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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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Timeout when use `getGEO` #85

Closed ShixiangWang closed 5 years ago

ShixiangWang commented 5 years ago

I google everywhere I can, but not fix this problem.

> gse <- getGEO('GSE10')
Error in open.connection(x, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
> gse <- getGEO('GSE10')
Error in open.connection(x, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
> gse <- getGEO('GSE10')
Error in open.connection(x, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
> gse <- getGEO('GSE10')
Error in open.connection(x, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds

Session info

> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 os       CentOS Linux 7 (Core)       
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Asia/Shanghai               
 date     2019-04-09                  

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version date       lib source        
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 3.5.1)
 backports      1.1.3   2018-12-14 [1] CRAN (R 3.5.1)
 Biobase      * 2.42.0  2018-10-30 [1] Bioconductor  
 BiocGenerics * 0.28.0  2018-10-30 [1] Bioconductor  
 callr          3.2.0   2019-03-15 [1] CRAN (R 3.5.2)
 cli            1.1.0   2019-03-19 [1] CRAN (R 3.5.1)
 crayon         1.3.4   2017-09-16 [2] CRAN (R 3.5.1)
 curl         * 3.3     2019-01-10 [1] CRAN (R 3.5.1)
 desc           1.2.0   2018-05-01 [1] CRAN (R 3.5.1)
 devtools       2.0.1   2018-10-26 [1] CRAN (R 3.5.2)
 digest         0.6.18  2018-10-10 [2] CRAN (R 3.5.1)
 dplyr          0.8.0.1 2019-02-15 [1] CRAN (R 3.5.2)
 fs             1.2.7   2019-03-19 [1] CRAN (R 3.5.2)
 GEOquery     * 2.50.5  2018-12-22 [1] Bioconductor  
 glue           1.3.1   2019-03-12 [1] CRAN (R 3.5.2)
 hms            0.4.2   2018-03-10 [1] CRAN (R 3.5.2)
 httr         * 1.4.0   2018-12-11 [1] CRAN (R 3.5.1)
 limma          3.38.3  2018-12-02 [1] Bioconductor  
 magrittr       1.5     2014-11-22 [2] CRAN (R 3.5.1)
 memoise        1.1.0   2017-04-21 [1] CRAN (R 3.5.1)
 pillar         1.3.1   2018-12-15 [1] CRAN (R 3.5.2)
 pkgbuild       1.0.3   2019-03-20 [1] CRAN (R 3.5.2)
 pkgconfig      2.0.2   2018-08-16 [1] CRAN (R 3.5.2)
 pkgload        1.0.2   2018-10-29 [1] CRAN (R 3.5.2)
 prettyunits    1.0.2   2015-07-13 [1] CRAN (R 3.5.1)
 processx       3.3.0   2019-03-10 [1] CRAN (R 3.5.1)
 ps             1.3.0   2018-12-21 [1] CRAN (R 3.5.1)
 purrr          0.3.2   2019-03-15 [1] CRAN (R 3.5.2)
 R6             2.4.0   2019-02-14 [1] CRAN (R 3.5.1)
 Rcpp           1.0.1   2019-03-17 [1] CRAN (R 3.5.2)
 readr          1.3.1   2018-12-21 [1] CRAN (R 3.5.2)
 remotes        2.0.2   2018-10-30 [1] CRAN (R 3.5.2)
 rlang          0.3.4   2019-04-07 [1] CRAN (R 3.5.1)
 rprojroot      1.3-2   2018-01-03 [1] CRAN (R 3.5.1)
 rstudioapi     0.10    2019-03-19 [1] CRAN (R 3.5.1)
 sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 3.5.1)
 testthat       2.0.1   2018-10-13 [1] CRAN (R 3.5.1)
 tibble         2.1.1   2019-03-16 [1] CRAN (R 3.5.2)
 tidyr          0.8.3   2019-03-01 [1] CRAN (R 3.5.2)
 tidyselect     0.2.5   2018-10-11 [1] CRAN (R 3.5.2)
 usethis        1.5.0   2019-04-07 [1] CRAN (R 3.5.2)
 withr          2.1.2   2018-03-15 [1] CRAN (R 3.5.1)
 xml2           1.2.0   2018-01-24 [1] CRAN (R 3.5.1)

[1] /public/R/library
[2] /opt/anaconda3/lib/R/library
ShixiangWang commented 5 years ago 
Error in open.connection(x, "rb"): Timeout was reached: Resolving timed out after 10000 milliseconds
Traceback:

1. getGEO("GSE10")
2. getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, 
 .     parseCharacteristics = parseCharacteristics)
3. getDirListing(sprintf(gdsurl, stub, GEO))
4. xml2::read_html(url)
5. read_html.default(url)
6. suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, 
 .     options = options))
7. withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8. read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9. read_xml.character(x, encoding = encoding, ..., as_html = TRUE, 
 .     options = options)
10. read_xml.connection(con, encoding = encoding, ..., as_html = as_html, 
  .     base_url = x, options = options)
11. open(x, "rb")
12. open.connection(x, "rb")
ShixiangWang commented 5 years ago

Finally this QA https://serverfault.com/questions/858649/slow-responses-with-curl-and-wget-on-centos-7?newreg=d2afef92c60a4553a77679a292d8d1ab fix my problem.

seandavi commented 5 years ago

Thanks for reporting that this fix worked for you.

bschilder commented 2 years ago

Hi @seandavi, it seems I'm having a similar issue, but only when I'm running getGET via GitHub Actions (link here):

Screenshot 2022-05-09 at 18 25 10

Oddly, this error occurs on Ubuntu, but works fine on MacOS.

Since I'm running the scripts on GitHub's servers, I don't think I have the necessary permissions to use the solution described by @ShixiangWang . Do you know of any alternative solutions?

Many thanks, Brian