getGEO error when downloading

[thyagoleal]

Dear developer,

I'm having issues with the main downloader function.

gset <- getGEO(GEO = "GSE35423", GSEMatrix = TRUE)

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35423/matrix/
OK
Found 2 file(s)
/geo/series/GSE35nnn/GSE35423/
**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/GSE35nnn/GSE35423/matrix//geo/series/GSE35nnn/GSE35423/: cannot open destfile '/tmp/RtmpqMvtBj//geo/series/GSE35nnn/GSE35423/', 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/RtmpqMvtBj//geo/series/GSE35nnn/GSE35423/': No such file or directory

I tried several different accessions and download methods in options() and none of them seem to work. I had this a lot in the past, but after a few tries it managed to download. Now, I can't download anything.

options(download.file.method.GEOquery = )

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
[1] GEOquery_2.42.0      Biobase_2.36.2       BiocGenerics_0.22.1 
[4] BiocInstaller_1.26.1

loaded via a namespace (and not attached):
[1] httr_1.3.1      compiler_3.4.4  R6_2.2.2        tools_3.4.4    
[5] RCurl_1.95-4.10 yaml_2.1.18     bitops_1.0-6    XML_3.98-1.11  

[thyagoleal]

It seems that a full upgrade fixed it. Sorry.

[seandavi]

Much better to get a report than to have users suffer. Thanks for the feedback and I am glad to hear that GEOquery is working for you again.