bioconductor install problem
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Di Wu ▴ 50
@di-wu-1709
Last seen 9.6 years ago
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
"Di Wu" <dxw51 at="" po.cwru.edu=""> writes: > Dear list, > > I have used bioconductor for several years. Recently, I moved to a new job > and wanted to install R and bioconductor in my new office pc. But I failed > to install bioconductor. R works well. > > Could you help me out? Or give some suggestion? You need to tell R how to access the internet using the web proxy used at your institution. You can read the man page for download.file and/or search the R-help and bioconductor mailing lists as this is a common issue. Perhaps someone who has recently solved this can chime in with a summary of the solution that worked for them. + seth
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I guess you are using R. Start it using the --internet2 option. See more details in the R FAQ (perhaps the R for Windows FAQ). You may have to look at the ?download help page. /Kasper On Jul 12, 2006, at 7:09 PM, Seth Falcon wrote: > "Di Wu" <dxw51 at="" po.cwru.edu=""> writes: > >> Dear list, >> >> I have used bioconductor for several years. Recently, I moved to a >> new job >> and wanted to install R and bioconductor in my new office pc. But >> I failed >> to install bioconductor. R works well. >> >> Could you help me out? Or give some suggestion? > > You need to tell R how to access the internet using the web proxy used > at your institution. > > You can read the man page for download.file and/or search the R-help > and bioconductor mailing lists as this is a common issue. > > Perhaps someone who has recently solved this can chime in with a > summary of the solution that worked for them. > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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Amy Mikhail ▴ 460
@amy-mikhail-1317
Last seen 9.6 years ago
Hi Di Wu, Right click on your R icon and go to the properties tab. You should see the file path written in the "target" box. Add --internet2 to the end of the filepath (this goes after the quotation marks and don't forget the 'space' before --internet2). Cheers, Amy ---------------------------------------------------------------------- ----- Dear list, I have used bioconductor for several years. Recently, I moved to a new job and wanted to install R and bioconductor in my new office pc. But I failed to install bioconductor. R works well. Could you help me out? Or give some suggestion? I use Dell (normal) PC. Our institute uses Novell Network. I use IE and Firefox both. The following is what I got: > source("http://www.bioconductor.org/biocLite.R") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. > utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Error in open.connection(file, "r") : unable to open connection In addition: Warning message: unable to connect to 'cran.r-project.org' on port 80. Warning: unable to access index for repository http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.3 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.3 Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, type = type) : no packages were specified > It seems there is problem to access internet. But I know my internet wokrs well, but it requires to log in each time when you open a new IE, not need to log in for Firefox. Thanks, Yours Di Wu ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab) 00-44-1224-273256 (office)
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