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3.1 years ago
Parham
★
1.6k
Hi,
I am following RnBeads tutorial and with Ziller2011_PLoSGen_450K data set. The tutorial says that the analysis takes 1 1/2 hours on two compute nodes but for me after overnight run with 4 cores it didn't finish so I had to terminate the process. It seems that there is a problem with some part of the job that the script throughs out Warning in cor(x[i[i <= N]], y) : the standard deviation is zero error for unlimited lines. It never ends and I couldn't stop it so I have to terminate whole R session by ending task on windows. Here I provide library(RnBeads) and sessionInfo()output if it can be helpful. I appreciate if someone can help to figure out the problem.
> library(RnBeads)
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’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: GenomicRanges
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
Loading required package: GenomeInfoDb
Loading required package: MASS
Loading required package: cluster
Loading required package: ff
Loading required package: bit
Attaching package: ‘bit’
The following object is masked from ‘package:base’:
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/POURBP~1/AppData/Local/Temp/RtmpIr52m7/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: ‘ff’
The following objects are masked from ‘package:utils’:
write.csv, write.csv2
The following objects are masked from ‘package:base’:
is.factor, is.ordered
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Attaching package: ‘grid’
The following object is masked from ‘package:ff’:
pattern
Spam version 2.7-0 (2021-06-25) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: ‘spam’
The following object is masked from ‘package:stats4’:
mle
The following objects are masked from ‘package:base’:
backsolve, forwardsolve
Loading required package: viridis
Loading required package: viridisLite
Try help(fields) to get started.
Loading required package: ggplot2
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:IRanges’:
space
The following object is masked from ‘package:S4Vectors’:
space
The following object is masked from ‘package:stats’:
lowess
Loading required package: gridExtra
Attaching package: ‘gridExtra’
The following object is masked from ‘package:BiocGenerics’:
combine
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: matrixStats
Loading required package: illuminaio
Loading required package: methylumi
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 objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Loading required package: scales
Attaching package: ‘scales’
The following object is masked from ‘package:viridis’:
viridis_pal
Loading required package: reshape2
Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:MASS’:
select
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db
Loading required package: minfi
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Attaching package: ‘MatrixGenerics’
The following object is masked from ‘package:Biobase’:
rowMedians
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: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:grid’:
pattern
The following objects are masked from ‘package:ff’:
mismatch, pattern
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)
Loading required package: plyr
Attaching package: ‘plyr’
The following object is masked from ‘package:XVector’:
compact
The following object is masked from ‘package:matrixStats’:
count
The following object is masked from ‘package:IRanges’:
desc
The following object is masked from ‘package:S4Vectors’:
rename
There were 19 warnings (use warnings() to see them)
0
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3.1 years ago by
Parham
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1.6k
