From renaud at mancala.cbio.uct.ac.za  Wed Apr 18 07:22:14 2012
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 18 Apr 2012 07:22:14 +0200 (SAST)
Subject: [Rd] url, readLines, source behind a proxy
In-Reply-To: <CAFDcVCQx1R7gJYnOPC3yzayJxi-Ts9zzaQd5T0bFSnLcOv8nCg@mail.gmail.com>
References: <4F8D234E.1070709@cbio.uct.ac.za>
	<CAFDcVCQx1R7gJYnOPC3yzayJxi-Ts9zzaQd5T0bFSnLcOv8nCg@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1204180705060.27275@mancala.cbio.uct.ac.za>

Hi Henrik,

I am sure it would time out indeed. I am fine with time out due to poor 
connection, but get a bit frustrated if my connection is fine and timeout 
occurs because proxy settings are not read. All the more if I have to run 
R CMD check multiple times and wait for the timeout.
But the issue might also be coming from my proxy, which somehow does not 
like the way url() reads remote content.

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?

Thanks.

Renaud 

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
> 



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