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

Asked 3/8, 2015 at 22:3 Answered 8/7, 2022 at 10:32

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.

Balbur answered 3/8, 2015 at 22:3 Comment(2)

You only get these two lines when your run dpkg -L libxml2-dev? If yes, libxml2 is probably not installed. – Eudy 3/8, 2015 at 22:33

@Pascal, No There are more I just added the two that seemed pertinent. I have added the full output from the call now for clarity. – Balbur 4/8, 2015 at 15:18

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.

Balbur answered 4/8, 2015 at 18:19 Comment(2)

Good to know. There is either a Debian/Ubuntu bug here, and/or a bug with the xml2 package. In either case you should really not change /usr/local to /usr as you now continue to mix local installations with package installations. That is generally a bad idea ... – Cessionary 4/8, 2015 at 20:55

This worked for me on Ubuntu 18.04 without doing anything after the wget step – Scutari 5/10, 2020 at 22:45

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.

Tincher answered 17/8, 2019 at 18:41 Comment(2)

Please note you might still get an error due to libxml2-dev not being installed properly if you go the apt-get, yum, etc. way. What worked for me on Ubuntu 18.04 was the command wget ftp://xmlsoft.org/libxml2/libxml2-2.9.2.tar.gz as @Balbur suggested above – Scutari 5/10, 2020 at 22:53

Thank you, this fixed a pip issue for me. Much better than manually building from source. – Newspaperwoman 16/10, 2022 at 0:49

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")

Effluent answered 6/8, 2015 at 13:3 Comment(2)

My specific problem seemed to be an issue with my system not recognising the configuration of libxml2-dev but +1 for the tip! – Balbur 7/8, 2015 at 19:20

I had the same problem. I tried this first before trying to install libxml2-dev manually, it helps – Effluent 7/8, 2015 at 23:17

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.

Cessionary answered 4/8, 2015 at 16:6 Comment(2)

Thanks for the answer but I think I'm missing something. If I do this and try again to install devtools the installation still fails with the same error.

* installing *source* package ‘xml2’ ... ** package ‘xml2’ successfully unpacked and MD5 sums checked 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

. Can you clarity for me please? – Balbur 4/8, 2015 at 16:31

Sorry, so it is package xml2, not package XML and the binary won't help you. My recommendation of installation dependencies one by one and checking their individual error logs still stands. All those packages install just fine on all my Ubuntu machines ... – Cessionary 4/8, 2015 at 16:56

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

Sarnoff answered 21/4, 2020 at 8:53 Comment(1)

Thanks, I was having issues installing tidyverse on MX Linux and this was one of the packages I was missing but the error message didn't mention libxml2-devel. – Heliotype 19/2, 2022 at 0:17

Today, 4 years and 2 months later, I was having exactly the same issue (even if in the context of the installation of a different package, xml2).

Looking closely at the .configure script of the package, I noticed that following one-line configuration test was failing:

echo "#include $PKG_TEST_HEADER" | ${CC} ${CPPFLAGS} ${PKG_CFLAGS} ${CFLAGS} -E -xc - >/dev/null 2>&1 || R_CONFIG_ERROR=1;

This is despite all the used parameters having correct and non-null values.

I'm not sure why exactly this test fails, but it seems to be a bug (so Dirk Eddelbuettel was right). Commenting out the test, allowed me to manually install the package without any further issues.

Morava answered 9/10, 2019 at 20:6 Comment(0)

if you used conda env R, then use conda to resolve this problem.

conda install -c anaconda libxml2

Ozmo answered 8/7, 2022 at 10:32 Comment(0)

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