Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
gravatar for martinguerrerog89
8 weeks ago by
martinguerrerog89240 wrote:

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

#Found 2 file(s)
#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}$", "nnn", GEO, perl = TRUE)
  gdsurl <- "https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/"
  b = getDirListing(sprintf(gdsurl, stub, GEO))
  message(sprintf("Found %d file(s)", length(b)))
  ret <- list()
  for (i in 1:length(b)) {
    destfile = file.path(destdir, b[i])
    if (file.exists(destfile)) {
      message(sprintf("Using locally cached version: %s", 
    else {
                            stub, GEO, b[i]), destfile = destfile, mode = "wb", 
                    method = getOption("download.file.method.GEOquery"))
    ret[[b[i]]] <- parseGSEMatrix(destfile, destdir = destdir, 
                                  AnnotGPL = AnnotGPL, getGPL = getGPL)$eset
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:


Now it should get going...

#Found 1 file(s)
#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)

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

[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 • 327 views
ADD COMMENTlink modified 7 weeks ago • written 8 weeks ago by martinguerrerog89240

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 7 weeks ago by Sean Davis24k

Tagging Sean Davis.

ADD REPLYlink written 8 weeks ago by h.mon12k
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