From edd at debian.org  Sat Oct 10 15:50:29 2009
From: edd at debian.org (edd at debian.org)
Date: Sat, 10 Oct 2009 15:50:29 +0200 (CEST)
Subject: [Rd] installing any package fails using 'install.packages()'
	(PR#13996)
Message-ID: <20091010135029.A41AF282EF42@mail.pubhealth.ku.dk>


On 10 October 2009 at 05:25, lmramba at gmail.com wrote:
| Dear all,
| I  installed my R-2.9.2 on my ubuntu version 9.04 successfully  using=
 the
| command
|=20
|    sudo apt-get install r-base-dev
|=20
| The problem is that I cannot install any package.

Huh?  This has _nothing_ to do with the error below.
=20
| See my details below:
|=20
|=20
|=20
| > install.packages("epicalc")
| Warning in install.packages("epicalc") :
|   argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'

This is suspicuous.=20

If you used the Ubuntu package, it would use /usr/local/lib/R/site-libr=
ary by
default.  So if you have a locally built version *you* need to figure o=
ut
what you broke there.

| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| Error in read.dcf(file =3D tmpf) : Line starting '<html> ...' is malf=
ormed!
| >
| > install.packages("lattice")
| Warning in install.packages("lattice") :
|   argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| Error in read.dcf(file =3D tmpf) : Line starting '<html> ...' is malf=
ormed!

No idea but you busted there. But it looks suspiciously like a local er=
ror on
your end.

Set an explicit argument for the repos, e.g. via ~/.Rprofile

    options("repos"=3D"http://cran.us.r-project.org")    ## US mirror

(as I am in the US, adapt accordingly for a close mirror for you) to av=
oid
the tcl/tk query. =20

That, again, works like a charm here on Ubuntu 9.10:

R> install.packages("epicalc")
Warning in install.packages("epicalc") :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://cran.us.r-project.org/src/contrib/epicalc_2.9.2.5.ta=
r.gz'
Content type 'application/x-gzip' length 201849 bytes (197 Kb)         =
    =20
opened URL                                                             =
    =20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D                         =20
downloaded 197 Kb                                                      =
    =20

* Installing *source* package =E2=80=98epicalc=E2=80=99 ...
** R                                      =20
** data                                   =20
** demo                                   =20
** preparing package for lazy loading     =20
Loading required package: splines         =20
** help                                   =20
*** installing help indices               =20
 >>> Building/Updating help pages for package 'epicalc'
     Formats: text html latex example                 =20
  ANCdata                           text    html    latex
[...]
  use                               text    html    latex   example
  zap                               text    html    latex   example
** building package indices ...
* DONE (epicalc)

The downloaded packages are in
        =E2=80=98/tmp/RtmpydkfiZ/downloaded_packages=E2=80=99
R>

If you install into /usr/local/lib/R/site-library, I recommend making t=
hat
directory's group mode one of the ones you have and set it to group-wri=
te.  I
typically make myself member of group 'staff' (or 'admin').

Again, in sum: not a bug in R and you just created extra work for R Cor=
e to
maintain the bug database.

Dirk


| > sessionInfo()
| R version 2.9.2 (2009-08-24)
| i486-pc-linux-gnu
|=20
| locale:
| LC_CTYPE=3Den_GB.UTF-8;LC_NUMERIC=3DC;LC_TIME=3Den_GB.UTF-8;LC_COLLAT=
E=3Den_GB.UTF-8;LC_MONETARY=3DC;LC_MESSAGES=3Den_GB.UTF-8;LC_PAPER=3Den=
_GB.UTF-8;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;LC_MEASUREMENT=3D=
en_GB.UTF-8;LC_IDENTIFICATION=3DC
|=20
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
|=20
| loaded via a namespace (and not attached):
| [1] tcltk_2.9.2 tools_2.9.2
| >
|=20
| =09[[alternative HTML version deleted]]
|=20
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel

--=20
Three out of two people have difficulties with fractions.



[Rd] installing any package fails using 'install.packages()' (PR#13996)
edd at debian.org