R Bioconductor installation error - Line starting '< DOCTYPE html PUBLI …' is malformed

StackOverflow https://stackoverflow.com/questions/10836371

Pregunta

I'm having trouble installing bioconductor packages in R. This is on MacOSX, a fresh install of R 2.15, and using bioconductor 1.4.4. Transcript follows:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.4, ?biocLite for help
> biocLite("Biobase")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.4.
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Installing package(s) 'Biobase'
Error: Line starting '<!DOCTYPE html PUBLI ...' is malformed!
> traceback()
6: read.dcf(file = tmpf)
5: available.packages(contriburl = contriburl, method = method)
4: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, 
       method = method, available = available, destdir = destdir, 
       dependencies = dependencies, ...)
3: install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)
2: biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos, suppressUpdates = suppressUpdates, 
       ...)
1: biocLite("Biobase")

Related questions I've found via google suggest an internet connection error (proxy, etc), but that doesn't seem to be the case here. I can install packages from CRAN just fine: (i.e. install.packages("foreach"))

Suggestions would be welcomed.

¿Fue útil?

Solución

I believe this is an error that will be corrected when our builds finish this morning at 10ish Seattle time -- the CRANextras repository is no longer available for Macs, and you're seeing the top of a redirect page. Look for BiocInstaller version > 1.4.5 after source("http://bioconductor.org/biocLite.R"). There is an email thread on the Bioconductor mailing list.

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