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Old 03-30-2016, 11:10 AM   #1
monadman46
LQ Newbie
 
Registered: Mar 2016
Posts: 2

Rep: Reputation: Disabled
libxml not found when installing XML package for R


Hi everybody, I am going crazy trying to solve this issue (been through every related thread about this with no luck). I am running Fedora release 20.
My trouble is that I try to install the XML package for R and get the following error message (using rStudio):
* 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/bin/pkg-config
checking for xml2-config... /opt/lampp/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 8, Patch 0 for 2.8.0
Located parser file -I/opt/lampp/include/libxml2/parser.h
Checking for 1.8: -I/opt/lampp/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package XML
* removing /home/juani/R/x86_64-redhat-linux-gnu-library/3.2/XML
Warning in install.packages :
installation of package XML had non-zero exit status

The downloaded source packages are in
/tmp/RtmpKfGruV/downloaded_packages



I tried playing around with export LIBXML_INCDIR and LIBXML_LIBDIR from bash and trying to install the package from there, but I get the error:

$ R CMD INSTALL XML
* installing to library /home/juani/R/x86_64-redhat-linux-gnu-library/3.2
* 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/bin/pkg-config
Checking directory of LIBXML_INCDIR
Located parser file /opt/lampp/include/parser.h
Checking for 1.8: /opt/lampp/include
Using libxml2.*
checking for gzopen in -lz... no
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/juani/R/x86_64-redhat-linux-gnu-library/3.2/XML

Any ideas how this can be solved?
Thanks in advance, any help is appreciated!
 
Old 03-30-2016, 01:16 PM   #2
monadman46
LQ Newbie
 
Registered: Mar 2016
Posts: 2

Original Poster
Rep: Reputation: Disabled
I could get in touch with a linux developer that solved this in two steps. First setting correctly LIBXML_INCDIR and LIBXML_LIBDIR, and then starting rstudio with privileges so that it could access the files (seems that not doing this was giving the exact same error that having the incorrect variables set). So problem solved!
 
  


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