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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
