From hkawakat at gmail.com  Wed Mar 11 14:57:27 2009
From: hkawakat at gmail.com (Hiroyuki Kawakatsu)
Date: Wed, 11 Mar 2009 13:57:27 +0000
Subject: [Rd] configure fail for XML package on freebsd
In-Reply-To: <49B7B930.9090003@wald.ucdavis.edu>
References: <307b90470903110428i1635c94btd2f457b893e3580c@mail.gmail.com>
	<49B7B930.9090003@wald.ucdavis.edu>
Message-ID: <307b90470903110657o14a7178ere9c5a5ea06b0d91d@mail.gmail.com>

On 3/11/09, Duncan Temple Lang wrote:
[...]
>
>  That should probably be
>   setenv  LIBXML_INCDIR -I/usr/local/include/libxml2
>
>  (rather than having the additional /libxml after it.)

OK, thanks. But this still fails.

>  Did you install libxml2 version 2.7.3 yourself,
>  i.e. separately from the installation of the operating system?

I did not install myself. It must have been installed as dependency of
some other package.

>  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.

erdos# ldd `which xmllint`
/usr/local/bin/xmllint:
        libxml2.so.5 => /usr/local/lib/libxml2.so.5 (0x80063e000)
        libz.so.4 => /lib/libz.so.4 (0x800884000)
        libiconv.so.3 => /usr/local/lib/libiconv.so.3 (0x800998000)
        libm.so.5 => /lib/libm.so.5 (0x800b91000)
        libc.so.7 => /lib/libc.so.7 (0x800cab000)


>  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.
[...]

Aha, thanks for the hint. Once I checked the config.log file, I found
the source of the error. XML was using a different version of gcc than
that used from building R-devel. So the solution was simply to do

R CMD INSTALL --configure-vars="MAKE=gmake CC=gcc44 ..." XML

Thanks very much for your help. Is there a way to automagically use
the configure-vars used to build R for any package installs without
having to explicitly pass them as above?

h.
-- 
+---
| Hiroyuki Kawakatsu
| Business School, Dublin City University
| Dublin 9, Ireland. Tel +353 (0)1 700 7496



[Rd] configure fail for XML package on freebsd
Hiroyuki Kawakatsu