Cannot install XML package in r

Question

I'm trying to install "XML" package in r, but an error occurs.
Please tell me what's wrong.

OS: OS X 10.11.6
R version: 3.3.2
The error message when executing "install.packages("XML") is the following.

* 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... /usr/local/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 2 for 2.9.2
Located parser file -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2/parser.h
Checking for 1.8:  -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’

And I set LIBXML_INCDIR=/usr/local/Cellar/libxml2/2.9.4, and tried again.
Then another error occurs.

* 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... /usr/local/bin/pkg-config
Checking directory of LIBXML_INCDIR
You specified LIBXML_INCDIR, but we couldn't find parser.h
Please specify it correctly and re-run the INSTALL'ation.
ERROR: configuration failed for package ‘XML’

Also tried with LIBXML_INCDIR=/usr/local/Cellar/libxml2/2.9.4/include
The result was same as above.

Regards

Answer 1

This worked for me in Mac OS X 10.11:

In the Terminal:

type xml2-config
xml2-config is /opt/local/bin/xml2-config

In R:

Sys.setenv(XML_CONFIG="/opt/local/bin/xml2-config")

Answer 2

Rather than forcing the linking of the libxml2 version from homebrew, you can edit the file $HOME/.R/Makevars to include:

CC=clang -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk CXX=clang++ -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk

Edit the SDK version (i.e. MacOSX10.13 in above example) to match your installed version. See https://forums.developer.apple.com/thread/87829 for (minimal) explanation.