[R-sig-Debian] warning with install.packages()

Dirk Eddelbuettel edd at debian.org
Wed Dec 5 19:28:19 CET 2007

On 5 December 2007 at 16:04, tyler wrote:
| I'm running R 2.5.1 on Debian Lenny. I'm the only user on a laptop, so
| I gave myself permission to write to /usr/local/lib/R/site-library. I
| can install packages without trouble using install.packages(), but I
| get the following warning:
| Warning message:
| cannot create HTML package index in: tools:::unix.packages.html(.Library) 
| Is this something I should be concerned about?

No -- it just wants to write somewhere else to update the help index. You
have to look inside the tools:::unix.packages.html() function and/or .Library
variable and basically give yourself write mods there too. Or only run
install.packages() when you're root (probably less secure....)

| On a related note, is there any reason to choose install.packages()
| rather than apt-get for installing packages that are available from
| the debian repositories?

No, not at all.  The pkg-bioc project (see the Debian wiki, and CCing the
list) tries to build all of CRAN as .deb files, but it isn't quite there
yet. You basically get to pick whichever way you want to do this.  Eg I at
work and on Ubuntu just let R itself update /usr/local/lib/R/site-packages
and don't use any r-cran-* packages, whereas at home I use a mix.

Hth, Dirk

Three out of two people have difficulties with fractions.

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