment':
cpm
--- finished re-building ‘de.Rmd’
--- re-building ‘doublets.Rmd’ using rmarkdown
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2834nnn/GSM2834500/suppl/GSM2834500%5FG%5F1%5Fbarcodes%2Etsv%2Egz'
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2834nnn/GSM2834500/suppl/GSM2834500%5FG%5F1%5Fgenes%2Etsv%2Egz'
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2834nnn/GSM2834500/suppl/GSM2834500%5FG%5F1%5Fmatrix%2Emtx%2Egz'
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: GenomicFeatures
'select()' returned 1:1 mapping between keys and columns
--- finished re-building ‘doublets.Rmd’
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’
--- re-building ‘misc.Rmd’ using rmarkdown
adding rname 'http://www.nature.com/nbt/journal/v33/n2/extref/nbt.3102-S7.xlsx'
Warning: download failed
web resource path: 'http://www.nature.com/nbt/journal/v33/n2/extref/nbt.3102-S7.xlsx'
local file path: 'raw_data/59793c2c1431_nbt.3102-S7.xlsx'
reason: Service Unavailable (HTTP 503).
Warning: bfcadd() failed; resource removed
rid: BFC10
fpath: 'http://www.nature.com/nbt/journal/v33/n2/extref/nbt.3102-S7.xlsx'
reason: download failed
Warning in value[[3L]](cond) :
trying to add rname 'http://www.nature.com/nbt/journal/v33/n2/extref/nbt.3102-S7.xlsx' produced error:
bfcadd() failed; see warnings()
Quitting from lines 109-113 (misc.Rmd)
Error: processing vignette 'misc.Rmd' failed with diagnostics:
not all 'rnames' found or unique.
--- failed re-building ‘misc.Rmd’
--- re-building ‘qc.Rmd’ using rmarkdown
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
sROC 0.1-2 loaded
--- finished re-building ‘qc.Rmd’
--- re-building ‘reads.Rmd’ using rmarkdown
--- finished re-building ‘reads.Rmd’
--- re-building ‘spike.Rmd’ using rmarkdown
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29087/suppl/GSE29087_L139_expression_tab.txt.gz'
--- finished re-building ‘spike.Rmd’
--- re-building ‘tenx.Rmd’ using rmarkdown
--- finished re-building ‘tenx.Rmd’
--- re-building ‘umis.Rmd’ using rmarkdown
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
--- finished re-building ‘umis.Rmd’
--- re-building ‘var.Rmd’ using rmarkdown
--- finished re-building ‘var.Rmd’
SUMMARY: processing the following file failed:
‘misc.Rmd’
Error: Vignette re-building failed.
Execution halted