error reading GSE using getGEO()

Question

[jaleh.amo]

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

[zx8754]

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

[h.mon]

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

[Kevin Blighe]

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

[jaleh.amo]

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

[h.mon]

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().

[jaleh.amo]

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

Answer 1

[h.mon]

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")

[jaleh.amo]

Thank you so much the upgrade worked

[WouterDeCoster]

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.