Finally! Everything seems to be working fine now. I didn't re-run the auto install script after installing libxml2-dev, I was just running the configure script for pathfinder, and attempting to "make" and "make install" manually (which wasn't working). But re-running the install script from the superball seems to have done the trick, so the problem was in fact just the missing libxml2-dev package. Thanks for the help, guys. If you want some more feedback on the process, let me know.

-Rob 

On Wed, Dec 1, 2010 at 2:07 PM, Stefan Manegold <Stefan.Manegold@cwi.nl> wrote:
On Tue, Nov 30, 2010 at 05:31:03PM +0000, Rob Fynes wrote:
> *Hi,*
> *
> *
> *Thanks to both of you for your quick responses. Ubuntu (lucid) does not
> have libxml2-dev installed by default, but it was a simple matter of
> searching for it in the Ubuntu Software Center and installing. The
> pathfinder configure script overcame the previous error and produced the
> following:*
>
> ...
> ...
> checking for xml2-config.32... no
> checking for xml2-32-config... no
> checking for xml2-config... /usr/bin/xml2-config
> checking for libxml/parser.h... yes
> checking for xmlParseDocument in -lxml2... yes
> checking libxml/SAX2.h usability... yes
> checking libxml/SAX2.h presence... yes
> checking for libxml/SAX2.h... yes
> configure: The following compiler options will be used to integrate
>            the libxml2 XML parsing library:
>            To find the libxml2 include files: -I/usr/include/libxml2
>            To find the libxml2 library:       -lxml2
>            SAX2 support:                      HAVE_SAX2=1
> checking for dlopen in -ldl... (cached) yes
> checking for pthread_create in -lpthread... yes
> checking gc.h usability... no
> checking gc.h presence... no
> checking for gc.h... no
> configure: WARNING: Unable to find the Hans Boehm garbage collector.
>                  Please go get it from
>                  http://www.hpl.hp.com/personal/Hans_Boehm/gc/
>                  (Compilation will use memory allocation only strategy
> instead.)
> checking time.h usability... yes
> checking time.h presence... yes
> ...
> ...
> ...
> config.status: creating src/sqlhelpers/xmlshred/Makefile
> config.status: creating pf_config.h
> config.status: executing depfiles commands
> config.status: executing libtool commands
>
> *The script ended with a series of config.status outputs as indicated above,
> with no mention of success or failure (but I assumed this to mean that the
> script was successful). Unfortunately, running Mserver with the pathfinder
> module again still produced the error mentioned in my last email. *

After the above (indeed successful, as far as I can see) configure, did the
`make` and `make install` for pathfinder work successfully, too?

Are MonetDB (Common), MonetDB4 (Mserver) and pathfinder installed in the
same prefix?

Do all of the following files exist after a successful build (woth prefix
<PREFIX>) of MonetDB incl.  pathfinder (XQuery):
<PREFIX>/lib64/MonetDB4/algebra.mil
<PREFIX>/lib64/MonetDB4/lib/lib_algebra.so
<PREFIX>/lib64/MonetDB4/pathfinder.mil
<PREFIX>/lib64/MonetDB4/lib/lib_pathfinder.so
?

Not being a Ubuntu user (let alone expert) myself, I cannot comment on the
remainder.

Stefan

> *
> *
> *I also tried installing using the pre-compiled binaries as you suggested,
> and I followed the steps successfully, creating the URL file, installing the
> public key, running update, none of which produced any errors. However, the
> following did: *
>
> *sudo apt-get install monetdb-xquery monetdb-client*
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Couldn't find package monetdb-xquery
>
> *I then tried the following:*
>
> *sudo apt-get install -y $(sed -n '/Build-Depends: */{s///;s/*([^)]*)//g;s/,
> */ /g;p;}' */debian/control | tr -s ' ' '\012' | sort -u | grep -v monetdb)*
> sed: can't read */debian/control: No such file or directory
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
>
>
> *Incidentally, the reason I want to use MonetDB is for an undergraduate XML
> data mining project in collaboration with the Interoperable Systems Group in
> DCU, Dublin. *
>
> Regards,
> -Rob
>
>
> On Tue, Nov 30, 2010 at 8:46 AM, Sjoerd Mullender <sjoerd@acm.org> wrote:
>
> > To make sure that you have installed all packages that you need for
> > building MonetDB, do this in the top-level directory of MonetDB (all on
> > one line):
> >
> > sudo apt-get install -y $(sed -n '/Build-Depends: */{s///;s/
> > *([^)]*)//g;s/, */ /g;p;}' */debian/control | tr -s ' ' '\012' | sort -u
> > | grep -v monetdb)
> >
> > What this does is install all packages that are mentioned as
> > Build-Depends in the Debian (and Ubuntu) configuration files.
> >
> > Leave out the -y if you want interaction (i.e. apt-get asking you
> > whether you want to install those packages).
> >
> > On 2010-11-30 01:56, Stefan Manegold wrote:
> > > Hi Rob,
> > >
> > > I'm everything but a Ubuntu expert, but on other Linux flavors like
> > Fedora
> > > and Debian, to use libxml2 for development, in addition to a libxml2
> > > package, also a libxml2-dev or libxml2-devel package needs to be
> > installed
> > > that among others provides the xml2-config script and the header files
> > that
> > > configure is looking for.
> > >
> > > Hence, could you please check, whether such libxml2-dev(el) package also
> > > exists for Ubuntu, and if so, whether it is installed on your machine?
> > >
> > > Alternatively, you could consider installing the prebuilt binary packages
> > as
> > > available from
> > > http://dev.monetdb.org/downloads/deb/
> > > instead of compiling MonetDB yourself.
> > >
> > > Stefan
> > >
> > > On Mon, Nov 29, 2010 at 11:54:04PM +0000, Rob Fynes wrote:
> > >> Hello,
> > >>
> > >> Apologies if this is the improper place to be asking this. I'm a new
> > user to
> > >> MonetDB, and I'm having trouble installing MonetDB/XQuery on Ubuntu
> > 10.04
> > >> 32-bit. Actually, the installation did seem to succeed (running the auto
> > >> install script from the super source tarball) and I can start MServer,
> > but
> > >> with the error:
> > >>
> > >> # MonetDB Server v4.40.2
> > >> # based on GDK   v1.40.2
> > >> # not released
> > >> # Copyright (c) 1993-July 2008, CWI. All rights reserved.
> > >> # Copyright (c) August 2008-2010, MonetDB B.V.. All rights reserved.
> > >> # Compiled for i686-pc-linux-gnu/32bit with 32bit OIDs; dynamically
> > linked.
> > >> # Detected 3.919 GiB (4208013312 bytes) main-memory.
> > >> # Visit http://monetdb.cwi.nl/ for further information.
> > >> !ERROR: moduleClient: module(pathfinder) load error.
> > >>
> > >> The problem, its seems anyway, is during the configuration of
> > pathfinder:
> > >>
> > >> ...
> > >> ...
> > >> checking for signal.h... yes
> > >> checking return type of signal handlers... (cached) void
> > >> checking for strings.h... (cached) yes
> > >> checking for strcasecmp... yes
> > >> checking for xml2-config.32... no
> > >> checking for xml2-32-config... no
> > >> checking for xml2-config... no
> > >> checking for libxml/parser.h... no
> > >> configure: error: in `/home/rob/MonetDB':
> > >> configure: error: The libxml2 XML parsing library and/or include files
> > were
> > >> not found or you have requested to not use it.
> > >>                 This is required dependence, core components like
> > >> the XML Schema import functionality depends on it.
> > >> See `config.log' for more details.
> > >>
> > >> I do have libxml2 installed (by default with Lucid). I've run the
> > pathfinder
> > >> configure script a few times, with the option --with-libxml2=*some
> > >> variations*, but I'm not really confident about what I'm doing. I was
> > >> wondering if anyone could point me in the right direction. Thanks.
> > >>
> > >> -Rob
> > >
> > >>
> > ------------------------------------------------------------------------------
> > >> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> > >> Tap into the largest installed PC base & get more eyes on your game by
> > >> optimizing for Intel(R) Graphics Technology. Get started today with the
> > >> Intel(R) Software Partner Program. Five $500 cash prizes are up for
> > grabs.
> > >> http://p.sf.net/sfu/intelisp-dev2dev
> > >
> > >> _______________________________________________
> > >> MonetDB-users mailing list
> > >> MonetDB-users@lists.sourceforge.net
> > >> https://lists.sourceforge.net/lists/listinfo/monetdb-users
> > >
> > >
> >
> >
> > --
> > Sjoerd Mullender
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> > Tap into the largest installed PC base & get more eyes on your game by
> > optimizing for Intel(R) Graphics Technology. Get started today with the
> > Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> > http://p.sf.net/sfu/intelisp-dev2dev
> > _______________________________________________
> > MonetDB-users mailing list
> > MonetDB-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/monetdb-users
> >
> >

> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> Tap into the largest installed PC base & get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev

> _______________________________________________
> MonetDB-users mailing list
> MonetDB-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/monetdb-users


--
| Stefan.Manegold @ CWI.nl | DB Architectures (INS1) |
| http://CWI.nl/~manegold/ | Science Park 123 (L321) |
| Tel.: +31 (0)20 592-4212 | 1098 XG Amsterdam  (NL) |

------------------------------------------------------------------------------
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
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