[BioC] stuck in biocLite("GEOquery")

[Dan Tenenbaum]

On Mon, Mar 7, 2011 at 1:19 PM, Jack Luo <jluo.rhelp at gmail.com> wrote:
> Dan,
>
> Thanks, it works. I guess it's just the network issue as you mentioned.
>
> -Jack


Thanks, glad to hear it. Are you saying that you can now install
GEOquery using the default mirror at bioconductor.org, or that it
works after you changed mirrors?

Dan

>
> On Fri, Mar 4, 2011 at 3:36 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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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>> >> >
>> >
>> >
>
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