Trying to install this package in R-3.2.2, and get the following error:

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

> biocLite("BSgenome.Hsapiens.UCSC.hg19")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
==================================================
downloaded 656.3 MB

* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: parseURI("")
  error: cannot parse URI
Error: loading failed
Execution halted
ERROR: loading failed

You need to show the output from sessionInfo() whenever you post about a problem. See the posting guide.

You probably have an outdated package somewhere. Try

library(BiocInstaller)

biocValid()

To figure out what the problem is, or simply

biocLite()

to fix it.

Hi. The BSgenome package has a dependency on the XML package (via rtracklayer). The XML package itself depends on the system library libxml2 which must be installed in your system with version 2.6.3 or higher. On my old Linux redhat system the library were too old. I can give hints how to solve this on linux, only.

On linux do:

echo $LD_LIBRARY_PATH 

and check each of the library entries (separated by : ) for the existence of lib.xml2* . You can do this to check for libxml2* in all of these paths:

for p in `echo $LD_LIBRARY_PATH | tr ':' '\n'` ; do find $p -name 'libxml2*' ; done

Id the full version number of the library is not printed you can get the version number for the libraries in a directory with like this:

 ldconfig -nv DIRECTORY

in my case: 

$ ldconfig -nv /usr/prog/pcsi/RH5/lib

/usr/prog/pcsi/RH5/lib:

    libxml2.so.2 -> libxml2.so.2.9.2

You need to arrange your LD_LIBRARY_PATH  so that the path with the libxml2 version >= 2.6.3 comes first, e.g. in my case I did edited my ~/.bashrc and set the following line:

export LD_LIBRARY_PATH=/usr/prog/pcsi/RH5/lib:$LD_LIBRARY_PATH

You may have to install this library if it is not found (you can install the libxml2 and libxml2-devel RPMs).

    hope this helps