On 14 October 2008 at 12:38, Prof Brian Ripley wrote: | The error is on installed.packages(): you have a faulty package installed.
Confirmed. That explains why my update.r from littler worked as it looked only at /usr/local/lib/R/. Being more explicit about lib.loc I get: > update.packages(repos="http://cran.r-project.org";, > lib.loc="/usr/lib/R/site-library") Error in read.dcf(pkgpath, fields = fields) : Line starting 'unix; ...' is malformed! > update.packages(repos="http://cran.r-project.org";, > lib.loc="/usr/lib/R/library") boot : Version 1.2-33 installed in /usr/lib/R/library Version 1.2-34 available at http://cran.r-project.org Update (y/N/c)? n [...] > But how do I find out which package this is, and why did R 2.7.2 didn't fall over? Dirk | | On Tue, 14 Oct 2008, Dirk Eddelbuettel wrote: | | > | > On 14 October 2008 at 10:09, Prof Brian Ripley wrote: | > | On Tue, 14 Oct 2008, Peter Dalgaard wrote: | > | | > | > [EMAIL PROTECTED] 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). | > | > Quite possible. This is a fresh failure picking the 'US (MI)' mirror: | > | >> 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! | >> traceback() | > 6: read.dcf(pkgpath, fields = fields) | > 5: .readPkgDesc(lib, fields) | > 4: installed.packages(lib.loc = lib.loc) | > 3: NROW(instPkgs) | > 2: old.packages(lib.loc = lib.loc, contriburl = contriburl, method = method, | > available = available, checkBuilt = checkBuilt) | > 1: update.packages() | >> | > | > But if I then re-run chooseCRANmirror() and pick Austria, it still fails: | > | >> chooseCRANmirror() | >> update.packages() | > Error in read.dcf(pkgpath, fields = fields) : | > Line starting 'unix; ...' is malformed! | >> | > | > yielding the same traceback. | > | > Dirk | > | > -- | > Three out of two people have difficulties with fractions. | > | | -- | Brian D. Ripley, [EMAIL PROTECTED] | 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 -- Three out of two people have difficulties with fractions. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
