[Bioc-devel] help with Win10 TLS problem?
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Thu Mar 19 21:46:15 CET 2020
Did it work?
On 3/18/20 15:41, Egon Willighagen wrote:
> Thanks, in going to try your suggestion tomorrow!
>
> On Wed, Mar 18, 2020, 23:22 Hervé Pagès <hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>> wrote:
>
> mmh.. for some reason the original post in this thread is only showing
> up now in my mailbox i.e. way after Steffen's answer (and even if
> Steffen's answer includes the original post, I must confess that I
> didn't really pay attention to it)
>
> Anyway, based on that original post I see now that Egon was using
> download.file() but this was not working on Windows 10 so he
> switched to
> the RCurl solution. And the RCurl solution works on Windows 10 but now
> fails on our Windows builders (Windows Server 2012 R2 Standard). Do I
> get the situation right?
>
> H.
>
>
> On 3/18/20 14:53, Hervé Pagès wrote:
> > The getBridgeNames() function in BridgeDbR uses the following
> code to
> > download the HTML page at
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bridgedb.github.io_data_gene-5Fdatabase_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw&s=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM&e=
>
> >
> > url <-
> >
> "https://urldefense.proofpoint.com/v2/url?u=https-3A__bridgedb.github.io_data_gene-5Fdatabase_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw&s=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM&e=
>
> > "
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__bridgedb.github.io_data_gene-5Fdatabase_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw&s=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM&e=
>
> > "
> > 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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
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: hpages using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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