Question: geGeo error - Error in .subset2(x, i) : subscript out of bounds
gravatar for yurigorelik
11 months ago by
yurigorelik10 wrote:


I was working with GEOquery,specifically with the getGEO function but it suddenly started crashing for every GSE I try to donwload unless I set the GSEMatrix to FALSE, I'm not sure what I did but I already even tried to reinstall R out of despair.

This is what it looks like:


> library(GEOquery)
Loading required package: Biobase
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,, basename, cbind, colMeans,
    colnames, colSums, dirname,, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax,,
    pmin,, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>  getGEO("GSE59071", GSEMatrix = TRUE)
Found 1 file(s)
trying URL ''
Content type 'application/x-gzip' length 20993787 bytes (20.0 MB)
downloaded 20.0 MB

Parsed with column specification:
Error in .subset2(x, i) : subscript out of bounds


Any ideas?

geoquery • 662 views
ADD COMMENTlink modified 11 months ago by James W. MacDonald51k • written 11 months ago by yurigorelik10

Thanks for the report. Others have noticed this problem, again apparently related to recent changes in readr. You can follow progress here:

ADD REPLYlink written 11 months ago by Sean Davis21k

Thanks for the rapid reposnse, installing readr directly from github currently seems to do the trick

ADD REPLYlink written 11 months ago by yurigorelik10
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