packrat::init() failed while installing dependent package XML on mac.

[cparsania]

Hi, I am trying to generate private project library using packrat::ini(). One my package depends on xml. Whenever it tries to install XML it stops. Below is the error I get. Can anyone tell how to get rid of this ?

Installing XML (3.98-1.19) ... 
[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T/RtmplUeUw6/XML' --library='/Users/chiragparsania/Documents/Projects/1_My_PhD/9_bioseqc/bioseqc/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package 'XML' ...\n** package 'XML' successfully unpacked and MD5 sums checked\nchecking for gcc... gcc\nchecking whether the C compiler works... yes\nchecking for C compiler default output file name... a.out\nchecking for suffix of executables... \nchecking whether we are cross compiling... no\nchecking for suffix of object files... o\nchecking whether we are using the GNU C compiler... yes\nchecking whether gcc accepts -g... yes\nchecking for gcc option to accept ISO C89... none needed\nchecking how to run the C preprocessor... gcc -E\nchecking for sed... /usr/bin/sed\nchecking for pkg-config... /usr/local/bin/pkg-config\nchecking for xml2-config... /usr/bin/xml2-config\nUSE_XML2 = yes\nSED_EXTENDED_ARG: -E\nMinor 9, Patch 4 for 2.9.4\nLocated parser file -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2/parser.h\nChecking for 1.8:  -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2\nUsing libxml2.*\nchecking for gzopen in -lz... yes\nchecking for xmlParseFile in -lxml2... no\nchecking for xmlParseFile in -lxml... no\nconfigure: error: \"libxml not found\"\nERROR: configuration failed for package 'XML'\n* removing '/Users/chiragparsania/Documents/Projects/1_My_PhD/9_bioseqc/bioseqc/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1/XML'"
Error: Command failed (1)

Failed to run system command:

	'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T/RtmplUeUw6/XML' --library='/Users/chiragparsania/Documents/Projects/1_My_PhD/9_bioseqc/bioseqc/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1' --install-tests --no-docs --no-multiarch --no-demo 

The command failed with output:
* installing *source* package 'XML' ...
** package 'XML' successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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/se
In addition: Warning messages:
1: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN package instead. 
2: In (function (theme = "cayman", highlight = NULL, css = NULL, fig_retina = NULL,  :
  theme not found, use default (cayman) instead