[Bioc-devel] RCurl on Windows

[Vincent Carey]

Curious situation, that we can hope will be resolved with action at CRAN.
FWIW RCurl for windows is building/checking without incident:

https://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html

The UniProt.ws check failure on malbec2 etc. seems unrelated, the URL noted
in the failure report

http://bioconductor.org/checkResults/3.13/bioc-LATEST/UniProt.ws/malbec2-buildsrc.html

resolves for me when attempted manually.

There are 59 bioc packages, some quite central, that declare "depends" or
"imports" on RCurl.

On Mon, Nov 23, 2020 at 12:54 PM James W. MacDonald <jmacdon using uw.edu> wrote:

> It's not something I need, per se, but what other packages that depend on
> RCurl need. This issue was brought to my attention because someone on the
> support site had a problem with the UniProt.ws package, which uses RCurl to
> download data. Given the reverse dependency tree for RCurl I assume this
> problem will have an outsized effect, at least amongst Windows users.
>
> I know that DTL wrote the package back in the day, but apparently the CRAN
> maintainers have been de facto maintainers/authors since 2013. So I sent
> them the same reproducible error. Anyway, there isn't a current version on
> Github (there is a two-year old version at github.com/cran/RCurl), so
> there isn't a more interactive way to report the error.
>
> On Mon, Nov 23, 2020 at 12:20 PM Vincent Carey <stvjc using channing.harvard.edu>
> wrote:
>
>> I reproduced the problem you noted.  Rebuilding RCurl with (an updated?)
>> openssl for
>> windows is not a slam-dunk for me at the moment.  Can the curl package do
>> what you need?
>>
>> On Mon, Nov 23, 2020 at 11:49 AM James W. MacDonald <jmacdon using uw.edu>
>> wrote:
>>
>>> FYI, there appears to be a problem with RCurl on Windows, most likely due
>>> to building against an old version of OpenSSL. Or at least that's what
>>> Google tells me. Anyway, reproducible code:
>>>
>>> > library(RCurl)
>>> > url <- "www.uniprot.org/mapping"
>>> > params <- c(from = "ACC+ID", to = "PDB_ID", format = "tab", query =
>>> "P31946 P62258")
>>> > getForm(url, .params = params, .opts = list(FOLLOWLOCATION = TRUE))
>>> Error in function (type, msg, asError = TRUE)  :
>>>   error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol
>>> version
>>>
>>> I sent the same to cran using r-project.org, which is the email for the
>>> maintainer. So they have been notified, but maybe somebody knows whomever
>>> is actually maintaining RCurl, and can pull a string?
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance HelpLine
>> at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

-- 
The information in this e-mail is intended only for the person to whom it 
is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline 
<http://www.partners.org/complianceline> . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender 
and properly
dispose of the e-mail.

	[[alternative HTML version deleted]]