R devtools fails as "Package libxml-2.0 was not found in the pkg-config search path"

Question

I am trying to install devtools in R version 3.2.1, however when I do the following error is thrown:

Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing libxml-2.0.pc
to the PKG_CONFIG_PATH environment variable

when I run dpkg -L libxml2-dev in a terminal I find:

/usr
/usr/bin
/usr/bin/xml2-config
/usr/share
/usr/share/aclocal
/usr/share/aclocal/libxml2.m4
/usr/share/doc
/usr/share/doc/libxml2-dev
/usr/share/doc/libxml2-dev/copyright
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/xml2-config.1.gz
/usr/share/man/man3
/usr/share/man/man3/libxml.3.gz
/usr/lib
/usr/lib/x86_64-linux-gnu
/usr/lib/x86_64-linux-gnu/libxml2.a
/usr/lib/x86_64-linux-gnu/pkgconfig
/usr/lib/x86_64-linux-gnu/pkgconfig/libxml-2.0.pc
/usr/lib/x86_64-linux-gnu/xml2Conf.sh
/usr/include
/usr/include/libxml2
/usr/include/libxml2/libxml
/usr/include/libxml2/libxml/globals.h
/usr/include/libxml2/libxml/schematron.h
/usr/include/libxml2/libxml/xlink.h
/usr/include/libxml2/libxml/HTMLparser.h
/usr/include/libxml2/libxml/pattern.h
/usr/include/libxml2/libxml/xmlexports.h
/usr/include/libxml2/libxml/xmlschemas.h
/usr/include/libxml2/libxml/list.h
/usr/include/libxml2/libxml/entities.h
/usr/include/libxml2/libxml/xmlstring.h
/usr/include/libxml2/libxml/encoding.h
/usr/include/libxml2/libxml/hash.h
/usr/include/libxml2/libxml/xmlmemory.h
/usr/include/libxml2/libxml/relaxng.h
/usr/include/libxml2/libxml/xmlsave.h
/usr/include/libxml2/libxml/SAX2.h
/usr/include/libxml2/libxml/xmlIO.h
/usr/include/libxml2/libxml/xmlschemastypes.h
/usr/include/libxml2/libxml/xpathInternals.h
/usr/include/libxml2/libxml/schemasInternals.h
/usr/include/libxml2/libxml/xmlmodule.h
/usr/include/libxml2/libxml/valid.h
/usr/include/libxml2/libxml/c14n.h
/usr/include/libxml2/libxml/xmlwriter.h
/usr/include/libxml2/libxml/tree.h
/usr/include/libxml2/libxml/xmlunicode.h
/usr/include/libxml2/libxml/nanohttp.h
/usr/include/libxml2/libxml/catalog.h
/usr/include/libxml2/libxml/xmlerror.h
/usr/include/libxml2/libxml/nanoftp.h
/usr/include/libxml2/libxml/xmlautomata.h
/usr/include/libxml2/libxml/xinclude.h
/usr/include/libxml2/libxml/HTMLtree.h
/usr/include/libxml2/libxml/chvalid.h
/usr/include/libxml2/libxml/parserInternals.h
/usr/include/libxml2/libxml/xpointer.h
/usr/include/libxml2/libxml/xmlversion.h
/usr/include/libxml2/libxml/dict.h
/usr/include/libxml2/libxml/xmlregexp.h
/usr/include/libxml2/libxml/DOCBparser.h
/usr/include/libxml2/libxml/parser.h
/usr/include/libxml2/libxml/xmlreader.h
/usr/include/libxml2/libxml/SAX.h
/usr/include/libxml2/libxml/threads.h
/usr/include/libxml2/libxml/debugXML.h
/usr/include/libxml2/libxml/xpath.h
/usr/include/libxml2/libxml/uri.h
/usr/share/doc/libxml2-dev/README
/usr/share/doc/libxml2-dev/NEWS.gz
/usr/share/doc/libxml2-dev/AUTHORS
/usr/share/doc/libxml2-dev/TODO.gz
/usr/share/doc/libxml2-dev/changelog.Debian.gz
/usr/lib/x86_64-linux-gnu/libxml2.so

to try and add this to the PKG_CONFIG_PATH I tried: env PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig however this does not seem to work.

Answer 1

OK so in the end I had to manually install libxml2 even though my system said it allready had the most up to date version installed after: sudo apt-get install libxml2 libxml2-dev

I manually installed based on info found here:

wget ftp://xmlsoft.org/libxml2/libxml2-2.9.2.tar.gz

Then uppack to a directory, e.g.:

tar -xvf libxml2-2.9.2.tar.gz
cd libxml2-2.9.2

Configure the install:

./configure --prefix=/usr --disable-static --with-history && make

and

sudo make install

after this the R command install.packages("devtools") completed with success.

Answer 2

Choose and Install suitable library from below as per your Linux flavor:-

• deb: libxml2-dev (Debian, Ubuntu, etc)
• rpm: libxml2-devel (Fedora, CentOS, RHEL)
• csw: libxml2_dev (Solaris)

Install with an appropriate command like apt-get, yum, etc.

Answer 3

From within R prompt, this command works provided that libxml2-dev has been installed:

Sys.setenv(PKG_CONFIG_PATH="/usr/lib/x86_64-linux-gnu/pkgconfig")

Answer 4

For the narrower problem of installing the R package "XML", just do

 sudo apt-get install r-cran-xml

Otherwise, start at the list of dependencies for "devtools" (eg from here) and install these dependencies one by one.

Answer 5

I had this problem on Fedora 31 (as of Apr 2020; error in xml2 installation). Installing libxml2-devel seems to solve it for me.

$ dnf install libxml2-devel