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
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.
Hi Vincent, Thank you very much. I am going to contact the STRINGdb package maintainer.
Any progress? Did you find out?
Hi Dimitris, Not yet. Will let you know when I do.
Hi Dimitris,
It was IP issue and it works for me now.