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Question: getGEO error when trying to download a series matrix file
1
gravatar for rubi
6 months ago by
rubi90
rubi90 wrote:

Hi,

I'm trying to use GEOquery's getGEO for downloading the series matrix file of several studies using their GEO accessions, from my linux cluster.

I originally tried:

geo.accession <- "GSE11675"
out.dir <- "~/Downloads/GSE11675"
GEOquery::getGEO(GEO = geo.accession, GSEMatrix = T, AnnotGPL = T, getGPL = T, destdir = out.dir)

 

And this is the output I get:

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11675/matrix/
OK
Found 2 file(s)
/geo/series/GSE11nnn/GSE11675/

downloaded 0 bytes

Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  cannot download all files
In addition: Warning message:
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/GSE11nnn/GSE11675/matrix//geo/series/GSE11nnn/GSE11675/': status was '404 Not Found'

 

The GEO accession GSE11675 is actually from the GEOquery vignette: https://kasperdanielhansen.github.io/genbioconductor/html/GEOquery.html

 

I get the same error even when just running:

GEOquery::getGEO(GEO = geo.accession)

 

Similarly, if I try to get a specific file, for example:

GEOquery::getGEOSuppFiles(GEO="GPL6244")

 

I get an error:

https://ftp.ncbi.nlm.nih.gov/geo/platform/GPL6nnn/GPL6244/suppl/
OK

downloaded 0 bytes

Error in download.file(file.path(url, i), destfile = file.path(storedir,  : 
  cannot download all files
In addition: Warning message:
In download.file(file.path(url, i), destfile = file.path(storedir,  :
  URL 'https://ftp.ncbi.nlm.nih.gov/geo/platform/GPL6nnn/GPL6244/suppl//mailto:%5bno%20address%20given%5d': status was '404 Not Found'

 

And both happen for both:

options(download.file.method='wget') 
options(download.file.method='curl') 
 

Here's my R session info

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8     
[8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0 data.table_1.10.4-3  limma_3.30.13        rhdf5_2.18.0         Matrix_1.2-7.1       GO.db_3.4.0          org.Hs.eg.db_3.4.0   AnnotationDbi_1.36.0 IRanges_2.8.1        S4Vectors_0.12.1   
[11] Biobase_2.34.0       BiocGenerics_0.20.0  ggplot2_2.2.1.9000   dplyr_0.7.4          bindrcpp_0.2        

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2              org.Ss.eg.db_3.4.0            biovizBase_1.22.0             htmlTable_1.9                 XVector_0.14.0                GenomicRanges_1.26.4          base64enc_0.1-3             
  [8] dichromat_2.0-0               affyio_1.44.0                 topGO_2.26.0                  bit64_0.9-7                   interactiveDisplayBase_1.12.0 codetools_0.2-15              oligoClasses_1.36.0         
[15] splines_3.3.2                 knitr_1.17                    Formula_1.2-2                 jsonlite_1.5                  Rsamtools_1.26.1              cluster_2.0.5                 graph_1.50.0                
[22] shiny_1.0.5                   httr_1.3.1                    backports_1.1.1               assertthat_0.2.0              lazyeval_0.2.1                org.Rn.eg.db_3.4.0            org.Mm.eg.db_3.4.0          
[29] org.Cf.eg.db_3.4.0            acepack_1.4.1                 htmltools_0.3.6               tools_3.3.2                   gtable_0.2.0                  glue_1.2.0                    affxparser_1.46.0           
[36] Rcpp_0.12.15                  org.Mmu.eg.db_3.4.0           Biostrings_2.42.1             preprocessCore_1.36.0         gdata_2.18.0                  rtracklayer_1.34.1            iterators_1.0.8             
[43] stringr_1.2.0                 mime_0.5                      ensembldb_1.6.2               gtools_3.5.0                  parsingUtils_0.1.0            XML_3.98-1.4                  AnnotationHub_2.6.4         
[50] zlibbioc_1.20.0               analysisUtils_0.0.0.9000      scales_0.5.0.9000             BSgenome_1.42.0               org.Sc.sgd.db_3.4.0           VariantAnnotation_1.20.2      SummarizedExperiment_1.2.3  
[57] GEOquery_2.40.0               annotationData_0.1.0          SparseM_1.72                  RColorBrewer_1.1-2            oligo_1.38.0                  yaml_2.1.16                   memoise_1.1.0               
[64] gridExtra_2.3                 biomaRt_2.30.0                rpart_4.1-10                  latticeExtra_0.6-28           stringi_1.1.6                 RSQLite_2.0                   org.Pt.eg.db_3.4.0          
[71] foreach_1.4.3                 checkmate_1.8.5               GenomicFeatures_1.26.0        caTools_1.17.1                BiocParallel_1.8.1            gageData_2.12.0               GenomeInfoDb_1.10.0         
[78] rlang_0.1.6.9003              pkgconfig_2.0.1               matrixStats_0.52.2            bitops_1.0-6                  lattice_0.20-34               purrr_0.2.4                   bindr_0.1                   
[85] GenomicAlignments_1.8.4       htmlwidgets_1.0               bit_1.1-12                    plyr_1.8.4                    magrittr_1.5                  R6_2.2.2                      gplots_3.0.1                
[92] Hmisc_4.0-3                   DBI_0.7                       pillar_1.1.0                  foreign_0.8-67                withr_2.1.1.9000              survival_2.40-1               RCurl_1.95-4.8              
[99] nnet_7.3-12                   tibble_1.4.2                  plottingUtils_0.1.0           KernSmooth_2.23-15            plotly_4.7.1.9000             org.Ce.eg.db_3.4.0            grid_3.3.2                  
[106] blob_1.1.0                    digest_0.6.15                 xtable_1.8-2                  ff_2.2-13                     tidyr_0.8.0                   httpuv_1.3.5                  setEnrichmentTests_0.1.0    
[113] munsell_0.4.3                 viridisLite_0.3.0             Gviz_1.18.1                  

 

ADD COMMENTlink modified 6 months ago • written 6 months ago by rubi90
2
gravatar for Sean Davis
6 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

It looks like you are using a pretty old version of R/Bioconductor. I suspect that an upgrade to R and then re-installing GEOquery will fix the problem. 

ADD COMMENTlink written 6 months ago by Sean Davis21k
0
gravatar for rubi
6 months ago by
rubi90
rubi90 wrote:

Thanks a lot

ADD COMMENTlink written 6 months ago by rubi90
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