I had 'cummeRbund' installed several months ago and had used without any problem.
Then, from this week, it stopped working.
When I tried to reinstall 'cummeRbund', I got following error.
> biocLite("cummeRbund") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'cummeRbund' trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/cummeRbund_2.4.1.tar.gz' Content type 'application/x-gzip' length 2273444 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb * installing *source* package ‘cummeRbund’ ... ** R ** data ** inst ** preparing package for lazy loading Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite' Error : package ‘Gviz’ could not be loaded ERROR: lazy loading failed for package ‘cummeRbund’ * removing ‘/home/bio1/R/x86_64-pc-linux-gnu-library/3.0/cummeRbund’ The downloaded source packages are in ‘/tmp/RtmpxMcEJQ/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘cummeRbund’ had non-zero exit status 2: installed directory not writable, cannot update packages 'DBI'
I have no idea what went wrong now.
Please, somebody help me!!!!!!
> sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.12.1 loaded via a namespace (and not attached):  tools_3.0.2