[RkWard-devel] installing packages hangs

[Thomas Friedrichsmeier]

Hi,

> 1) When running CRAN.packages() in the terminal, I get no window, but am
> provided with a text list of mirrors in the terminal.  I can select a
> mirror by giving its number, and then a list of available packages is
> shown.
>
> 2) When re-creating the error in question in rkward, I entered "42" at the
> "Selection:" prompt (in the terminal), and the list appeared as it should
> in the graphical window of rkward.  I was then able to select packages. 

ok, then. The good news is, I know how to fix this problem (i.e. pop up a 
dialog showing the selection), and it's already on the TODO-list. The bad 
news is, this is not something to whip up in a few minutes, so don't expect a 
solution too soon.

> However, this led me to another bug and another question.
>
> First, the bug:  when I select packages and then attempt to install them, I
> get the following error:
>
> running command: .rk.get.CRAN.packages ()
> Selection: 42
> running command: download.packages (pkgs=c ("g.data", "gdata", "gplots",
> "gregmisc", "gstat", "gtools"), destdir="/root/.rkward/.packagetemp") *
> Installing *source* package 'g.data' ...
> ** R
> ** help
>
>  >>> Building/Updating help pages for package 'g.data'
>
>      Formats: text html latex example
>   g.data.save                       text    html    latex   example
>   g.data.upgrade                    text    html    latex
> ** building package indices ...
> Warning: cannot open file '/tmp/RtmpQWOWbJ/Rf327b23c6'
> Error in file(open = "w+") : unable to open connection
> Execution halted
> ERROR: installing package indices failed
>
>
> For some reason, when it gets to building the package indices, it's looking
> for something in a directory that doesn't exist (/tmp/RtmpQWOWbJ/Rf327b23c6
> does not exist on my system, and I'm not sure what it's looking for there
> anyway.  In fact, the directory /tmp/RtmpQWOWbJ doesn't exist either).

Hmm, this is somewhat strange. Could you, again, try the same thing in a plain 
R session (i.e.:

download.packages (pkgs=c ("g.data", "gdata", "gplots", "gregmisc", "gstat", 
"gtools"), destdir="/root/.rkward/.packagetemp")

) and see whether it works there?
Also, I notice, you seem to be running rkward as root. Maybe R does not behave 
as expected for the root user. Could you try running rkward as a regular 
user, instead?

> Now, the question.  Am I able to set custom mirrors?  For instance, I would
> like to be able to browse the bioconductor repositories, but am not able to
> specify them.

Sorry, no, it simply hasn't been implemented, yet. I'll add this to the 
TODO-list. The workaround should be to specify the "repos" option manually, 
i.e. run this command in the R console:

options (repos=c ("http://my.repository.org/location/", 
"http://another.repository.org/"))

after that packages from both repositories should show up in the dialog (I 
have not tested this myself, though).

Thomas