STRINGdb : error with string_db$plot_network()
Entering edit mode
Last seen 1 day ago

Dear experts,

suddenly I'm encountering an error when trying to visualize/plot a network with the package STRINGdb.

Here's what I ran (based on the package vignette) :

Any hints ?


head(diff_exp_example1)     # as in vignette
string_db <- STRINGdb$new( version="11.0b", species=9606, score_threshold=200, input_directory="")
example1_mapped <- string_db$map( diff_exp_example1, "gene", removeUnmappedRows = TRUE )

example1_mapped$STRING_id[1:5]      # mapping was successful
## I get : "9606.ENSP00000362560" "9606.ENSP00000481721" "9606.ENSP00000479355" "9606.ENSP00000369699" "9606.ENSP00000361072"

## try to plot
string_db$plot_network( example1_mapped$STRING_id[1:5] )
## Error in function (type, msg, asError = TRUE)  : 
##  error:1408F119:SSL routines:SSL3_GET_RECORD:decryption failed or bad record mac

## For completeness :

sessionInfo( )
## returns 
#R version 4.1.2 (2021-11-01)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 19042)
#Matrix products: default
#[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
#[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
#[5] LC_TIME=French_France.1252    
#attached base packages:
#[1] stats     graphics  grDevices utils     datasets  methods   base     
#other attached packages:
#[1] STRINGdb_2.4.2
#loaded via a namespace (and not attached):
# [1] igraph_1.2.8       hash_2.2.6.1       Rcpp_1.0.7         magrittr_2.0.1    
# [5] bit_4.0.4          rlang_0.4.12       fastmap_1.1.0      blob_1.2.2        
# [9] plyr_1.8.6         tools_4.1.2        caTools_1.18.2     png_0.1-7         
#[13] plotrix_3.8-2      KernSmooth_2.23-20 DBI_1.1.2          gtools_3.9.2      
#[17] bit64_4.0.5        RColorBrewer_1.1-2 vctrs_0.3.8        bitops_1.0-7      
#[21] RCurl_1.98-1.5     memoise_2.0.1      cachem_1.0.6       RSQLite_2.2.9     
#[25] gsubfn_0.7         compiler_4.1.2     gplots_3.1.1       chron_2.3-56      
#[29] sqldf_0.4-11       proto_1.0.0        pkgconfig_2.0.3

Thank's in advance, Wolfgang Raffelsberger

STRINGdb • 77 views
Entering edit mode

I just realized that there is a more recent version of STRING (it seems the vignette is not up to date), ie 11.5, but I still get a similar "SSL certificate problem" when starting by declaring STRINGdb$new(version="11.5" ...

Entering edit mode

Dear Wolfgang,

As far as I know we haven't changed anything in our certificate setup. However it is not the first time that some users experience issues with trying to use secure protocol, it's usually curl/OS version dependent and I can't reproduce it. I'll submit a bug fix that adds an ability to connect to STRING server via standard http. This should solve the issue you are experiencing.

I'll write again when the bugfix goes public (should be beginning of next week).

Best, Damian.

Entering edit mode

Dear Wolfgang,

The bugfix has now been published. If you still can't plot the network in STRINGdb version >= 2.6.1 you can now add parameter protocol="http" when you create the STRINGdb object:

string_db <- STRINGdb$new( version="11.5", species=9606, score_threshold=200, input_directory="", protocol="http")

This should fix the issue with the certificates.


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