title: Cannot install XML package in R/RStudio
body: <p>[Environment: macOS 10.12.6, RStudio 1.1.383, R 3.4.2 (via homebrew)]</p>
  
  <p><strong>Please note this is <em>not</em> a duplicate of <a href="https://stackoverflow.com/questions/40682615/cannot-install-xml-package-in-r">this question</a> - solutions there do not work for me.</strong></p>
  
  <p>I am getting install errors when I attempt to install the XML package in RStudio:</p>
  
  <pre><code>&gt; install.packages("XML")
  Installing package into ‘/usr/local/lib/R/3.4/site-library’
  (as ‘lib’ is unspecified)
  trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
  Content type 'application/x-gzip' length 1599437 bytes (1.5 MB)
  ==================================================
  downloaded 1.5 MB
  
  * 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 4 for 2.9.4
  Located parser file -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2/parser.h
  Checking for 1.8:  -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.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’
  * removing ‘/usr/local/lib/R/3.4/site-library/XML’
  </code></pre>
  
  <p>OK - so I installed libxml2 (2.9.7) via homebrew and force-linked:</p>
  
  <pre><code>&gt;brew install libxml2
  &gt;brew link libxml2 --force
  </code></pre>
  
  <p>and I added this code to <code>~/.Renviron</code>:</p>
  
  <pre><code>LIBXML_INCDIR=/usr/local/opt/libxml2
  LIBXML_LIBDIR=/usr/local/opt/libxml2
  PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig
  LDFLAGS=-L/usr/local/opt/libxml2/lib
  CPPFLAGS=-I/usr/local/opt/libxml2/include
  </code></pre>
  
  <p>I quit &amp; restart RStudio; try again:</p>
  
  <pre><code>&gt; install.packages("XML")
  Installing package into ‘/usr/local/lib/R/3.4/site-library’
  (as ‘lib’ is unspecified)
  trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
  Content type 'application/x-gzip' length 1599437 bytes (1.5 MB)
  ==================================================
  downloaded 1.5 MB
  
  * 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’
  * removing ‘/usr/local/lib/R/3.4/site-library/XML’
  </code></pre>
  
  <p><code>parser.h</code> does exist at <code>/usr/local/opt/libxml2/include/libxml2/libxml/parser.h</code> (placed there by brew), and I even symlinked it to <code>/usr/local/opt/libxml2/include/parser.h</code>, but to no avail.</p>
  
  <p>So I pretty much can't figure out how to get RStudio to recognize both the lib <code>libxml2</code> and <code>parser.h</code>.</p>
  
  <p>RStudio Environment:</p>
  
  <pre><code>&gt; Sys.getenv()
  __CF_USER_TEXT_ENCODING    0x535:0x0:0x0
  Apple_PubSub_Socket_Render
                             /private/tmp/com.apple.launchd.oqvtmxMkmV/Render
  CLICOLOR_FORCE             1
  CPPFLAGS                   -I/usr/local/opt/libxml2/include
  DISPLAY                    /private/tmp/com.apple.launchd.z0UbJdCqkr/org.macosforge.xquartz:0
  DYLD_FALLBACK_LIBRARY_PATH
                             /usr/local/Cellar/r/3.4.2/lib/R/lib:/Users/conrad/lib:/usr/local/lib:/usr/lib:::/lib
  EDITOR                     vi
  GIT_ASKPASS                rpostback-askpass
  HOME                       /Users/conrad
  LANG                       en_US.UTF-8
  LC_CTYPE                   en_US.UTF-8
  LDFLAGS                    -L/usr/local/opt/libxml2/lib
  LIBXML_INCDIR              /usr/local/opt/libxml2
  LIBXML_LIBDIR              /usr/local/opt/libxml2
  LN_S                       ln -s
  LOGNAME                    conrad
  MAKE                       make
  PAGER                      /usr/bin/less
  PATH                       /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/MacGPG2/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands
  PKG_CONFIG_PATH            /usr/local/opt/libxml2/lib/pkgconfig
  R_BROWSER                  /usr/bin/open
  R_BZIPCMD                  /usr/bin/bzip2
  R_DOC_DIR                  /usr/local/Cellar/r/3.4.2/lib/R/doc
  R_GZIPCMD                  /usr/bin/gzip
  R_HOME                     /usr/local/Cellar/r/3.4.2/lib/R
  R_INCLUDE_DIR              /usr/local/Cellar/r/3.4.2/lib/R/include
  R_LIBS_SITE                
  R_LIBS_USER                ~/Library/R/3.4/library
  R_PAPERSIZE                a4
  R_PDFVIEWER                /usr/bin/open
  R_PLATFORM                 x86_64-apple-darwin16.7.0
  R_PRINTCMD                 lpr
  R_RD4PDF                   times,inconsolata,hyper
  R_SESSION_TMPDIR           /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T//RtmpvNqwQA
  R_SHARE_DIR                /usr/local/Cellar/r/3.4.2/lib/R/share
  R_SYSTEM_ABI               osx,gcc,gxx,gfortran,?
  R_TEXI2DVICMD              /usr/bin/texi2dvi
  R_UNZIPCMD                 /usr/bin/unzip
  R_ZIPCMD                   /usr/bin/zip
  RMARKDOWN_MATHJAX_PATH     /Applications/RStudio.app/Contents/Resources/resources/mathjax-26
  RS_RPOSTBACK_PATH          /Applications/RStudio.app/Contents/MacOS/rpostback
  RS_SHARED_SECRET           &lt;redacted&gt;
  RSTUDIO                    1
  RSTUDIO_CONSOLE_COLOR      256
  RSTUDIO_CONSOLE_WIDTH      91
  RSTUDIO_PANDOC             /Applications/RStudio.app/Contents/MacOS/pandoc
  RSTUDIO_SESSION_PORT       9090
  RSTUDIO_USER_IDENTITY      conrad
  RSTUDIO_WINUTILS           bin/winutils
  SED                        /usr/bin/sed
  SHELL                      /bin/tcsh
  SSH_ASKPASS                rpostback-askpass
  SSH_AUTH_SOCK              /private/tmp/com.apple.launchd.wBdDUnzsja/Listeners
  TAR                        /usr/bin/tar
  TERM                       xterm-256color
  TMPDIR                     /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T/
  USER                       conrad
  XPC_FLAGS                  0x0
  XPC_SERVICE_NAME           0
  </code></pre>