[Bioc-devel] help with Win10 TLS problem?

[Hervé Pagès]

The getBridgeNames() function in BridgeDbR uses the following code to 
download the HTML page at https://bridgedb.github.io/data/gene_database/

   url <- "https://bridgedb.github.io/data/gene_database/"
   library(RCurl)
   CURL_SSLVERSION_TLSv1_2 <- 6L
   opts <- curlOptions(sslversion=CURL_SSLVERSION_TLSv1_2)
   site <- basicTextGatherer()
   curlPerform(url=url, writefunction=site$update, .opts=opts)
   html <- site$value()

Not sure why this fails on our Windows builder but if it fails there it 
might fail on other Windows systems. A more portable/reliable way to get 
that HTML document is to use download.file():

   url <- "https://bridgedb.github.io/data/gene_database/"
   destfile <- tempfile()
   download.file(url, destfile)
   html2 <- paste0(readLines(destfile), "\n", collapse="")

   identical(html, html2)  # TRUE

This works everywhere I tested e.g. my laptop, malbec1, merida1, tokay2, 
etc... and doesn't rely on some obscure RCurl/SSL settings.

By doing the same kind of change in their getDatabase() function, the 
BridgeDbR maintainers can get rid of their dependency on RCurl.

Hope this helps,
H.


On 3/18/20 12:20, Neumann, Steffen wrote:
> Hi,
> 
> can you get me the URL that wants to be downloaded ?
> 
> The "tlsv1 alert protocol version" indicates that the proper
> solution might be to notify the server to reconfigure
> the web server supported TLS versions.
> 
> Yours,
> Steffen
> 
> 
> On Wed, 2020-03-18 at 19:55 +0100, Egon Willighagen wrote:
>> Hi all,
>>
>> in the BridgeDbR package I have a TSL issue, just on Windows10 [0]:
>>
>>> location <- getDatabase("Bacillus subtilis")
>>
>> Error in function (type, msg, asError = TRUE)  :
>>    error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert
>> protocol version
>> Calls: getDatabase ... getBridgeNames -> curlPerform -> <Anonymous>
>> -> fun
>> Execution halted
>>
>> This method is using the download.file() method (see [1]). I am not
>> sure
>> what this method uses by default. I have been googling and found a
>> number
>> of suggestions on how to get RCurl to use other SSL version, such as:
>>
>> CURL_SSLVERSION_TLSv1_2 <- 1Lopts <- RCurl::curlOptions(  verbose =
>> TRUE, sslversion = CURL_SSLVERSION_TLSv1_2)download.file(url, file,
>> mode = "wb", .opts=opts)
>>
>>
>> But I haven't found something that works. Error messages are very
>> cryptic,
>> and I'm running out of ideas.
>>
>> Does someone have a suggestion how to debug this? Maybe even have a
>> solution?
>>
>> All feedback is very much appreciated!
>>
>> Egon
>>
>>
>>
>> 0.
>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_BridgeDbR_tokay1-2Dchecksrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU&s=SDaSu90TFdkKtZZR37pGYXHlqzxNF52W5cEYLNRIl88&e=
>> 1.
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bridgedb_BridgeDbR_blob_master_R_getDatabase.R-23L23&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU&s=IIwoUM7vnfvLY_e0j7jr4Vd3-EFsgGD1khuegLj83KI&e=
>>
>>
>>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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