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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