Hi Guys,

I was not able to properly install the package variant from bioconductor in R

So I ran 

source("http://bioconductor.org/workflows.R")
workflowInstall("variants")

and a bunch of errors show up, I was able to fix some but there are a few I have no clue to it. Here is one of a problematic package:

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... no
checking for xml2-config... /Applications/anaconda/anaconda3/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 7 for 2.9.7
Located parser file -I/Applications/anaconda/anaconda3/include/libxml2 -I/Applications/anaconda/anaconda3/include/parser.h
Checking for 1.8:  -I/Applications/anaconda/anaconda3/include/libxml2 -I/Applications/anaconda/anaconda3/include
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package ‘XML’

System info:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS High Sierra 10.13.3

libxml2 2.9.7

Try to re-install libxml2:

brew update
brew uninstall libxml2
brew install libxml2 --with-xml2-config