From @|mon@@ndrew@ @end|ng |rom b@br@h@m@@c@uk  Thu Sep 12 17:06:50 2024
From: @|mon@@ndrew@ @end|ng |rom b@br@h@m@@c@uk (Simon Andrews)
Date: Thu, 12 Sep 2024 15:06:50 +0000
Subject: [Rd] Can gzfile be given the same method option as file
In-Reply-To: <20240912172737.1202b2bd@arachnoid>
References: <CWXP123MB619012B710931D02CF91B812D0642@CWXP123MB6190.GBRP123.PROD.OUTLOOK.COM>
 <20240912172737.1202b2bd@arachnoid>
Message-ID: <CWXP123MB6190D38EB374D47862DC5E52D0642@CWXP123MB6190.GBRP123.PROD.OUTLOOK.COM>

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 <ikrylov at disroot.org> 
Sent: 12 September 2024 15:28
To: Simon Andrews via R-devel <r-devel at r-project.org>
Cc: Simon Andrews <simon.andrews at babraham.ac.uk>
Subject: Re: [Rd] Can gzfile be given the same method option as file

? Thu, 12 Sep 2024 12:01:54 +0000
Simon Andrews via R-devel <r-devel at r-project.org> ?????:

> 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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[Rd] Can gzfile be given the same method option as file
Simon Andrews