Trying to install the XML package as follows I get the error configure: error: "libxml not found". It seems that R is picking up the libxml2 installation from Anaconda. How can I fix this?
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> install.packages("XML")
Installing package into ‘/home/bravegag/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.19.tar.gz'
Content type 'application/x-gzip' length 1600788 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 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... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... /opt/dev/anaconda/2018.12/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 8 for 2.9.8
Located parser file -I/opt/dev/anaconda/2018.12/include/libxml2 -I/opt/dev/anaconda/2018.12/include/parser.h
Checking for 1.8: -I/opt/dev/anaconda/2018.12/include/libxml2 -I/opt/dev/anaconda/2018.12/include
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 ‘/home/bravegag/R/x86_64-pc-linux-gnu-library/3.4/XML’
The downloaded source packages are in
‘/tmp/RtmpannHh6/downloaded_packages’
Warning message:
In install.packages("XML") :
installation of package ‘XML’ had non-zero exit status
>
I also get this:
$ type xml2-config
xml2-config is /opt/dev/anaconda/2018.12/bin/xml2-config
but setting the config in the R environment doesn't help:
Sys.setenv(XML_CONFIG="/opt/dev/anaconda/2018.12/bin/xml2-config")
UPDATE I already had libxml2 installed in the system see:
bravegag@zeus:~$ sudo apt-get install libxml2
Reading package lists... Done
Building dependency tree
Reading state information... Done
libxml2 is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
bravegag@zeus:~$ sudo apt-get install libxml2-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libxml2-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Make sure your system has the libxml-dev or libxml2-dev package installed. i.e.
sudo apt-get install libxml2-dev
I'm unable to determine which is the right version (libxml or libxml2) for 14.04 but you'll want to make sure you have the -dev version installed.