On 08/25/2015 01:30 PM, Kevin Ushey wrote:
Hi Martin,
Indeed it does (and I should have confirmed myself with R-patched and R-devel
before posting...)
actually I don't know that it does -- it addresses the symptom but I think there
should be an error from libcurl on the 403 / 404 rather than from read.dcf on
error page...
Martin
Thanks, and sorry for the noise.
Kevin
On Tue, Aug 25, 2015, 13:11 Martin Morgan <mtmor...@fredhutch.org
<mailto:mtmor...@fredhutch.org>> wrote:
On 08/25/2015 12:54 PM, Kevin Ushey wrote:
> Hi all,
>
> The following fails for me (on OS X, although I imagine it's the same
> on other platforms using libcurl):
>
> options(download.file.method = "libcurl")
> options(repos = c(CRAN = "https://cran.rstudio.com/";, CRANextra =
> "http://www.stats.ox.ac.uk/pub/RWin";))
> install.packages("lattice") ## could be any package
>
> gives me:
>
> > options(download.file.method = "libcurl")
> > options(repos = c(CRAN = "https://cran.rstudio.com/";, CRANextra
> = "http://www.stats.ox.ac.uk/pub/RWin";))
> > install.packages("lattice") ## coudl be any package
> Installing package into ‘/Users/kevinushey/Library/R/3.2/library’
> (as ‘lib’ is unspecified)
> Error: Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
>
> This seems to come from a call to `available.packages()` to a URL that
> doesn't exist on the server (likely when querying PACKAGES on the
> CRANextra repo)
>
> Eg.
>
> > URL <- "http://www.stats.ox.ac.uk/pub/RWin";
> > available.packages(URL, method = "internal")
> Warning: unable to access index for repository
> http://www.stats.ox.ac.uk/pub/RWin
> Package Version Priority Depends Imports LinkingTo Suggests
> Enhances License License_is_FOSS
> License_restricts_use OS_type Archs MD5sum NeedsCompilation
> File Repository
> > available.packages(URL, method = "libcurl")
> Error: Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
>
> It looks like libcurl downloads and retrieves the 403 page itself,
> rather than reporting that it was actually forbidden, e.g.:
>
> >
download.file("http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/mavericks/contrib/3.2/PACKAGES.gz";,
> tempfile(), method = "libcurl")
> trying URL
'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/mavericks/contrib/3.2/PACKAGES.gz'
> Content type 'text/html; charset=iso-8859-1' length 339 bytes
> ==================================================
> downloaded 339 bytes
>
> Using `method = "internal"` gives an error related to the inability to
> access that URL due to the HTTP status 403.
>
> The overarching issue here is that package installation shouldn't fail
> even if libcurl fails to access one of the repositories set.
>
With
> R.version.string
[1] "R version 3.2.2 Patched (2015-08-25 r69179)"
the behavior is to warn with an indication of the repository for which the
problem occurs
> URL <- "http://www.stats.ox.ac.uk/pub/RWin";
> available.packages(URL, method="libcurl")
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin:
Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Package Version Priority Depends Imports LinkingTo Suggests Enhances
License License_is_FOSS License_restricts_use OS_type Archs MD5sum
NeedsCompilation File Repository
> available.packages(URL, method="internal")
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/PACKAGES'
Package Version Priority Depends Imports LinkingTo Suggests Enhances
License License_is_FOSS License_restricts_use OS_type Archs MD5sum
NeedsCompilation File Repository
Does that work for you / address the problem?
Martin
>> sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.4 (Yosemite)
>
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] testthat_0.8.1.0.99 knitr_1.11 devtools_1.5.0.9001
> [4] BiocInstaller_1.15.5
>
> loaded via a namespace (and not attached):
> [1] httr_1.0.0 R6_2.0.0.9000 tools_3.2.2 parallel_3.2.2
whisker_0.3-2
> [6] RCurl_1.95-4.1 memoise_0.2.1 stringr_0.6.2 digest_0.6.4
evaluate_0.7.2
>
> Thanks,
> Kevin
>
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>
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