i am trying to install the sequence analysis package through the commands as given on the web site: 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' -- Sent via the guest posting facility at bioconductor.org.

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

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

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 >