Re: [Rd] Recursive dependencies(Rcmdr)

From: John Fox <jfox_at_mcmaster.ca>
Date: Fri 11 Nov 2005 - 16:47:45 GMT


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 install.packages().

Thanks for bringing this to my attention.

John



John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox

> -----Original Message-----
> From: r-devel-bounces@r-project.org
> [mailto:r-devel-bounces@r-project.org] On Behalf Of Prof Brian Ripley
> Sent: Friday, November 11, 2005 10:45 AM
> To: Peter Dalgaard
> Cc: r-devel@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
> 'Suggests'
> 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':
> > /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()
> > [1] "/home/bs/pd/Rlibrary" "/usr/lib64/R/library"
> >
> > --
> > O__ ---- Peter Dalgaard ุster Farimagsgade 5, Entr.B
> > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> > (*) \(*) -- University of Copenhagen Denmark Ph:
> (+45) 35327918
> > ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)
> FAX: (+45) 35327907
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
> --
> Brian D. Ripley, ripley@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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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Sat Nov 12 03:53:38 2005

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