##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BeadArrayUseCases
###
##############################################################################
##############################################################################


* checking for file ‘BeadArrayUseCases/DESCRIPTION’ ... OK
* preparing ‘BeadArrayUseCases’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘BeadArrayUseCases.rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element,
    setdiff, setequal, union


Attaching package: ‘BiocGenerics’

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, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames,
    sapply, saveRDS, table, tapply, unique, unsplit,
    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: hexbin
Registered S3 method overwritten by 'bit64':
  method          from 
  print.bitstring tools
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: org.Hs.eg.db



Sample Sheet /tmp/RtmpZLQWOP/Rinstdb59265917fc9/BeadArrayUseCases/extdata/Chips/sampleSheet.csv will be used to read the data
Processing section 4613710017_B
Processing section 4613710052_B
Processing section 4613710054_B
Processing section 4616443079_B
Processing section 4616443093_B
Processing section 4616443115_B
Processing section 4616443081_B
Processing section 4616443081_H
Processing section 4616443092_B
Processing section 4616443107_A
Processing section 4616443136_A
Processing section 4616494005_A
HULKing section 4613710017_B
Calculating Neighbourhood
Using locs file to generate neighbours matrix
Loading required package: illuminaHumanv3.db

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Loading required package: Biostrings
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: GenomicRanges

Attaching package: ‘limma’

The following object is masked from ‘package:beadarray’:

    imageplot

The following object is masked from ‘package:BiocGenerics’:

    plotMA

Found 19 file(s)
GSE5350-GPL1355_series_matrix.txt.gz
GSE5350-GPL1708_series_matrix.txt.gz

Error: processing vignette 'BeadArrayUseCases.rnw' failed with diagnostics:
 chunk 48 (label = readFromGEO) 
Error in httr2::req_perform(req) : Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Transferred a partial file [www.ncbi.nlm.nih.gov]

--- failed re-building ‘BeadArrayUseCases.rnw’

SUMMARY: processing the following file failed:
  ‘BeadArrayUseCases.rnw’

Error: Vignette re-building failed.
Execution halted