cderv
January 9, 2020, 8:33am
5
It seems you are right. I did not see that at first. It seems the R installation is using the python libxml2 installation. It may not be the same. You should check that.
You may be able to use environment variable to precise the path to your libxml library to change the one change by pkg-config
--with-libxml use the libxml library (default)
--with-expat use expat library (off by default)
--with-xml-output-buffer use ADD_XML_OUTPUT_BUFFER_CODE (conditionally on)
--with-xmlsec add support (experimental) for XML security with xmlsec. Specify no, xmlsec1 or xmlsec1-openssl
Some influential environment variables:
CC C compiler command
CFLAGS C compiler flags
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CPP C preprocessor
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
_ACEOF
ac_status=$?
fi
There are also other environment variables that could be used to configure the compilation.XML/configure at 1200e8d2e2cd4910537b700245c9d58350c3e351 · omegahat/XML · GitHub
I did not find a lot of documentation for changing the default.
I guess you can also change you pkgconfig configuration so that the python one is not found by default.
For xml2, the configuration can use --configure-vars installation option, to precise INCLUDE_DIR and LIB_DIR (see configure too)
Hope you'll find how to do this. I think you are on the right track.