On 14 October 2008 at 07:27, Dirk Eddelbuettel wrote: | | 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?
Found it -- it was the non-CRAN package 'sg' for the Shogun toolbox. Soeren: There is a bug the in the DESCRIPTION file of shogun-r version 0.6.3-1: It needs to keep this on one line: Built: 2.7.1; i486-pc-linux-gnu; > .Platform[1] unix; or else R's internal updates fail on R 2.8.0 onwards as reported by Simon on r-sig-debian yesterday. R-Core: Please close the bug report on R's side, and thanks as always to BDR for being spot-on in the analysis. Dirk | 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. -- Three out of two people have difficulties with fractions. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel