connection to stringdb database server failed
0
0
Entering edit mode
julie • 0
@julie-19182
Last seen 2.9 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 • 500 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Any progress? Did you find out?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi Dimitris, 

It was IP issue and it works for me now. 

ADD REPLY

Login before adding your answer.

Traffic: 338 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6