[BioC] regarding the installation of packages

[Dan Tenenbaum]

On Tue, Oct 2, 2012 at 10:55 PM, shivam agrawal
<shivam.bioinfo at gmail.com> wrote:
> This is the session info of my system.:
>
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ALL_1.4.12           genefilter_1.38.0    GSEABase_1.18.0
> [4] graph_1.34.0         annotate_1.34.1      AnnotationDbi_1.18.4
> [7] Biobase_2.16.0       BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5        IRanges_1.14.4   RSQLite_0.11.2   splines_2.15.1
> [5] stats4_2.15.1    survival_2.36-14 tools_2.15.1     XML_3.9-4.1
> [9] xtable_1.7-0
>
>

See this FAQ:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-Internet-download-functions-fail_002e

Dan


> On Wed, Oct 3, 2012 at 11:22 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Tue, Oct 2, 2012 at 10:49 PM, shivam agrawal
>> <shivam.bioinfo at gmail.com> wrote:
>> > I have a LAN connection in my lab and facing this prblm of
>> > firewall/proxy.
>> > Kindly guide me how can i resolve this prblm.
>>
>> The answer depends on what operating system you have.
>> If you send the output of sessionInfo() we can have more information
>> about your situation.
>> On windows, for example, you can start R as follows:
>>
>> R --internet2
>>
>> Dan
>>
>>
>> >
>> > On Oct 3, 2012 11:11 AM, "Dan Tenenbaum" <dtenenba at fhcrc.org> wrote:
>> >>
>> >> Hi,
>> >>
>> >>
>> >> On Tue, Oct 2, 2012 at 10:38 PM, shivam agrawal [guest]
>> >> <guest at bioconductor.org> wrote:
>> >> >
>> >> > i am trying to install the sequence analysis package
>> >>
>> >> Which package?
>> >>
>> >> >through the commands as given on the web site:
>> >>
>> >> Which web page:
>> >>
>> >> >
>> >> > source("http://bioconductor.org/scratch-repos/pkgInstall.R")
>> >> >
>> >> > Kindly help me out with this...
>> >> >
>> >> >  -- output of sessionInfo():
>> >> >
>> >> > it shows the following error message:
>> >> >
>> >> > Error in file(filename, "r", encoding = encoding) :
>> >> >   cannot open the connection
>> >> > In addition: Warning message:
>> >> > In file(filename, "r", encoding = encoding) :
>> >> >   unable to resolve 'bioconductor.org'
>> >>
>> >> You're missing a command here...what's the actual command that causes
>> >> the
>> >> error?
>> >>
>> >> It looks like you're not connected to the internet, or maybe there is
>> >> a proxy/firewall issue.
>> >> Please post the output of the
>> >> sessionInfo()
>> >>
>> >> command.
>> >> Dan
>> >>
>> >>
>> >> >
>> >> > --
>> >> > Sent via the guest posting facility at bioconductor.org.
>> >> >
>> >> > _______________________________________________
>> >> > Bioconductor mailing list
>> >> > Bioconductor at r-project.org
>> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> > Search the archives:
>> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
> --
> REGARDS
> SHIVAM AGRAWAL
>  M.Sc. BIOINFORMATICS
> DEPARTMENT OF BIOINFORMTICS
> INSTITUTE OF INTER-DISCIPLINARY STUDIES
> UNIVERSITY OF ALLAHABAD
>