[BioC] stuck in biocLite("GEOquery")

[Dan Tenenbaum]

On Fri, Mar 4, 2011 at 11:46 AM, Jack Luo <jluo.rhelp at gmail.com> wrote:
> Hi Dan,
>
> Thanks for your reply. You are right that I am using windows and my OS is
> win7.
> Do you think the version of R might be a problem? I use 2.12.2 and the first
> sentence showing after I type biocLite("GEOquery") is:
> Using R version 2.12.2, biocinstall version 2.7.4.
>
> In addition, I am not clear how to figure out which file(s) get stuck, it
> just shows a sliding window with something like:
> xxx/bioc/bin/windows/contrib/2.12/GEO_query2.17.4.zip
>
> I looked at the folder with downloaded packages and can not find GEOquery,
> so I presume it will only show in that folder when all the downloads are
> complete.
>
> The output from sessionInfo() is:
>
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.2
>
> Thanks a bunch,
>
> -Jack


Hi Jack,

It sounds like a network issue, a timeout perhaps. I'm not sure what
else it could be. The repository seems to be working ok.

You might try chooseBioCmirror() and see if there is a mirror closer
to you, then try installing GEOquery again.

Let us know if that works.
Dan


>
>
>
> On Fri, Mar 4, 2011 at 1:50 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Fri, Mar 4, 2011 at 10:44 AM, Jack Luo <jluo.rhelp at gmail.com> wrote:
>> > Hi,
>> >
>> > I am trying to use install GEOquery package in R and type:
>> >
>> > source("http://bioconductor.org/biocLite.R")
>> > biocLite("GEOquery")
>> >
>> > The sliding bar stops at some point, then I stopped the task and repeat
>> > it,
>> > then it stops in another place ..., but still not 100%. I keep doing
>> > this
>> > for many times and it is still not successful yet. For some other
>> > packages,
>> > I've encountered similar problem before, but at most 3 times I repeated,
>> > the
>> > download should be 100% finished.
>> >
>> > Does anyone have similar problem?
>>
>> I'm guessing you're on Windows (but you should post the output of
>> sessionInfo() so that we can know this, plus other information helpful
>> to diagnose the problem).
>>
>> I was just able to install GEOquery using biocLite() on windows and it
>> didn't take long.
>> Of course, I am here at FHCRC; you may be encountering network latency
>> issues.
>>
>> Several files may be downloaded when you install GEOquery. If you
>> could let us know which ones seem to be getting stuck, that would also
>> help.
>>
>> Thanks
>> Dan
>>
>>
>> >
>> > Thanks,
>> >
>> > -Jack
>> >
>> >        [[alternative HTML version deleted]]
>> >
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>> >
>
>