Hi Hiroyuki
Hiroyuki Kawakatsu wrote:> Hi,
>
> I am having problems installing the XML package with R-devel on
> freebsd. If I simply do install.packages("XML"), it says that the
> parser.h file is not found. After reading the INSTALL file, I have set
>
> setenv XML_CONFIG /usr/local/bin/xml2-config
> setenv LIBXML_LIBDIR -L/usr/local/lib
> setenv LIBXML_INCDIR -I/usr/local/include/libxml2/libxml
That should probably be
setenv LIBXML_INCDIR -I/usr/local/include/libxml2
(rather than having the additional /libxml after it.)
Did you install libxml2 version 2.7.3 yourself,
i.e. separately from the installation of the operating system?
Is /usr/local/lib being searched for .so files by your dynamic
loader?
Try
ldd `which xmllint`
to see what shared libraries it finds? Does it list
libxml2.so.2 and if so, where is the file to which it points -
/usr/lib or /usr/local/lib ? If it is /usr/lib, that is the
problem.
If this doesn't identify the problem, please download
the XML_2.3-0.tar.gz file and issue the commands
tar zxf XML_2.3-0.tar.gz
R CMD INSTALL XML
and send me the file XML/config.log and I can try to
find out what is going wrong form the details in that.
Thanks,
D.
>
> and install.packages("XML") fails with
>
> checking for stdint.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for libxml/parser.h... (cached) no
> checking for gnome-xml/parser.h... (cached) no
> Located parser file -I/usr/local/include/libxml2/libxml/parser.h
> 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 '/usr/local/share/R-devel/library/XML'
> Warning in install.packages("XML", clean = TRUE) :
> installation of package 'XML' had non-zero exit status
>
> Some version info on my machine:
>
> erdos# portversion -F "libxml*"
> libxml2-2.7.3 >
> erdos# xml2-config --version
> 2.7.3
>
> erdos# ls /usr/local/lib/libxml*
> /usr/local/lib/libxml2.a /usr/local/lib/libxmlparse.so@
> /usr/local/lib/libxml2.la* /usr/local/lib/libxmlparse.so.1*
> /usr/local/lib/libxml2.so@ /usr/local/lib/libxmltok.a
> /usr/local/lib/libxml2.so.5* /usr/local/lib/libxmltok.la*
> /usr/local/lib/libxmlparse.a /usr/local/lib/libxmltok.so@
> /usr/local/lib/libxmlparse.la* /usr/local/lib/libxmltok.so.1*
>
> The header LIBXML_INCDIR/xmlversion.h does define version as 2.7.3.
> Does anyone have an idea of what may be going wrong?
>
> h.