I tried to install
biocLite but keep having some error messages. I have been able to install and use it in the past but I had to reinstall R in the meantime. I have checked that all dependancies are installed (
> source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help > biocLite("IlluminaHumanMethylation450k.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1. Installing package(s) 'IlluminaHumanMethylation450k.db' trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/IlluminaHumanMethylation450k.db_2.0.7.tar.gz' Content type 'application/x-gzip' length 63268195 bytes (60.3 Mb) opened URL ================================================= downloaded 60.3 Mb * installing *source* package ‘IlluminaHumanMethylation450k.db’ ... ** R ** inst ** preparing package for lazy loading Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'createSimpleBimap' not found Error : unable to load R code in package ‘IlluminaHumanMethylation450k.db’ ERROR: lazy loading failed for package ‘IlluminaHumanMethylation450k.db’ * removing ‘/home/benhur/R/x86_64-pc-linux-gnu-library/3.1/IlluminaHumanMethylation450k.db’ The downloaded source packages are in ‘/tmp/RtmpSVWOdr/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘IlluminaHumanMethylation450k.db’ had non-zero exit status
> sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C  LC_MESSAGES=C LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.16.0 loaded via a namespace (and not attached):  tools_3.1.1
Hopefully someone would be able to help me :).