Thank you very much, Simon.
I did notice that, when trying to install a relatively small package from
the console, Mac OS believes that R freezes for some time. However, if you
let it be, than the console comes back operational and Mac OS sees R again.
Perhaps a warning message to the new users won't hurt.
I am going to report on genefilter on the BioC list.
Cheers again.
Massimo
On Tue, Apr 14, 2009 at 4:34 PM, Simon Urbanek
<simon.urba...@r-project.org>wrote:
>
> On Apr 14, 2009, at 9:26 , Massimo Pinto wrote:
>
> Hi Simon,
>> Thank you. It's a several minutes hang, on a relatively fast 'university'
>> LAN. But more interestingly, perhaps, Mac OS 'believes' that R is not
>> responding while it goes ahead and installs packages. Does that suffice to
>> claim that installation of extra packages is dysfunctional on my platform?
>>
>
> No, that is (sort of) normal. The installation is synchronous, i.e. R won't
> come back until the installation has finished, so the R GUI won't be able to
> respond to the OS until R handles the control back. The OS interprets this
> as not responding, since the GUI cannot process event while R is installing
> away happily.
>
>
> I have successfully managed to install packages by hand, few days ago,
>> after I had dowloaded them manually, and this had worked - but for
>> "genefilter". Since I was getting stuck with the installation of genefilter,
>> I erased R (following instructions) and re-installed it from the .dmg
>> package. That, however, does not seem to have helped much.
>>
>>
> Well, why don't you tell us what is your problem with genefilter? (Actually
> you may even take this to the BioC list since this appears to be really a
> BioC question ...).
>
> Cheers,
> Simon
>
>
>
>
> Cheers again.
>> Massimo
>>
>> On Tue, Apr 14, 2009 at 3:10 PM, Simon Urbanek <
>> simon.urba...@r-project.org> wrote:
>>
>> On Apr 14, 2009, at 8:57 AM, Massimo Pinto wrote:
>>
>> Greetings,
>> I am having troubles getting R to work on a Mac OS X 10.5.6, Leopard. I
>> have
>> installed R 2.8.1 (R 2.8.1 GUI 1.27 Tiger build 32-bit) from a .dmg file
>> using the Mac OS installer, and, apparently, everything went smoothly.
>> >From R, I would like to install a few basic packages that I will need to
>> run
>> in conjunction with "Agi4x44PreProcess" which I need to use to preprocess
>> my
>> cDNA microarray data. This is what I do from the R console:
>>
>> source("http://bioconductor.org/biocLite.R";)
>> biocLite()
>>
>> I do get a list of the packages that will be installed, but then the
>> system
>> hangs and I have to resort to a "Force Quit".
>> I get the same behaviour when I try the package installer, right from the
>> R
>> GUI. Again, I got a hang.
>>
>>
>> How long is the "hang"? Note that the installation can take a while
>> depending on your connection since some of the packages are big. If R hangs
>> for a while even installing one package, then there may be some problem with
>> your internet connection. In that case you may want to download the files
>> manually (e.g. thorough a proxy) and install them from local files.
>>
>> Cheers,
>> Simon
>>
>>
>> I would greatly appreciate any suggestion toward the resolution of this
>> problem.
>> Yours,
>> Massimo
>>
>> --
>> Massimo Pinto
>> Post Doctoral Research Fellow
>> Enrico Fermi Centre and Italian Public Health Research Institute (ISS),
>> Rome
>> http://claimid.com/massimopinto
>>
>> [[alternative HTML version deleted]]
>>
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>> R-SIG-Mac@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>>
>>
>>
>>
>> --
>> Massimo Pinto
>> Post Doctoral Research Fellow
>> Enrico Fermi Centre and Italian Public Health Research Institute (ISS),
>> Rome
>> http://claimid.com/massimopinto
>>
>
>
--
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto
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