I get an error when installing biovizBase, that seems to come from the package R code itself:

> biocLite("biovizBase")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'biovizBase'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/biovizBase_1.14.0.tar.gz'
Content type 'application/x-gzip' length 2429664 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb

* installing *source* package ‘biovizBase’ ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness
/usr/include/string.h:146: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Error : unable to load R code in package ‘biovizBase’
ERROR: lazy loading failed for package ‘biovizBase’
* removing ‘/usr/lib64/R/library/biovizBase’

The downloaded source packages are in
    ‘/tmp/Rtmp9Ubt7U/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biovizBase’ had non-zero exit status

I dont seem to get around this problem, since it's not dependent on missing libraries etc..  

Here's my system info:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-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=fi_FI.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fi_FI.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_1.16.1

loaded via a namespace (and not attached):
[1] tools_3.1.2

The problem has to do with a recent change to the RColorBrewer package. It works with an older version which you can get here:

http://cran.r-project.org/src/contrib/Archive/RColorBrewer/RColorBrewer_1.0-5.tar.gz

I will contact the RColorBrewer and biovizBase maintainers and let them know about this issue.

Dan

That's a bit of a mystery. It seems like the error occurs when R is trying to update installed packages. I notice that the installation directory is /usr/lib64/R/library/, which is not specific to a particular version of R; maybe you are installing over an old (ancient?) R? This also implies that you are installing packages as super-user, whereas it is better practice to install packages as a regular user, perhaps to a directory where other users have read access.

As a test, you might try using .libPaths() to point to a non-system directory, something like .libPaths('/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1') before running biocLite().

If this seems like it's in the right direction, see the help page ?.libPaths for approaches to making this kind of separation of R installation and user package installation more permanent; for my own use the default R library path is 'read only', and when R tries to install it's first new package it prompts me to create the appropriate 'personal' directory.

Hi Martin, thanks for suggestion for ville.q.rantanen. I tried it myself (I'm using R-3.1.2.) - .libPaths to a non-system directory, and sadly I still get the same error at the ** preparing package for lazy loading** stage