From ripley at stats.ox.ac.uk  Tue Oct 14 11:09:15 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 14 Oct 2008 10:09:15 +0100 (BST)
Subject: [Rd] [R-sig-Debian] problem with update.packages (PR#13161)
In-Reply-To: <48F44CE8.3080409@biostat.ku.dk>
References: <20081014004005.F12F2282EF48@mail.pubhealth.ku.dk>
	<48F44CE8.3080409@biostat.ku.dk>
Message-ID: <alpine.LFD.2.00.0810140845150.20953@gannet.stats.ox.ac.uk>

On Tue, 14 Oct 2008, Peter Dalgaard wrote:

> edd at debian.org wrote:
>> On 14 October 2008 at 09:39, Simon Blomberg wrote:
>> | Hi, is anyone else getting this error? Could this be a bug?:
>> | | > update.packages(ask=FALSE)
>> | Error in read.dcf(pkgpath, fields = fields) : |   Line starting 'unix; 
>> ...' is malformed!
>> | | > sessionInfo()
>> | R version 2.8.0 RC (2008-10-12 r46696) | x86_64-pc-linux-gnu 
>> Confirmed in plain R using the same package built this morning from last
>> night's tarball from Denmark:  Running update.packages() yields:
>> 
>>> update.packages()
>> --- Please select a CRAN mirror for use in this session ---
>> Loading Tcl/Tk interface ... done
>> Error in read.dcf(pkgpath, fields = fields) :
>>   Line starting 'unix; ...' is malformed!
>> 
>> 
>> OTOH I don't have a problem running my 'update.r' script (included in 
>> littler as
>> /usr/share/doc/littler/examples/update.r) which just downloaded / upgraded
>> ten packages. It is equivalent to calling 
>>> repos <- "http://cran.r-project.org"
>>> lib.loc <- "/usr/local/lib/R/site-library"
>>> update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)
>> 
>> and that sequence also works in plain R.  Could someone please dig into
>> update.packages() ? 
>> Dirk 
>
> Hmm, some of us are wary of running update.packages() in non-production 
> versions. Is the problem perhaps originating in getCRANmirors() or 
> chooseCRANmirror()?

(Neither of those read DCF files: my expectation is that this is 
available.packages() reading a DCF file downloaded from a CRAN mirror.)

I do use update.packages() daily on pre-2.8.0 and I have not seen a 
problem.  (I keep a separate package installation for test versions.)

Can we please have some useful debugging info, e.g. the result of 
traceback() and which CRAN mirror is being used?  I suspect a problem with 
downloading PACKAGES.gz resulting in a corrupt file (possibly because it 
was corrupt on the mirror).

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] [R-sig-Debian] problem with update.packages (PR#13161)
Prof Brian Ripley