Hello,

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:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.12.1

loaded via a namespace (and not attached):
[1] tools_3.0.2

The solution to this is to upgrade to R-3.1.2 and Bioconductor 3.0, the most up-to-date release versions of both.

After installing R-3.1.2, enter these commands:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

Dan

Thank you for your quick reply!

So I removed 'r-base' and downloaded tar package of 'R-3.1.2'.

After untar, './configure' gave me an another error.

configure: error: --with-x=yes (default) and X11 headers/libs are not available

What could be a problem here?

You need the X11 development headers installed. 

Rather than try and build the the tarball from source, consider using apt-get to install the necessary packages, see these instructions:

http://cran.fhcrc.org/bin/linux/ubuntu/

It looks from http://cran.fhcrc.org/bin/linux/ubuntu/trusty/ like R-3.1.2 is available but 3.1.1 would do in a pinch.

Dan

Hi Dan

Just FYI, I got the same error (i.e. can't install biovizBase and hence Gviz) despite using R-3.1.2 and bioconductor 3.0 - Martin Morgan was going to look into it I think (see: https://support.bioconductor.org/p/63510/#63522)

Cheers

Amit

I just found the easiest way to upgrade R from here.