STRINGdb r package blocked by antivirus and changes output?
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Entering edit mode
3.1 years ago
DN99 ▴ 20

I have code that I've used for months to get some gene's STRINGdb identifiers. I haven't changed the code in any way but recently, when I use the R package STRINGdb and its functions that download data from STRINGdb, it' being blocked by my antivirus software, and when I unblock it and run it the results are different to what I used to always get previously. I don't change my data or my code, is there anything that could make this happen?

Specifically the functions I use from STRINGdb are:

library(data.table)
library(STRINGdb)
library(dplyr)
library(plyr)
library(tidyverse)
library(sqldf)

Genelist <- fread("Genelist.txt") #one column of HGNC gene symbols

string_db <- STRINGdb$new(version = "11", species = 9606,
                          score_threshold = 0, input_directory = "")

genes_mapped <- string_db$map(Genelist, "Gene", removeUnmappedRows = TRUE)

Not sure if helpful but the antivirus blocking message I get if I run this with it on is:

trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
Error in download.file(urlStr, temp) : 
  cannot open URL 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
In addition: Warning message:
In download.file(urlStr, temp) :
  InternetOpenUrl failed: 'A connection with the server could not be established'

If I unblock it and run it I get:

 genes_mapped <- string_db$map(Genelist, "Gene", removeUnmappedRows = TRUE)
trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 13253303 bytes (12.6 MB)
downloaded 12.6 MB

trying URL 'https://stringdb-static.org/download/protein.info.v11.0/9606.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 1894048 bytes (1.8 MB)
downloaded 1.8 MB

Which is a message I've always gotten but now the output after this code is different.

STRINGdb R • 970 views
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Entering edit mode

Hi, I imagine that this would be better put [as a question] to the STRING developers, and / or try to contact, directly, the developer of the STRINGdb package.

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