Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
2
gravatar for martinguerrerog89
5 months ago by
martinguerrerog89250 wrote:

Recently getGEO function of the package GEOquery suddenly started throwing the following error:

gse=getGEO("GSE106977",GSEMatrix=T)
#https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/
#OK
#Found 2 file(s)
#/geo/series/GSE106nnn/GSE106977/
#Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
 #cannot open destfile 'C:\Users\Marti\AppData\Local\Temp\Rtmp8cEqMH//geo/series/GSE106nnn/GSE106977', reason 'No such file or directory'

After some debuging I found that there was an error in the getAndParseGSEMatrices hidden function To overcome this issue I made a patch, that fix the issue.

First copy this code into Rstudio or worpad

getAndParseGSEMatrices=function (GEO, destdir, AnnotGPL, getGPL = TRUE) 
{
  GEO <- toupper(GEO)
  stub = gsub("\\d{1,3}$", "nnn", GEO, perl = TRUE)
  gdsurl <- "https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/"
  b = getDirListing(sprintf(gdsurl, stub, GEO))
  b=b[-1]
  message(sprintf("Found %d file(s)", length(b)))
  ret <- list()
  for (i in 1:length(b)) {
    message(b[i])
    destfile = file.path(destdir, b[i])
    if (file.exists(destfile)) {
      message(sprintf("Using locally cached version: %s", 
                      destfile))
    }
    else {
      download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", 
                            stub, GEO, b[i]), destfile = destfile, mode = "wb", 
                    method = getOption("download.file.method.GEOquery"))
    }
    ret[[b[i]]] <- parseGSEMatrix(destfile, destdir = destdir, 
                                  AnnotGPL = AnnotGPL, getGPL = getGPL)$eset
  }
  return(ret)
}
environment(getAndParseGSEMatrices)<-asNamespace("GEOquery")
assignInNamespace("getAndParseGSEMatrices", getAndParseGSEMatrices, ns="GEOquery")

Save the file as GEOpatch.R in your working directory and then, when loading the GEOquery library, source the saved file:

library(GEOquery)
source("GEOpatch.R")

Now it should get going...

gse=getGEO("GSE106977",GSEMatrix=T)
#https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/
#OK
#Found 1 file(s)
#GSE106977_series_matrix.txt.gz
#trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/GSE106977_series_matrix.txt.gz'
#Content type 'application/x-gzip' length 32707196 bytes (31.2 MB)

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GEOquery_2.40.0      Biobase_2.34.0       BiocGenerics_0.20.0 
[4] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] httr_1.3.1      R6_2.2.2        tools_3.3.2     RCurl_1.95-4.10
[5] bitops_1.0-6    XML_3.98-1.9
microarray geoquery tutorial R geo • 904 views
ADD COMMENTlink modified 3 months ago by Sean Davis24k • written 5 months ago by martinguerrerog89250
2

You have not include the output of sessionInfo(), but I suspect that you are using an outdated version of R/Bioconductor. Updating to the most recent Bioconductor release and R version should fix the problem that you are noticing.

As just an aside, rather than submitting a "tutorial" for how to patch an unknown version of GEOquery, the recommended approach is to report the error or problem via the official bug reporting mechanism to the author. In the case of GEOquery, that is a new issue on GitHub (which you did, I noticed). This way, everyone can benefit from any required code changes. In addition, having users copy-and-paste code without version information, testing, and build checks sidesteps the significant testing that occurs during the GEOquery and Bioconductor build processes.

ADD REPLYlink written 5 months ago by Sean Davis24k

Tagging Sean Davis.

ADD REPLYlink written 5 months ago by h.mon15k

Tnx a lot Martin. i was struggling alot with this prob and now i can finally do my stuff in relief.

ADD REPLYlink written 3 months ago by farzaneafzali10

Upgrading R to the current release version (3.4.) and then installing the matching GEOquery version will fix the problem noted in the original post.

ADD REPLYlink modified 3 months ago • written 3 months ago by Sean Davis24k
2
gravatar for Sean Davis
3 months ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

Sorry for the late reply. Upgrading R and GEOquery will fix the issue noted here.

ADD COMMENTlink written 3 months ago by Sean Davis24k
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