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