Question: Getgeo Error
0
gravatar for nazaninhoseinkhan
7.2 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan410 wrote:

Hi Thanks for comments, but the problem has not been solved yet. When I type this command: gds = getGEO('GDS2478'), I get the following error:

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS2nnn/GDS2478/soft/GDS2478.soft.gz'
In addition: Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  InternetOpenUrl failed: 'The server name or address could not be resolved.

Could it be related to slow internet connection or something similar? Thanks anyway for your response. Nazanin

error • 3.7k views
ADD COMMENTlink modified 7.2 years ago by Devon Ryan98k • written 7.2 years ago by nazaninhoseinkhan410

It would be better to use a comment thread at your original question to resolve these issues. You have now posted a variation of the same question 3 times.

ADD REPLYlink written 7.2 years ago by Neilfws49k

Note: this and related questions are now resolved. Questioner posted the resolution as yet another question...with yet more unhelpful tags...which was deleted.

ADD REPLYlink written 7.2 years ago by Neilfws49k
2
gravatar for Sean Davis
7.2 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Your question has nothing to do with GEOquery, really. It looks like you are likely behind a firewall or do not have internet connectivity. Assuming that other software is able to connect to the internet, you will likely need to set up a proxy to get through your firewall. The help page for download.file documents this process.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Sean Davis26k
1

Sometimes, getGEO ( even GEOquery 2.33.8) is really slow even loadings series_matrix file locally.  Update: The reason is indeed the internet connectivity to GEO website is poor. I found getGEO must download GPL from internet if GPL=TRUE but cannot use local GPL file.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Zhilong Jia1.6k
1

GEOquery should use a locally cached GPL now (as of version 2.35.1 or later).  

ADD REPLYlink written 5.9 years ago by Sean Davis26k
1

I had the same problem and this really worked for me. Thanks Sean.

ADD REPLYlink written 5.8 years ago by mpereraalberto10
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