Re: [Bioc-devel] help with Win10 TLS problem?
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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[Bioc-devel] BiSeq package
Hello, I am Katja Hebestreit, and the maintainer of the package BiSeq. I saw that the package is deprecated for Bioc 3.11. Unfortunately I realized just now that the email in the description file is outdated, it should be katja.hebestr...@gmail.com. That's probably why I never received any notification about the errors. Could you let me know what I can do so the package will be part of version 3.11? Thank you very much. Katja [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] help with Win10 TLS problem?
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] Change associated email/github
Redirecting you to bioc-devel for a better response on this. > On Mar 18, 2020, at 3:51 PM, Russell Bainer wrote: > > Sorry, one last question. Is there a way to change the email associated with > my user on the support site? > > https://support.bioconductor.org/u/10923/ > > -R > > On Wed, Mar 18, 2020 at 10:56 AM Russell Bainer wrote: > Oh, great- I think I am in and have updated my profile credentials. Thanks so > much for all of the n00b question help. > > Stay safe > > -R > > On Wed, Mar 18, 2020 at 10:50 AM Turaga, Nitesh > wrote: > It seems you already have an account with that email. > > You can just hit forgot password to > https://git.bioconductor.org/BiocCredentials/password_reset/ reset. > > > > > On Mar 18, 2020, at 1:47 PM, Russell Bainer wrote: > > > > Thank you, this one is fine. > > > > russ.bai...@gmail.com > > github ID is RussBainer > > > > On Wed, Mar 18, 2020 at 10:46 AM Turaga, Nitesh > > wrote: > > I can just change the email for you. > > > > Can you tell me which email you'd like you account to be associated with? > > > > > On Mar 17, 2020, at 5:40 PM, Russell Bainer wrote: > > > > > > Thanks very much for the response. Can you recommend a way to do password > > > recovery? I no longer have access to the registered email address, and > > > I'm afraid that I registered long enough ago that I don't have the > > > password that I used. > > > > > > > > > On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh > > > wrote: > > > Hi, > > > > > > There are a couple of things you'd have to do, > > > > > > 1. In the BiocCredentials app, you'd have to change your email address > > > registered. And update your SSH keys if needed, add your personal Github > > > ID as well. > > > > > > 2. In the DESCRIPTION file of the package, you'd have to change your > > > email address to reflect where you'll be able to receive emails as a > > > maintainer. > > > > > > 3. Update your email address on Bioc-devel mailing list if it is not > > > already registered. > > > > > > Best, > > > > > > Nitesh > > > > > > > On Mar 17, 2020, at 1:34 PM, Russell Bainer > > > > wrote: > > > > > > > > I'd like to change the email address associated with my > > > > Bioconductor account, and also update the ownership of my packages to my > > > > personal Github account (I originally registered both of these with my > > > > employer, and I have since left the company). Could you please direct > > > > me to > > > > documentation that will help me do this? > > > > > > > > Thanks very much > > > > > > > > -R > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > ___ > > > > Bioc-devel@r-project.org mailing list > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > > This email message may contain legally privileged and/or confidential > > > information. If you are not the intended recipient(s), or the employee > > > or agent responsible for the delivery of this message to the intended > > > recipient(s), you are hereby notified that any disclosure, copying, > > > distribution, or use of this email message is prohibited. If you have > > > received this message in error, please notify the sender immediately by > > > e-mail and delete this email message from your computer. Thank you. > > > > > > > > This email message may contain legally privileged and/or confidential > > information. If you are not the intended recipient(s), or the employee or > > agent responsible for the delivery of this message to the intended > > recipient(s), you are hereby notified that any disclosure, copying, > > distribution, or use of this email message is prohibited. If you have > > received this message in error, please notify the sender immediately by > > e-mail and delete this email message from your computer. Thank you. > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___
Re: [Bioc-devel] help with Win10 TLS problem?
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
---
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Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 Tel. +49 (0) 345 5582 - 1470
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[Bioc-devel] help with Win10 TSL problem?
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
--
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Re: [Bioc-devel] Change associated email/github
I can just change the email for you. Can you tell me which email you'd like you account to be associated with? > On Mar 17, 2020, at 5:40 PM, Russell Bainer wrote: > > Thanks very much for the response. Can you recommend a way to do password > recovery? I no longer have access to the registered email address, and I'm > afraid that I registered long enough ago that I don't have the password that > I used. > > > On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh > wrote: > Hi, > > There are a couple of things you'd have to do, > > 1. In the BiocCredentials app, you'd have to change your email address > registered. And update your SSH keys if needed, add your personal Github ID > as well. > > 2. In the DESCRIPTION file of the package, you'd have to change your email > address to reflect where you'll be able to receive emails as a maintainer. > > 3. Update your email address on Bioc-devel mailing list if it is not already > registered. > > Best, > > Nitesh > > > On Mar 17, 2020, at 1:34 PM, Russell Bainer wrote: > > > > I'd like to change the email address associated with my > > Bioconductor account, and also update the ownership of my packages to my > > personal Github account (I originally registered both of these with my > > employer, and I have since left the company). Could you please direct me to > > documentation that will help me do this? > > > > Thanks very much > > > > -R > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Deploy a critical patch
On Tue, Mar 17, 2020 at 11:48 PM Julian Flesch wrote: > Hi Bioc team, > > > I am the maintainer of the package /waddR/. > > We have had built issues on the active branch recently, due a dependency > being unavailable. After pushing a patch, the issues were resolved on > the devel branch. > > Is it possible to merge these critical changes (version 1.1.4) to the > active branch of Bioconductor? > Hi, Julian. If I understand you correctly, you want to fix the RELEASE version as well as the DEVEL version of your package. See http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Sean > > > Best, > > Julian > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
