Question: error reading GSE using getGEO()
0
gravatar for jaleh.amo
2.6 years ago by
jaleh.amo0
jaleh.amo0 wrote:

I am trying to read a GSE file and getting this following error.

 gg = getGEO("GSE6929", GSEMatrix = TRUE)

but I receive the following error

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6929/matrix/
OK
Found 2 file(s)
/geo/series/GSE6nnn/GSE6929/
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  URL https://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6929/matrix//geo/series/GSE6nnn/GSE6929/: cannot open destfile '/tmp/RtmpFquqz8//geo/series/GSE6nnn/GSE6929/', reason 'No such file or directory'
2: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  download had nonzero exit status
3: In file(con, "r") :
  cannot open file '/tmp/RtmpFquqz8//geo/series/GSE6nnn/GSE6929/': No such file or directory

In case you are wondering this is the version of R I am using

sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
R • 1.3k views
ADD COMMENTlink modified 2.6 years ago by zx87549.9k • written 2.6 years ago by jaleh.amo0
1

You might get better response at: https://support.bioconductor.org/

ADD REPLYlink written 2.6 years ago by zx87549.9k
1

In case your GEOquery is old, update it and try again.

Your sessionInfo()is incomplete, as it doesn't show the versions of the packages loaded. I can download without problems the dataset you pointed to, here is my sessionInfo():

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
[1] bindrcpp_0.2.2      GEOquery_2.46.15    Biobase_2.38.0      BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17     tidyr_0.8.1      dplyr_0.7.6      assertthat_0.2.0 R6_2.2.2        
 [6] magrittr_1.5     pillar_1.3.0     stringi_1.2.3    rlang_0.2.1      curl_3.2        
[11] limma_3.34.9     xml2_1.2.0       tools_3.5.1      readr_1.1.1      glue_1.3.0      
[16] purrr_0.2.5      hms_0.4.2        yaml_2.1.19      compiler_3.5.1   pkgconfig_2.0.1 
[21] tidyselect_0.2.4 bindr_0.1.1      tibble_1.4.2
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by h.mon32k
1

I downloaded the dataset without error on my computer. The errors that you have remind me of a R session that just needs to be restarted because it's full of variables and its memory is full-up.

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

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

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

other attached packages:
[1] bindrcpp_0.2.2       GEOquery_2.49.0      Biobase_2.41.1      
[4] BiocGenerics_0.27.1  BiocInstaller_1.31.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17     tidyr_0.8.1      crayon_1.3.4     dplyr_0.7.6     
 [5] assertthat_0.2.0 R6_2.2.2         magrittr_1.5     pillar_1.3.0    
 [9] stringi_1.2.3    rlang_0.2.1      curl_3.2         limma_3.37.3    
[13] xml2_1.2.0       tools_3.5.1      readr_1.1.1      glue_1.2.0      
[17] purrr_0.2.5      hms_0.4.2        compiler_3.5.1   pkgconfig_2.0.1 
[21] tidyselect_0.2.4 bindr_0.1.1      tibble_1.4.2
ADD REPLYlink written 2.6 years ago by Kevin Blighe71k

Sorry I didn't realize it was uploaded incomplete

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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   base     

other attached packages:
[1] GEOquery_2.42.0     Biobase_2.36.2      BiocGenerics_0.22.1

loaded via a namespace (and not attached):
[1] httr_1.3.1      compiler_3.5.0  R6_2.2.2        tools_3.5.0     RCurl_1.95-4.11 bitops_1.0-6    XML_3.98-1.12
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by jaleh.amo0

I don't see something like GEOquery_2.46.15 like in my session, or GEOquery_2.49.0 like in Kevin Blighe session. First load GEOquery with library( GEOquery ), then issue sessionInfo().

ADD REPLYlink written 2.6 years ago by h.mon32k

Sorry fixed it.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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   base     

other attached packages:
[1] GEOquery_2.42.0     Biobase_2.36.2      BiocGenerics_0.22.1

loaded via a namespace (and not attached):
[1] httr_1.3.1      compiler_3.5.0  R6_2.2.2        tools_3.5.0     RCurl_1.95-4.11 bitops_1.0-6    XML_3.98-1.12
ADD REPLYlink written 2.6 years ago by jaleh.amo0
3
gravatar for h.mon
2.6 years ago by
h.mon32k
Brazil
h.mon32k wrote:

Your GEOquery is old (GEOquery_2.42.0), you need to update it:

source("https://bioconductor.org/biocLite.R")
biocLite()

You may have to upgrade BioConductor:

biocLite("BiocUpgrade")
ADD COMMENTlink written 2.6 years ago by h.mon32k

Thank you so much the upgrade worked

ADD REPLYlink written 2.6 years ago by jaleh.amo0
1

I have moved the comment from h.mon to an answer so you can accept it to mark this question as solved.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 2.6 years ago by WouterDeCoster45k
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