Question: geGeo error - Error in .subset2(x, i) : subscript out of bounds
1
gravatar for yurigorelik
6 months ago by
yurigorelik10
yurigorelik10 wrote:

Hello,

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, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, 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)
GSE59071_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59071/matrix/GSE59071_series_matrix.txt.gz'
Content type 'application/x-gzip' length 20993787 bytes (20.0 MB)
downloaded 20.0 MB

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

 

Any ideas?

geoquery • 385 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald50k • written 6 months ago by yurigorelik10
1

Thanks for the report. Others have noticed this problem, again apparently related to recent changes in readr. You can follow progress here: https://github.com/seandavi/GEOquery/issues/78

ADD REPLYlink written 6 months ago by Sean Davis21k

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

ADD REPLYlink written 6 months ago by yurigorelik10
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