This page was generated on 2021-05-06 12:33:35 -0400 (Thu, 06 May 2021).
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### Running command:
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### chmod a+r sesame -R && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data sesame
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* checking for file 'sesame/DESCRIPTION' ... OK
* preparing 'sesame':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'QC.Rmd' using rmarkdown
Loading required package: sesameData
Loading required package: ExperimentHub
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: rmarkdown
Loading sesameData.
----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". This needs to be done only
| once per SeSAMe installation.
----------------------------------------------------------
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
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: 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
The following object is masked from 'package:ExperimentHub':
cache
The following object is masked from 'package:AnnotationHub':
cache
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
snapshotDate(): 2021-05-05
snapshotDate(): 2021-05-05
--- finished re-building 'QC.Rmd'
--- re-building 'datasanitization.Rmd' using rmarkdown
trying URL 'http://zhouserver.research.chop.edu//sesameData/raw/3999492009_R01C01_Grn.idat'
Content type ' C·'ý' length 8095289 bytes (7.7 MB)
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downloaded 7.7 MB
trying URL 'http://zhouserver.research.chop.edu//sesameData/raw/3999492009_R01C01_Red.idat'
Content type ' C·'ý' length 8095289 bytes (7.7 MB)
==================================================
downloaded 7.7 MB
Quitting from lines 40-49 (datasanitization.Rmd)
Error: processing vignette 'datasanitization.Rmd' failed with diagnostics:
cannot allocate vector of size 76.3 Gb
--- failed re-building 'datasanitization.Rmd'
--- re-building 'largeData.Rmd' using rmarkdown
--- finished re-building 'largeData.Rmd'
--- re-building 'mammal.Rmd' using rmarkdown
Attaching package: 'dplyr'
The following object is masked from 'package:minfi':
combine
The following objects are masked from 'package:Biostrings':
collapse, intersect, setdiff, setequal, union
The following object is masked from 'package:XVector':
slice
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:matrixStats':
count
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:dbplyr':
ident, sql
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
trying URL 'http://zhouserver.research.chop.edu//sesameData/raw/GSM4411982_Grn.idat.gz'
Content type 'application/x-gzip' length 391803 bytes (382 KB)
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downloaded 382 KB
trying URL 'http://zhouserver.research.chop.edu//sesameData/raw/GSM4411982_Red.idat.gz'
Content type 'application/x-gzip' length 393052 bytes (383 KB)
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downloaded 383 KB
--- finished re-building 'mammal.Rmd'
--- re-building 'minfi.Rmd' using rmarkdown
--- finished re-building 'minfi.Rmd'
--- re-building 'mouse.Rmd' using rmarkdown
--- finished re-building 'mouse.Rmd'
--- re-building 'sesame.Rmd' using rmarkdown
Loading required package: DNAcopy
Loading required package: scales
--- finished re-building 'sesame.Rmd'
SUMMARY: processing the following file failed:
'datasanitization.Rmd'
Error: Vignette re-building failed.
Execution halted