[Bioc-devel] RCurl on Windows
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Mon Nov 23 19:35:49 CET 2020
Curious situation, that we can hope will be resolved with action at CRAN.
FWIW RCurl for windows is building/checking without incident:
The UniProt.ws check failure on malbec2 etc. seems unrelated, the URL noted
in the failure report
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>
>> 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>
>>> 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
>>> 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?
>>> James W. MacDonald, M.S.
>>> 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
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> James W. MacDonald, M.S.
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
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