[Rd] Recursive dependencies(Rcmdr)
jfox at mcmaster.ca
Fri Nov 11 17:47:45 CET 2005
Dear Brian and Peter,
I guess that this problem didn't surface before because most use of the
Rcmdr package is on Windows using the package binaries.
I think that I can simply remove mvtnorm (and probably some others as well)
from the Rcmdr dependencies. I'll check more carefully when I have some
time, but I believe that mtvnorm is there just for multcomp, and its
inclusion probably dates to a period before dependencies were resolved by
Thanks for bringing this to my attention.
Department of Sociology
Canada L8S 4M4
> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Prof Brian Ripley
> Sent: Friday, November 11, 2005 10:45 AM
> To: Peter Dalgaard
> Cc: r-devel at stat.math.ethz.ch
> Subject: Re: [Rd] Recursive dependencies(Rcmdr)
> On Fri, 11 Nov 2005, Peter Dalgaard wrote:
> > Something might have slipped by me, but I got into the following
> > situation installing Rcmdr:
> install.packages() does indeed have code to check for
> dependencies of dependencies. I got the message
> also installing the dependencies 'acepack', 'scatterplot3d',
> 'quadprog', 'fBasics', 'Hmisc', 'mlbench', 'randomForest',
> 'SparseM', 'xtable', 'oz', 'leaps', 'dynlm', 'e1071',
> 'tseries', 'chron', 'fCalendar', 'its', 'DAAG', 'abind',
> 'car', 'effects', 'lmtest', 'multcomp', 'mvtnorm', 'relimp',
> 'sandwich', 'strucchange', 'zoo'
> The problem is the ordering. Rcmdr does have mvtnorm in the
> list, and has it after 'multcomp', and install.packages does
> not check that the Suggests list does not have inter-dependencies.
> So we do `do something smarter', but not smart enough.
> > < install.packages("Rcmdr",depend=TRUE) >
> > Oodles of Output, until:
> > * Installing *source* package 'multcomp' ...
> > ** R
> > ** data
> > ** inst
> > ** preparing package for lazy loading
> > Error in dyn.load(x, as.logical(local), as.logical(now)) :
> > unable to load shared library
> > /home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so: cannot open shared
> > object file: No such file or directory Execution halted
> > .... Several oodles more for remaining packages ....
> > ** building package indices ...
> > * DONE (strucchange)
> > The downloaded packages are in
> > /tmp/RtmpF23254/downloaded_packages
> > Warning messages:
> > 1: installation of package 'multcomp' had non-zero exit status in:
> > install.packages("Rcmdr", depend = TRUE)
> > 2: cannot create HTML package index in:
> > tools:::unix.packages.html(.Library)
> > OK, so we start Rcmdr
> >> library(Rcmdr)
> > Loading required package: tcltk
> > Loading required package: car
> > it then detects that multcomp is missing and asks for permission to
> > install it, giving the same result.
> > The thing appears to be that multcomp depends on mvtnorm, but the
> > extra dependency goes undetected. Manual installation of the two
> > works.
> > A workaround is that John adds mvtnorm to the Suggested list for
> > Rcmdr, but I wonder if we couldn't do something smarter.
> >> version
> > _
> > platform x86_64-unknown-linux-gnu
> > arch x86_64
> > os linux-gnu
> > system x86_64, linux-gnu
> > status
> > major 2
> > minor 2.0
> > year 2005
> > month 10
> > day 06
> > svn rev 35749
> > language R
> >> .libPaths()
> >  "/home/bs/pd/Rlibrary" "/usr/lib64/R/library"
> > --
> > O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
> > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> > (*) \(*) -- University of Copenhagen Denmark Ph:
> (+45) 35327918
> > ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)
> FAX: (+45) 35327907
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 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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