Hello, I have been trying to wrap R-based tool to download data from GEO database and I have tried different methods (wget, curl, libcurl, auto) and still get same error. None of these work. Do you have any idea what I'm doing wrong or maybe someone have same issue with "download.file" function?
Fatal error: Exit code 1 () 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, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, 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")'. Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums Attaching package: ‘SummarizedExperiment’ The following objects are masked from ‘package:IRanges’: acbind, arbind locfit 1.5-9.1 2013-03-22 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Warning messages: 1: multiple methods tables found for ‘arbind’ 2: multiple methods tables found for ‘acbind’ 3: replacing previous import ‘IRanges::arbind’ by ‘SummarizedExperiment::arbind’ when loading ‘GenomicAlignments’ 4: replacing previous import ‘IRanges::acbind’ by ‘SummarizedExperiment::acbind’ when loading ‘GenomicAlignments’ 5: replacing previous import ‘SummarizedExperiment::acbind’ by ‘IRanges::acbind’ when loading ‘minfi’ 6: replacing previous import ‘SummarizedExperiment::arbind’ by ‘IRanges::arbind’ when loading ‘minfi’ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51547/matrix/ Found 1 file(s) GSE51547_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51547/matrix/GSE51547_series_matrix.txt.gz'
ftp data connection made, file length 50127506 bytes
downloaded 47.8 MB Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL13534&form=text&view=full' Calls: getGenomicRatioSetFromGEO ... parseGSEMatrix -> getGEO -> getGEOfile -> download.file Execution halted