##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RegParallel
###
##############################################################################
##############################################################################


* checking for file ‘RegParallel/DESCRIPTION’ ... OK
* preparing ‘RegParallel’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RegParallel.Rmd’ using rmarkdown
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: data.table
Loading required package: stringr
Loading required package: survival
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

arm (Version 1.11-2, built: 2020-7-27)

Working directory is /tmp/Rtmp1oq6Hl/Rbuild20634501f675e/RegParallel/vignettes

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

The following objects are masked from 'package:data.table':

    first, second

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

##############################
#RegParallel
##############################

System is:
-- Linux
Blocksize:
-- 500
101 variables have all zeros! Removing these...
Now testing 1890 variables
Cores / Threads:
-- 3
Terms included in model:
-- cell
First 5 formulae:
-- ENSG00000000003 ~ cell
-- ENSG00000000419 ~ cell
-- ENSG00000000457 ~ cell
-- ENSG00000000460 ~ cell
-- ENSG00000000938 ~ cell
Processing 500 formulae, batch 1 of 4
-- index1: 1; index2: 500
Processing 500 formulae, batch 2 of 4
-- index1: 501; index2: 1000
Processing 500 formulae, batch 3 of 4
-- index1: 1001; index2: 1500
Processing final batch 4 of 4
-- index1: 1501; index2: 1890
Done!

##############################
#RegParallel
##############################

System is:
-- Linux
Blocksize:
-- 500
101 variables have all zeros! Removing these...
Now testing 1890 variables
Cores / Threads:
-- 3
Terms included in model:
-- cell
First 5 formulae:
-- ENSG00000000003 ~ cell
-- ENSG00000000419 ~ cell
-- ENSG00000000457 ~ cell
-- ENSG00000000460 ~ cell
-- ENSG00000000938 ~ cell
Processing 500 formulae, batch 1 of 4
-- index1: 1; index2: 500
Processing 500 formulae, batch 2 of 4
-- index1: 501; index2: 1000
Processing 500 formulae, batch 3 of 4
-- index1: 1001; index2: 1500
Processing final batch 4 of 4
-- index1: 1501; index2: 1890
Done!
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE2990_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2990/matrix/GSE2990_series_matrix.txt.gz'
Content type 'application/x-gzip' length 16680570 bytes (15.9 MB)
==================================================
downloaded 15.9 MB

Quitting from lines 187-222 (RegParallel.Rmd) 
Error: processing vignette 'RegParallel.Rmd' failed with diagnostics:
The size of the connection buffer (131072) was not large enough
to fit a complete line:
  * Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`
--- failed re-building ‘RegParallel.Rmd’

SUMMARY: processing the following file failed:
  ‘RegParallel.Rmd’

Error: Vignette re-building failed.
Execution halted