Re: [Rd] [R-sig-Debian] problem with update.packages (PR#13161)

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue, 14 Oct 2008 10:09:15 +0100 (BST)

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

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