Question: download.file function error
0
gravatar for testtoolshed
16 months ago by
testtoolshed30
testtoolshed30 wrote:

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

download.file R • 516 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by testtoolshed30
1
gravatar for Hotz, Hans-Rudolf
16 months ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

I suspect this is due to the general problems accessing the NCBI resources today

Regards, Hans-Rudolf

ADD COMMENTlink written 16 months ago by Hotz, Hans-Rudolf1.8k
0
gravatar for testtoolshed
16 months ago by
testtoolshed30
testtoolshed30 wrote:

Hi Hans-Rudolf,

I try today and have this error again. It is same with other scripts based on "download.file" function (GSE, GSM accession doesn't matter). They used to work before and on my local galaxy. I checked my scripts and xml few times just in case and everything looks fine (no R errors or warnings, no xml issues). What can I do to solve this problem, maybe you have better idea for GEO data download?

Thank you for your support, Kate

ADD COMMENTlink written 16 months ago by testtoolshed30

Have you looked into "Extract reads in Fastq/a format from NCBI SRA" from the toolshed?

Regards, Hans-Rudolf

ADD REPLYlink written 16 months ago by Hotz, Hans-Rudolf1.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 120 users visited in the last hour