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.
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