BioC 3.4: BUILD report for CAGEr on tokay1

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### Running command:
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###   chmod a+r CAGEr -R && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CAGEr
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* checking for file 'CAGEr/DESCRIPTION' ... OK
* preparing 'CAGEr':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"C:/Users/biocbuild/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: BSgenome
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce,
    anyDuplicated, append, as.data.frame, cbind,
    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, rownames,
    sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer

Reading in file: C:/Users/biocbuild/bbs-3.4-bioc/tmpdir/RtmpOqFCmZ/Rinstc4467544df7/CAGEr/extdata/Zf.30p.dome.chr17.ctss...

Reading in file: C:/Users/biocbuild/bbs-3.4-bioc/tmpdir/RtmpOqFCmZ/Rinstc4467544df7/CAGEr/extdata/Zf.high.chr17.ctss...

Reading in file: C:/Users/biocbuild/bbs-3.4-bioc/tmpdir/RtmpOqFCmZ/Rinstc4467544df7/CAGEr/extdata/Zf.prim6.rep1.chr17.ctss...

Reading in file: C:/Users/biocbuild/bbs-3.4-bioc/tmpdir/RtmpOqFCmZ/Rinstc4467544df7/CAGEr/extdata/Zf.prim6.rep2.chr17.ctss...

Reading in file: C:/Users/biocbuild/bbs-3.4-bioc/tmpdir/RtmpOqFCmZ/Rinstc4467544df7/CAGEr/extdata/Zf.unfertilized.egg.chr17.ctss...

Normalizing tag count...
	-> zf_unfertilized_egg
	-> zf_high
	-> zf_30p_dome
	-> zf_prim6

Filtering CTSSs below threshold...
Clustering...
	-> zf_unfertilized_egg
	-> zf_high
	-> zf_30p_dome
	-> zf_prim6

Calculating cumulative sum of CAGE signal along clusters...
	-> zf_unfertilized_egg
	-> zf_high
	-> zf_30p_dome
	-> zf_prim6

Getting positions of quantiles within clusters...
	-> zf_unfertilized_egg
	-> zf_high
	-> zf_30p_dome
	-> zf_prim6

Calculating cumulative sum of CAGE signal along clusters...
	-> zf_unfertilized_egg
	-> zf_high
	-> zf_30p_dome
	-> zf_prim6

Calculating shifting score...
Testing for significance using Kolmogorov-Smirnov test...

Fetching sample: Astrocyte_-_cerebellum__donor1...
Warning in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  :
  InternetOpenUrl failed: 'A connection with the server could not be established'

Error: processing vignette 'CAGEr.Rnw' failed with diagnostics:
 chunk 39 
Error in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  : 
  cannot open the connection
Execution halted
BioC 3.4: BUILD report for CAGEr on tokay1

Summary

Command output
