From renaud at mancala.cbio.uct.ac.za  Thu May 10 10:25:05 2012
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 10 May 2012 10:25:05 +0200
Subject: [Rd] url, readLines, source behind a proxy
In-Reply-To: <CAFDcVCQ4y=1wjz-mc0KUjhyTvgBW929Ja3qFHk2W615rSyeARw@mail.gmail.com>
References: <4F8D234E.1070709@cbio.uct.ac.za>
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	<Pine.LNX.4.64.1204180705060.27275@mancala.cbio.uct.ac.za>
	<CAPPM_gS7LA-rv=__y_QbUi4ketxT9dn3PU=6dm+Sv9q5nU8nkw@mail.gmail.com>
	<4F957794.5090806@stats.ox.ac.uk> <4F96A0B9.4090108@cbio.uct.ac.za>
	<CAFDcVCQ4y=1wjz-mc0KUjhyTvgBW929Ja3qFHk2W615rSyeARw@mail.gmail.com>
Message-ID: <4FAB7B61.6090106@cbio.uct.ac.za>

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
> <renaud at 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
>>>> <renaud at 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
>>>>>> <renaud at 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
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] url, readLines, source behind a proxy
Renaud Gaujoux