connection to stringdb database server failed
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julie • 0
@julie-19182
Last seen 5.9 years ago

When I run the command string_db$plot_network( hits ), I got the following error: Error in function (type, msg, asError = TRUE) :Failed to connect to version10.string-db.org port 80: Connection timed out. When I pasted version10.string-db.org to webbrowser, it can't connect either with the error message "Unable to round-trip http request to upstream: dial tcp 194.94.44.34:80: i/o timeout". It seems to me that this server is down, anybody know what I should do, or whom I should report this error? Thank you a lot! 

 

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] STRINGdb_1.22.0

loaded via a namespace (and not attached):
 [1] igraph_1.2.2       hash_2.2.6         Rcpp_1.0.0         magrittr_1.5      
 [5] bit_1.1-14         blob_1.1.1         plyr_1.8.4         tools_3.5.2       
 [9] caTools_1.17.1.1   png_0.1-7          plotrix_3.7-4      KernSmooth_2.23-15
[13] DBI_1.0.0          gtools_3.8.1       bit64_0.9-7        digest_0.6.18     
[17] RColorBrewer_1.1-2 bitops_1.0-6       RCurl_1.95-4.11    memoise_1.1.0     
[21] RSQLite_2.1.1      gsubfn_0.7         gdata_2.18.0       compiler_3.5.2    
[25] gplots_3.0.1       sqldf_0.4-11       chron_2.3-53       pkgconfig_2.0.2   
[29] proto_1.0.0       

sringdb problem with connection • 1.4k views
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I can confirm this with the current version in devel branch.  There may be an issue with the URL generated in the call to plot_network.  I conjecture this because the api seems to work when used directly ... e.g., with https://string-db.org/api/image/network?identifiers=TP53%0dEGFR&add_white_nodes=10&network_flavor=actions.  You should contact the STRINGdb package maintainer.

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Hi Vincent, Thank you very much. I am going to contact the STRINGdb package maintainer. 

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Any progress? Did you find out?

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Hi Dimitris, Not yet. Will let you know when I do. 

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Hi Dimitris, 

It was IP issue and it works for me now. 

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