Thankyou! This helped a lot. I had mis-understood some of the chain of
functions which got to the eventual failure. I can confirm that it does indeed
work if you create a url() first and it picks the appropriate back end as long
as the url.method option is set.
For the schannel back end I have:
> libcurlVersion()
[1] "8.6.0"
attr(,"ssl_version")
[1] "(OpenSSL/3.2.1) Schannel"
attr(,"libssh_version")
[1] "libssh2/1.11.0"
However I can't get either of the curl related methods to work.
> download.file('https://seurat.nygenome.org/azimuth/references/homologs.rds',
> destfile = "c:/Users/andrewss/homologs.rds", method="libcurl")
trying URL 'https://seurat.nygenome.org/azimuth/references/homologs.rds'
Error in
download.file("https://seurat.nygenome.org/azimuth/references/homologs.rds";, :
cannot open URL 'https://seurat.nygenome.org/azimuth/references/homologs.rds'
In addition: Warning message:
In download.file("https://seurat.nygenome.org/azimuth/references/homologs.rds";,
:
URL 'https://seurat.nygenome.org/azimuth/references/homologs.rds': status was
'SSL connect error'
> download.file('https://seurat.nygenome.org/azimuth/references/homologs.rds',
> destfile = "c:/Users/andrewss/homologs.rds", method="curl")
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (35) schannel: next InitializeSecurityContext failed:
CRYPT_E_NO_REVOCATION_CHECK (0x80092012) - The revocation function was unable
to check revocation for the certificate.
Error in
download.file("https://seurat.nygenome.org/azimuth/references/homologs.rds";, :
'curl' call had nonzero exit status
I realise that this may not be as simple as the certificate not being seen, and
that the system here may not fake the revocation infrastructure too, but I
don't see that this is going to change, and it's only the winet method which
actually allows anything to connect.
Simon.
-----Original Message-----
From: Ivan Krylov <ikry...@disroot.org>
Sent: 12 September 2024 15:28
To: Simon Andrews via R-devel <r-devel@r-project.org>
Cc: Simon Andrews <simon.andr...@babraham.ac.uk>
Subject: Re: [Rd] Can gzfile be given the same method option as file
В Thu, 12 Sep 2024 12:01:54 +0000
Simon Andrews via R-devel <r-devel@r-project.org> пишет:
> readRDS('https://seurat.nygenome.org/azimuth/references/homologs.rds')
> Error in gzfile(file, "rb") : cannot open the connection
I don't think that gzfile works with URLs. gzcon(), on the other hand, does
work with url() connections, which accepts the 'method' argument and the
getOption('url.method') default.
h <- readRDS(url(
'https://seurat.nygenome.org/azimuth/references/homologs.rds'
))
But that only works with gzip-compressed files. For example, CRAN's
PACKAGES.rds is xz-compressed, and I don't see a way to read it the same way:
readBin(
index <- file.path(
contrib.url(getOption('repos')['CRAN']),
'PACKAGES.rds'
), raw(), 5
) |> rawToChar()
# [1] "\xfd7zXZ" <-- note the "7zXZ" header
readRDS(url(index))
# Error in readRDS(url(index)) : unknown input format
> 2. Given the warnings we're getting when using wininet, are their
> plans to make windows certficates be supported in another way?
What does libcurlVersion() return for you? In theory, it should be possible to
make libcurl use schannel and therefore the system certificate store for TLS
verification purposes.
--
Best regards,
Ivan
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