Thanks Henrik for the work around.
It worked perfectly and save me lots of check time.
Renaud
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
On 24/04/2012 17:57, Henrik Bengtsson wrote:
Looking at the source code (src/library/tools/R/check.R and
src/library/tools/R/QC.R), I found that...
WORKAROUND:
You can trick 'R CMD check' to quickly skip the
"check_package_CRAN_incoming" test by providing it with invalid URLs
to repositories by setting system environment
'_R_CHECK_XREFS_REPOSITORIES_' to a non-empty URL. For example:
% export _R_CHECK_XREFS_REPOSITORIES_="invalidURL"
% R CMD check --as-cran ...
gives:
* checking CRAN incoming feasibility ...NB: need Internet access to
use CRAN incoming checks
OK
/Henrik
On Tue, Apr 24, 2012 at 5:46 AM, Renaud Gaujoux
<ren...@mancala.cbio.uct.ac.za> wrote:
On 23/04/2012 17:39, Prof Brian Ripley wrote:
On 18/04/2012 16:04, Joshua Ulrich wrote:
Hi Renaud,
On Wed, Apr 18, 2012 at 12:22 AM, Renaud Gaujoux
<ren...@mancala.cbio.uct.ac.za> wrote:
Hi Henrik,
<snip>
Could anybody behind a proxy check if the issue can be reproduced?
My proxy is in fact provided by cntml, which acts as a local proxy that
takes care of tricky authentication protocols with the actual university
proxy, not natively supported by my system (Ubuntu). Anybody in this
case?
I can replicate this on a WinXP system, where I normally have to use
the --internet2 flag to get internet access through a proxy.
?download.file has a section on "Setting Proxies", which describes how
to use environment variables to set proxy information. Setting
http_proxy='http://my.proxy.com/' was enough for me to get R CMD
check to run successfully with the --as-cran flag.
I guess that the simplest way on Windows is to ensure that --internet2 is
set. In R-patched there is a new environment variable R_WIN_INTERNET2 which
lets you do that (set it in ~/.R/check.Renviron).
[Setting proxies is so 20th century -- even moderately competent sysadmins
worked out how to use transparent caching proxies ca 1995. Which is why the
R developers give it a low priority.]
I completely understand the low priority -- fast-illimited-internet based --
point of view. I wish I could live without such a fussy proxy, but I have
not much choice.
I like to understand why things work and do not work though.
Is there any special feature my proxy should have to allow readLines/source
to correctly read remote data? What makes its access different from wget?
Thank you for your insights on this.
Thanks.
Renaud
Best,
--
Joshua Ulrich | FOSS Trading: www.fosstrading.com
R/Finance 2012: Applied Finance with R
www.RinFinance.com
On Tue, 17 Apr 2012, Henrik Bengtsson wrote:
On Tue, Apr 17, 2012 at 1:01 AM, Renaud Gaujoux
<ren...@mancala.cbio.uct.ac.za> wrote:
Hi,
when I run R CMD check with flag --as-cran, the process hangs at
stage:
* checking CRAN incoming feasibility ...
Doesn't it time-out eventually? I'm not behind a proxy but when I've
been running 'R CMD check' whenon very poor 3G connection, it had
eventually timed out.
/Henrik
I am pretty sure it is a proxy issue.
I looked at the check code in the tools package and it seems that the
issue
is in the local function `.repository_db()` (defined in
`tools:::.check_package_CRAN_incoming()`), which eventually calls
`url()`
with argument open="rb", that hangs probably because it does not use
the
proxy settings.
I had a similar issue with `source()`, which apparently uses internal
network functions (not as download.file), but is supposed to work
behind a
proxy (correct?).
Does anybody else have this problem?
I was wondering if there is a way around, as I would like to be able
to use
--as-cran for my checks.
Thank you.
Renaud
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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