Download.file R Wb Mode

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Answer 1

@rgentleman-7725

Last seen 6.6 years ago

United States

Dear Fabio, Almost surely there is some local problem (to you). You will need to speak with someone there to find out what that problem might be. Not being able to open a URL from inside of R, suggests that you examine the relevant documentation on setting up other means of downloading (perhaps your site requires the use of a proxy server?), such as wget, etc. which you would need to configure. best wishes Robert Fabio Passetti wrote: > Dear bioconductor developers and mainteiners, > > I have been trying to download since last week some packages either from > the web site or inside R. First, I tried to install inside R, as follows: > > > source("http://bioconductor.org/biocLite.R") > > biocLite("annaffy") > Running biocinstall version 2.1.8 with R version 2.6.0 > Your version of R requires version 2.1 of Bioconductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/storage/carma/R/x86_64-unknown-linux-gnu-library/2.6' > also installing the dependency AnnotationDbi > > trying URL > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi _1.0.6.tar.gz' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL > > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi _1.0.6.tar.gz' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb") : > cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(p0, destdir = tmpd, available = available, : > download of package 'AnnotationDbi' failed > trying URL > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/annaffy_1.10. 0.tar.gz' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL > > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/annaffy_1.10. 0.tar.gz' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb") : > cannot open: HTTP status was '403 Forbidden' > Warning in download.packages(p0, destdir = tmpd, available = available, : > download of package 'annaffy' failed > > Then I have tried to download manually these packages from the > bioconductor web site, but they came corrupted. > > Any help is appreciated. > > Regards, > > Fabio > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Answer 2

@nothing-24422

Last seen 11 months ago

I am writing this who come across the problem regarding downloading. For this you have to download the source package to your local from the bioconductor download site. then use:

                    install.packages(path_to_file, repos = NULL, type="source")

May this helps, Thank you

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Download.file R Wb Mode