Re: [Bioc-devel] help with Win10 TLS problem?

2020-03-19 Thread Hervé Pagès 

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 > 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_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM=

 >
 >    url <-
 >

"https://urldefense.proofpoint.com/v2/url?u=https-3A__bridgedb.github.io_data_gene-5Fdatabase_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM=

 > "
 >    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_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM=

 > "
 >    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 -> 
 >>> -> 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=SDaSu90TFdkKtZZR37pGYXHlqzxNF52W5cEYLNRIl88=

 >>
 >>> 1.
 >>>

Re: [Bioc-devel] help with Win10 TLS problem?

2020-03-18 Thread Hervé Pagès 
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_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM= 

   url <- 
"https://urldefense.proofpoint.com/v2/url?u=https-3A__bridgedb.github.io_data_gene-5Fdatabase_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM= 
"

   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_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=GbdGtFXiT4WW33h7Un9R0XL7r4I1e4JAb9uSyup82Sw=qywf3a1JViBPl5ArNq4vLqt8_csFrFDG_G2MREAWwpM= 
"

   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 -> 
-> 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=SDaSu90TFdkKtZZR37pGYXHlqzxNF52W5cEYLNRIl88= 


1.
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bridgedb_BridgeDbR_blob_master_R_getDatabase.R-23L23=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=IIwoUM7vnfvLY_e0j7jr4Vd3-EFsgGD1khuegLj83KI= 









--
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

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Re: [Bioc-devel] help with Win10 TLS problem?

2020-03-18 Thread 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 -> 
-> 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=SDaSu90TFdkKtZZR37pGYXHlqzxNF52W5cEYLNRIl88=

1.
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bridgedb_BridgeDbR_blob_master_R_getDatabase.R-23L23=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=IIwoUM7vnfvLY_e0j7jr4Vd3-EFsgGD1khuegLj83KI=





--
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

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Re: [Bioc-devel] help with Win10 TLS problem?

2020-03-18 Thread Neumann, Steffen 
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 -> 
> -> 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://bioconductor.org/checkResults/release/bioc-LATEST/BridgeDbR/tokay1-checksrc.html
> 1.
> https://github.com/bridgedb/BridgeDbR/blob/master/R/getDatabase.R#L23
> 
> 
> 
-- 

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB
  
https://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/wissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd/
 

* PSI Spring Meeting Online, 23.-25.03.2020, 
  http://www.psidev.info/hupo-psi-meeting-2020

* Annual symposium of German Society for Metabolomics e.V. (DGMet)
  in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020


---
IPB HalleBioinformatics and Scientific Data
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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