getGEO - cannot Open URL issue
2
1
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alptaciroglu ▴ 50
@alptaciroglu-8859
Last seen 4.6 years ago
Turkey

Dear All,

 

I am trying to download GEO data using getGEO function. Below are the code and error message. I would appreciate if you could let me know whats going on with it. I already tried options('download.file.method'='curl') and it did not work. Thanks. 

 

gse_retrieval<-function(Tumor_gse, GPLs)
{
    basedir=paste(getwd(),'processed_data',sep='/')

#########    1: Libraries########
library(GEOquery)

##########    2: Download Series Matrix and Raw data###########
for(j in 1:length(Tumor_gse))
{
    ######    3: Create GSE names directory########    
    gse_names= as.character(Tumor_gse[j])
    dir.create(gse_names)
    setwd(gse_names)

        #########    4: Series File Retrieval and GPL assignment ############
        series_file=getGEO(gse_names,GSEMatrix=T)
        number_series=1        #will be updated in block if there will be more then one series file
    #If there are more then one series matrix usually they have GPL name in their series matrix file name e.g. GSE19885_GPL96_series_matrix.txt.gz. So we can find our all required GPLs from the names but here in this case there is only one GPL. 
   ################################################################################################

source('GEO_retrieval.R')
source('qualityControl.R')
source('normalization_after_georetrieval.R')
source('pdataAdjustment.R')
gse_try1=c('GSE5586','GSE46844','GSE31712')

GPL='GPL1319'
#dir.create('processed_data')
gse_retrieval(gse_try1,GPL)

 

#############################################################################################    

 

 Error in download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/GSE5586_series_matrix.txt.gz' 

 

##############################################################################################

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] GEOquery_2.34.0     Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] tools_3.2.2    RCurl_1.95-4.7 bitops_1.0-6   XML_3.98-1.3  
getGEO R GEOquery • 7.5k views
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Make sure that you are not behind a firewall (where you would need to set a proxy).  Otherwise, try again in a few hours.  

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I was able to download using a USB modem but I cant download connected to the internet my institute provides. That would mean I need to alter something in my connection right. Can you tell me how to bypass this using institutes internet ?

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See the help for download.file(), and specifically the section on setting proxies.  You may need to consult with your IT support folks to get the proxy correct:

http://stat.ethz.ch/R-manual/R-patched/library/utils/html/download.file.html

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alptaciroglu ▴ 50
@alptaciroglu-8859
Last seen 4.6 years ago
Turkey

I was unable to use getGEO because of institutions proxy settings. Thanks to James W. MacDonald and Sean Davis for helping me out.
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@james-w-macdonald-5106
Last seen 44 minutes ago
United States

There are sometimes weird hiccups when trying to download things, and sometimes you have to try more than once.

> z <- getGEO("GSE5586")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/
Found 1 file(s)
GSE5586_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/GSE5586_series_matrix.txt.gz'
downloaded 455 KB

File stored at:
C:\Users\jmacdon\AppData\Local\Temp\RtmpQX1v3B/GPL1319.soft
Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  downloaded length 9046455 != reported length 200
> z[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 15617 features, 10 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM130391 GSM130392 ... GSM130400 (10 total)
  varLabels: title geo_accession ... data_row_count (34 total)
  varMetadata: labelDescription
featureData
  featureNames: AFFX-BioB-3_at AFFX-BioB-5_at ... DrAffx.3.1.S1_at (15617 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL1319
>

Not sure about the error about file size - AFAICT it's the full length data set.
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I tried at least 10 times and It is not working. I also removed the option of GSEMatrix = T from the code and it did not work that either. (which was the only thing that is different in your code and mine)

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The difference is that I tested on Windows and you are on some sort of *nix OS.

This works:

> z <- getGEO("GSE5586")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/
Found 1 file(s)
GSE5586_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/GSE5586_series_matrix.txt.gz'
downloaded 455 KB

File stored at:
C:\Users\jmacdon\AppData\Local\Temp\Rtmp6x61KH/GPL1319.soft
Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  downloaded length 9046455 != reported length 200
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

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_2.34.0     Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.7 bitops_1.0-6   XML_3.98-1.3


This doesn't:

> z <- getGEO("GSE5586")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/
Error in function (type, msg, asError = TRUE)  :
  Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Connection refused
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GEOquery_2.34.0     Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.7 bitops_1.0-6   XML_3.98-1.3

The obvious differences are that on Linux it is using curl to download, and on Windows it is using 'auto', which defaults to wininet.

On Windows:

> options(download.file.method.GEOquery = "curl")
> z <- getGEO("GSE5586")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/
Found 1 file(s)
GSE5586_series_matrix.txt.gz
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: running command 'curl  "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/GSE5586_series_matrix.txt.gz"  -o "C:\Users\jmacdon\AppData\Local\Temp\RtmpOKvIPn/GSE5586_series_matrix.txt.gz"' had status 127
2: In download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  download had nonzero exit status
3: In file(con, "r") :
  cannot open file 'C:\Users\jmacdon\AppData\Local\Temp\RtmpOKvIPn/GSE5586_series_matrix.txt.gz': No such file or directory
> options(download.file.method.GEOquery = "auto")
> z <- getGEO("GSE5586")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/
Found 1 file(s)
GSE5586_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5586/matrix/GSE5586_series_matrix.txt.gz'
downloaded 455 KB

File stored at:
C:\Users\jmacdon\AppData\Local\Temp\RtmpOKvIPn/GPL1319.soft
Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  downloaded length 9046455 != reported length 200

So evidently there is some problem using curl (or wget, which I tried on Linux as well) to get this file, and wininet is magically delicious. This is beyond my ken, and hopefully Sean Davis will step in soon...

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I also tried copy-pasting the URL in a browser which automatically downloaded the desired file to my computer.

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