From minc-users@bic.mni.mcgill.ca  Mon Jan  5 02:22:58 2004
From: minc-users@bic.mni.mcgill.ca (Andre MATOS)
Date: Sun, 4 Jan 2004 21:22:58 -0500 (EST)
Subject: [MINC-users] mritotal freezes
In-Reply-To: <20031217160322.GA5938@sickkids.ca>
Message-ID: <Pine.LNX.4.44.0401042121100.10776-100000@hydra.bic.mni.mcgill.ca>

Hi John,

great!!! I changed the environment variable LANG to LANG=C and worked, but 
why this happen?

Thanks!

Andre Matos
amatos@mrs.mni.mcgill.ca


On Wed, 17 Dec 2003, John G. Sled wrote:

> 
> 
> I have had a similar problem with mritotal on Redhat 9 that seemed to
> be an issue with unicode characters and perl.  Try setting the
> environment variable LANG=C before running mritotal.
> 
> John
> 
> On Wed, Dec 17, 2003 at 09:33:45AM -0500, Andrew Janke wrote:
> > On Mon, 15 Dec 2003, Andre MATOS wrote:
> > 
> > > I installed the mni_autoreg and when I run mritotal <input> <output.xfm>
> > > my Linux Red Hat 9 freezes. I tried to use the options "-verbose" and also
> > > "-debug" to see messages, but the mritotal didn't wrote any output, just
> > > freeze.
> > >
> > > The others tools such as mritoself is working perfect.
> > 
> > This on surface value appears very strange (as mritotal and mritoself are very
> > similar -- both perl scripts that both call other MINC programs)
> > 
> > However a few questions..
> > 
> >   1. When you say redhat "freezes" does just the window you run mritotal in
> > freeze or does the whole computer freeze up?
> > 
> >   2. Is there any output with mritotal -noexecute -debug -verbose ?
> > or with mritotal -version ?
> > 
> > 
> > --
> > Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
> > Australia->University of Queensland->Centre for Magnetic Resonance
> > W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581
> > 
> > 
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > 
> > 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 

-- 
Andre Matos
amatos@mrs.mni.mcgill.ca



From minc-users@bic.mni.mcgill.ca  Mon Jan  5 02:56:01 2004
From: minc-users@bic.mni.mcgill.ca (Peter NEELIN)
Date: Sun, 4 Jan 2004 21:56:01 -0500
Subject: [MINC-users] minc 1.2 errors on Mac OS X
In-Reply-To: <Pine.LNX.4.44.0312221056170.6849-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0401042152240.292791-100000@shadow.bic.mni.mcgill.ca>

On Mon, 22 Dec 2003, Andre MATOS wrote:

> After I compiled the mimc version 1.2 into the Mac OS X 10.2.8 without
> errors, I runned "make check" to be sure that it was compiled ok, but I
> got this:
> ...
> make  check-TESTS
> Testing minc_types
> Segmentation fault

'Looks like the test program minc_types in testdir is crashing. Try
running it on its own to see if it produces any output. If you have a
debugger, then try to find out where the problem happens. You may need to
recompile it with the -g flag.

            Peter
----
            Peter Neelin (neelin@bic.mni.mcgill.ca)


From minc-users@bic.mni.mcgill.ca  Sun Jan  4 22:43:43 2004
From: minc-users@bic.mni.mcgill.ca (Jeff ATKINSON)
Date: Sun, 4 Jan 2004 17:43:43 -0500
Subject: [MINC-users] compiling register on OS X
Message-ID: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca>

I have Mac OS 10.3.2.  I received the binaries at the workshop and they
installed fine.  However as described on you web page Display works but
register does not.  In fact in loads and creates a window fine but never
shows the minc volume and does not respond to mouse controls.

I thought I would try to recomplie register to see if this would fix the
problem but I am having difficulty.

Without sending the whole output of configure the problem is related to
the gl and glut libraries.  I can fix some of the problem by making a
sympolic link from /usr/include/GL to
/System/Libraries/Frameworks/OpenGL.framework/Headers and
/System/Libraries/Frameworks/GLUT.framework/Headers so it can find gl.h,
glu.h and glut.h.  As well symbolic links from /usr/lib to
/System/Libraries/Frameworks/OpenGL.framework/Libraries for all the gl
libraries seems to work but I am still stuck at configure looking for a
glut library.  There are no libraries in
/System/Libraries/Frameworks/OpenGL.framework/ so I am not sure where to
point it.

Any ideas?

Jeff Atkinson



From minc-users@bic.mni.mcgill.ca  Wed Jan  7 16:11:21 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 7 Jan 2004 11:11:21 -0500
Subject: [MINC-users] compiling register on OS X
In-Reply-To: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca>

Hello Jeff,

frameworks are a OS X specific thing; the current version of register 
does not use them but instead relies on the OpenGL libraries in 
/usr/X11R6 and the GLUT libraries installed using FINK. It is possible 
to get register to work by using the frameworks and bypassing X11, but 
there were some issues there I have yet to figure out.

Cheers,

Jason

On Jan 4, 2004, at 5:43 PM, Jeff ATKINSON wrote:

> I have Mac OS 10.3.2.  I received the binaries at the workshop and they
> installed fine.  However as described on you web page Display works but
> register does not.  In fact in loads and creates a window fine but 
> never
> shows the minc volume and does not respond to mouse controls.
>
> I thought I would try to recomplie register to see if this would fix 
> the
> problem but I am having difficulty.
>
> Without sending the whole output of configure the problem is related to
> the gl and glut libraries.  I can fix some of the problem by making a
> sympolic link from /usr/include/GL to
> /System/Libraries/Frameworks/OpenGL.framework/Headers and
> /System/Libraries/Frameworks/GLUT.framework/Headers so it can find 
> gl.h,
> glu.h and glut.h.  As well symbolic links from /usr/lib to
> /System/Libraries/Frameworks/OpenGL.framework/Libraries for all the gl
> libraries seems to work but I am still stuck at configure looking for a
> glut library.  There are no libraries in
> /System/Libraries/Frameworks/OpenGL.framework/ so I am not sure where 
> to
> point it.
>
> Any ideas?
>
> Jeff Atkinson
>
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Wed Jan  7 17:26:26 2004
From: minc-users@bic.mni.mcgill.ca (James Dessart)
Date: Wed, 7 Jan 2004 12:26:26 -0500
Subject: [MINC-users] compiling register on OS X
In-Reply-To: <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca> <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <9F24C508-4136-11D8-8BD2-000A95A6E01C@rogue-research.com>

On 7-Jan-04, at 11:11 AM, Jason Lerch wrote:

> frameworks are a OS X specific thing; the current version of register 
> does not use them but instead relies on the OpenGL libraries in 
> /usr/X11R6 and the GLUT libraries installed using FINK. It is possible 
> to get register to work by using the frameworks and bypassing X11, but 
> there were some issues there I have yet to figure out.

I think the biggest issue would be replacing X11.  It will always need 
to use the GL and GLUT that works with X11 as long as all the windowing 
is X11.

James


From minc-users@bic.mni.mcgill.ca  Wed Jan  7 18:19:35 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 7 Jan 2004 13:19:35 -0500
Subject: [MINC-users] compiling register on OS X
In-Reply-To: <9F24C508-4136-11D8-8BD2-000A95A6E01C@rogue-research.com>
References: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca> <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca> <9F24C508-4136-11D8-8BD2-000A95A6E01C@rogue-research.com>
Message-ID: <0C4082EC-413E-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca>

On Jan 7, 2004, at 12:26 PM, James Dessart wrote:

>
> On 7-Jan-04, at 11:11 AM, Jason Lerch wrote:
>
>> frameworks are a OS X specific thing; the current version of register 
>> does not use them but instead relies on the OpenGL libraries in 
>> /usr/X11R6 and the GLUT libraries installed using FINK. It is 
>> possible to get register to work by using the frameworks and 
>> bypassing X11, but there were some issues there I have yet to figure 
>> out.
>
> I think the biggest issue would be replacing X11.  It will always need 
> to use the GL and GLUT that works with X11 as long as all the 
> windowing is X11.

That actually wasn't an issue at all. It took a few hacks on the 
linking line, but register compiled and ran just fine without X11. It 
was only happy with certain MINC files, however; I havn't the foggiest 
idea why, and since that experiment happened a few days before the 
workshop I gave up and just compiled against X11. I'll try to get back 
to getting a quartz version of Display and Register soon, however 
(unless someone beats me to it - I would not complain).

Jason


From minc-users@bic.mni.mcgill.ca  Thu Jan  8 03:39:10 2004
From: minc-users@bic.mni.mcgill.ca (Jeffrey Atkinson)
Date: Wed, 7 Jan 2004 22:39:10 -0500
Subject: [MINC-users] compiling register on OS X
References: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca> <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca> <9F24C508-4136-11D8-8BD2-000A95A6E01C@rogue-research.com> <0C4082EC-413E-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <002601c3d598$fa2a0930$0100a8c0@FIGARO>

I was actually able to get register to compile with the frameworks links and
some GLUT links from /usr/local/mni/external-libs but same problem as the
binary. Register window opens but no volume appears.

Also lots of trouble with xdisp.  Bruce seems to link against a bunch of
dynamic libraries in /sw/lib  -- a directory tree that does not exist on my
netcdf installation -- from the MAC OS X distribution package on the CD.

Jeff



From minc-users@bic.mni.mcgill.ca  Thu Jan  8 22:14:47 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 8 Jan 2004 17:14:47 -0500
Subject: [MINC-users] compiling register on OS X
In-Reply-To: <002601c3d598$fa2a0930$0100a8c0@FIGARO>
References: <Pine.SGI.4.44.0401041737030.292005-100000@shadow.bic.mni.mcgill.ca> <22589A7A-412C-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca> <9F24C508-4136-11D8-8BD2-000A95A6E01C@rogue-research.com> <0C4082EC-413E-11D8-B4D7-000A95DBBFD8@bic.mni.mcgill.ca> <002601c3d598$fa2a0930$0100a8c0@FIGARO>
Message-ID: <11D4B28A-4228-11D8-BD30-000A95DBBFD8@bic.mni.mcgill.ca>

/sw is where the fink installs its stuff. Check out fink.sourceforge.net

Jason


On Jan 7, 2004, at 10:39 PM, Jeffrey Atkinson wrote:

> I was actually able to get register to compile with the frameworks 
> links and
> some GLUT links from /usr/local/mni/external-libs but same problem as 
> the
> binary. Register window opens but no volume appears.
>
> Also lots of trouble with xdisp.  Bruce seems to link against a bunch 
> of
> dynamic libraries in /sw/lib  -- a directory tree that does not exist 
> on my
> netcdf installation -- from the MAC OS X distribution package on the 
> CD.
>
> Jeff
>
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Sun Jan 11 23:28:01 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Sun, 11 Jan 2004 18:28:01 -0500
Subject: [MINC-users] Basic question about shared and static Minc libraries
In-Reply-To: <Pine.LNX.4.44.0312221114110.6849-100000@hydra.bic.mni.mcgill.ca>; from amatos@mrs.mni.mcgill.ca on Mon, Dec 22, 2003 at 11:19:06AM -0500
References: <Pine.LNX.4.44.0312221114110.6849-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <20040111182801.C757679@shadow.bic.mni.mcgill.ca>

On Mon, Dec 22, 2003 at 11:19:06AM -0500, Andre MATOS wrote:
> Hi Minc Users,
> 
> Can anyone give me a little explanation about shared and static libraries 
> in the minc tools and in which way should I use each one?

Conveniently, the short answer is: "you shouldn't have to worry about it."

While it is true that shared libraries have several advantages
(see e.g. http://www.tldp.org/HOWTO/Program-Library-HOWTO/index.html),
there is one usability issue with shared libraries: the system has to
know where to find them.  This isn't a problem for the shared libs that
come from your vendor (generally the ones in /lib and /usr/lib on a
unix system) as the vendor has set things up for you.  

However, for libraries built by third parties such as MINC, the
system configuration may need tweaking after installing them.  This
tweaking varies across systems and is often a source of confusion.
For that reason, we decided to build only static libs by default.
That's why you see the quoted output during the configure run:
 
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes

If you desire shared libs, simply configure using

	--enable-shared

and do the appropriate things after installing.

-Steve

 

From minc-users@bic.mni.mcgill.ca  Sun Jan 11 23:52:43 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Sun, 11 Jan 2004 18:52:43 -0500
Subject: [MINC-users] mni_autoreg compilation failed
In-Reply-To: <Pine.LNX.4.44.0312221312290.6849-100000@hydra.bic.mni.mcgill.ca>; from amatos@mrs.mni.mcgill.ca on Mon, Dec 22, 2003 at 01:19:34PM -0500
References: <20031220071951.C1044432@shadow.bic.mni.mcgill.ca> <Pine.LNX.4.44.0312221312290.6849-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <20040111185243.D757679@shadow.bic.mni.mcgill.ca>

On Mon, Dec 22, 2003 at 01:19:34PM -0500, Andre MATOS wrote:
> Hi Steve
> 
> The version of the gcc here (Linux Red Hat 7) is 2.96 and the "patch" 
> solved the compilation problem.
> 
> This is really interesting becouse at home (Linux Red Hat 9) I compilled 
> without errors and without this patch. Do you think that the gcc version 
> could be the problem?

It's possible.  "2.96" is the infamous prematurely-released version
of GCC by Redhat which is notoriously buggy.

However, there's nothing lost by moving the function declaration
in question.  I've applied the patch to the CVS of mni_autoreg so it
should be fixed in the next release.

-S


From minc-users@bic.mni.mcgill.ca  Mon Jan 12 00:05:59 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Sun, 11 Jan 2004 19:05:59 -0500
Subject: [MINC-users] MNI_PERLLIB failed
In-Reply-To: <Pine.LNX.4.44.0312222206380.24924-100000@hydra.bic.mni.mcgill.ca>; from amatos@mrs.mni.mcgill.ca on Mon, Dec 22, 2003 at 10:16:55PM -0500
References: <Pine.LNX.4.44.0312222206380.24924-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <20040111190559.F757679@shadow.bic.mni.mcgill.ca>

On Mon, Dec 22, 2003 at 10:16:55PM -0500, Andre MATOS wrote:
> Hi List,
> 
> when I runned "make test" into the mni_perllib version 0.07, I got the 
> error below. I did these steps:

Don't worry about any error arising from "batch" tests.  Those are
tests for the UCSF batch queuing system, which has a program named
"batch".  Unfortunately, there is also a standard unix command named
"batch" that is related to the "cron" / "at" system.  The failures
you see come from running the latter kind of "batch" command.

Other errors should should vanish if you (1) don't run as root, (2) install
mni_autoreg (volume_cog), and (3) install N3 (volume_stats).  

-S

 
> $ wget ftp://ftp.bic.mni.mcgill.ca/pub/minc/mni_perllib-0.07.tar.gz
> $ tar -xvzf mni_perllib-0.07.tar.gz
> $ cd mni_perllib-0.07
> $ make /usr/local/mni/data
> $ perl Makefile.PL PREFIX=/usr/local/mni/ INSTALLDIRS=perl
> $ make 
> $ make test
>  
> Before runned "make test", when I runned "make" I got the message:
> 
> Default directory for model data [/usr/local/mni/data]?
> Checking if your kit is complete...
> Looks good
> Makefile.PL: I don't grok the manifypods section, so can't tweak the 
> pod2man args at Makefile.PL line 162.
> Writing Makefile for mni_perllib
> 
> 
> 
> [root@pataxo mni_perllib-0.07]# make test
> rm -f t/datadir.t
> sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/data|' t/datadir.t.in > 
> t/datadir.t
> chmod 444 t/datadir.t
> rm -f t/toy_ls
> sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls
> chmod 555 t/toy_ls
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/batch-0........ok
> t/batch-1......../usr/bin/getopt: opção inválida -- J
> /usr/bin/getopt: opção inválida -- Q
> /usr/bin/getopt: opção inválida -- S
> /usr/bin/getopt: opção inválida -- s
> /usr/bin/getopt: opção inválida -- o
> /usr/bin/getopt: opção inválida -- e
> batch: error parsing command-line arguments
> Error closing pipe to batch:
>  at t/batch-1.t line 36
> `batch' exited with non-zero status code: 256
>  at t/batch-1.t line 36
> t/batch-1........NOK 1tail: .out29611: Arquivo ou diretório não 
> encontrado
> /usr/bin/getopt: opção inválida -- J
> /usr/bin/getopt: opção inválida -- Q
> /usr/bin/getopt: opção inválida -- S
> /usr/bin/getopt: opção inválida -- s
> /usr/bin/getopt: opção inválida -- o
> /usr/bin/getopt: opção inválida -- e
> batch: error parsing command-line arguments
> t/batch-1........dubious
>         Test returned status 0 (wstat 13, 0xd)
> DIED. FAILED tests 1-21
>         Failed 21/21 tests, 0.00% okay
> t/batch-2......../usr/bin/getopt: opção inválida -- J
> /usr/bin/getopt: opção inválida -- Q
> /usr/bin/getopt: opção inválida -- l
> /usr/bin/getopt: opção inválida -- S
> /usr/bin/getopt: opção inválida -- s
> /usr/bin/getopt: opção inválida -- o
> /usr/bin/getopt: opção inválida -- e
> batch: error parsing command-line arguments
> t/batch-2........dubious
>         Test returned status 0 (wstat 13, 0xd)
> DIED. FAILED tests 1-3
>         Failed 3/3 tests, 0.00% okay
> t/checkdirs......warning: running test suite as root means not all tests 
> will be run
> t/checkdirs......FAILED tests 41-42
>         Failed 2/42 tests, 95.24% okay
> t/checkfiles.....warning: running test suite as root means not all tests 
> will be run
> t/checkfiles.....FAILED tests 24-25
>         Failed 2/41 tests, 95.12% okay
> t/datadir........ok
> t/mincutil.......ok 3/22mincutil.t: couldn't find volume_stats; pretending 
> to pass all tests that depend on it
> t/mincutil.......ok 4/22mincutil.t: couldn't find volume_cog; pretending 
> to pass all tests that depend on it
> t/mincutil.......ok
> t/miscutil.......ok
> t/numutil........ok
> t/pathutil.......ok
> t/searchfiles....warning: running test suite as root means not all tests 
> will be run
> t/searchfiles....ok
> t/spawn..........FAILED tests 13-15, 19-25
>         Failed 10/56 tests, 82.14% okay
> t/startup........ok
> t/tagset.........ok
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/batch-1.t       0    13    21   21 100.00%  1-21
> t/batch-2.t       0    13     3    3 100.00%  1-3
> t/checkdirs.t                42    2   4.76%  41-42
> t/checkfiles.t               41    2   4.88%  24-25
> t/spawn.t                    56   10  17.86%  13-15 19-25
> Failed 5/14 test scripts, 64.29% okay. 38/381 subtests failed, 90.03% 
> okay.
> make: ** [test_dynamic] Erro 29
> 
> 
> 
> Linux: Red Hat 9
> gcc --version
> gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
> 
> PERL version: perl5 (revision 5.0 version 8 subversion 0)
> 
> Thanks!!!
> 
> -- 
> Andre Matos
> amatos@mrs.mni.mcgill.ca
> 
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From minc-users@bic.mni.mcgill.ca  Mon Jan 12 22:23:17 2004
From: minc-users@bic.mni.mcgill.ca (minc-users@bic.mni.mcgill.ca)
Date: Mon, 12 Jan 2004 17:23:17 -0500
Subject: [MINC-users] register and OS X
Message-ID: <20040112222317.OGMS23238.tomts31-srv.bellnexxia.net@smtp.bellnexxia.net>

I am not sure what other peoples problems with OS X and register were but mine were specifically that 
the X window opened, the volume loading window opened and loaded, and the volume was never 
displayed.

The quick fix, courtesy of Roch Comeau, is to click in the main register Window while the volume is 
loading to restore focus to this window.

The precompiled binary from the web site works fine with this trick.

Obviously this is not a permanent solution but it appears to work.

Jeff Atkinson


From mdesco@cim.mcgill.ca  Tue Jan 13 20:36:48 2004
From: mdesco@cim.mcgill.ca (Maxime Descoteaux)
Date: Tue, 13 Jan 2004 15:36:48 -0500 (EST)
Subject: [MINC-users] "Not implemented yet in cache_volume_range_has_changed()"
Message-ID: <33089.132.206.73.105.1074026208.squirrel@www.cim.mcgill.ca>

Hi all,

My program has always run fine on minc volumes up to 181 x 217 x 181.
But today, I tried to run on a 256 x 256 x 181 and on a 384 x 512 x 90
volumes I get this weird output and finally a bus error:

Outputting Volume:  46% done. (41/90)   Time: 20.8 sec out of approx 45.4 sec
Outputting Volume: DONE in 29.9 sec
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
writing /tmp/max/I_yy.mnc ...
Bus error


Any idea what is causing this.  As the process runs, I do a top and watch
the %mem and how big it is and everything seems as expected.

Thanks

Max



From minc-users@bic.mni.mcgill.ca  Wed Jan 14 11:32:05 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Wed, 14 Jan 2004 11:32:05 +0000
Subject: [MINC-users] make build problem with mni_n3
Message-ID: <400528B5.60707@sghms.ac.uk>

Dear mni_n3 support,

I have a make build problem:

  env NETCDF_INCLUDE=/usr/local/netcdf-3.5.0/include/ 
MINC_INCLUDE=/usr/local/mni/include MINC_LIB=/usr/local/mni/lib 
VOLUMEIO_INCLUDE=/usr/local/mni/include VOLUMEIO_LIB=/usr/local/mni/lib 
MNI_DATAPATH=/usr/local/mni/data ./configure --prefix=/usr/local/n3

and get this error at the end :

make[3]: *** [volumeStats.o] Error 1
make[3]: Leaving directory `/space/N3/src/VolumeStats'
umask 022;
make[2]: Leaving directory `/space/N3/src'
make[1]: Leaving directory `/space/N3/src'

and

even make test fails,eg
MNI_DATAPATH=/usr/local/mni/data with all the files,ie


  ls -l /usr/local/mni/data/N3
total 126
-rw-r--r--   1 root     other      64270 Jan  8 15:30 
average_305_mask_1mm.mnc.gz
  ls -l /usr/local/mni/data/testing/
total 126
-rw-r--r--   1 root     other      64270 Jan  8 16:22 
average_305_mask_1mm.mnc.gz

make test
(cd testing; ./do_test test.log )

---------------------------------------------------------------------
  Testing MNI N3 software package

---------------------------------------------------------------------

do_test: couldn't find program "field2imp"
do_test: couldn't find program "imp2field"
do_test: couldn't find program "sharpen_volume"
do_test: couldn't find program "nu_estimate_np_and_em"
do_test: couldn't find program "nu_evaluate"
do_test: couldn't find program "nu_evaluate"
do_test: couldn't find program "nu_estimate"
do_test: couldn't find program "evaluate_field"
do_test: couldn't find program "extracttag"
do_test: couldn't find program "sharpen_hist"
do_test: couldn't find program "spline_smooth"
do_test: couldn't find program "volume_hist"
do_test: couldn't find program "volume_stats"
Cannot find the file N3/testing/average_305_mask_1mm.mnc.gz.  The data 
for the test suite
does not appear to be installed correctly.
make: *** [test] Error 1


..help would be much appreciated ..!
-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



-- 
This message has been scanned for viruses and
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From minc-users@bic.mni.mcgill.ca  Wed Jan 14 11:36:28 2004
From: minc-users@bic.mni.mcgill.ca (Anders Bertil Rodell)
Date: 14 Jan 2004 12:36:28 +0100
Subject: [MINC-users] MicroPET conversion to MINC
In-Reply-To: <200401051701.i05H16Bi328710@shadow.bic.mni.mcgill.ca>
References: <200401051701.i05H16Bi328710@shadow.bic.mni.mcgill.ca>
Message-ID: <1074080188.14178.8.camel@kafka>

Does anybody have a conversion program to take  MicroPET R4 files into
MINC format?

best regards Anders 


-- 
Anders Bertil Rodell <rodell@pet.auh.dk>
PET Centre Aarhus General Hospital


From minc-users@bic.mni.mcgill.ca  Wed Jan 14 15:22:06 2004
From: minc-users@bic.mni.mcgill.ca (Andre MATOS)
Date: Wed, 14 Jan 2004 10:22:06 -0500 (EST)
Subject: [MINC-users] make build problem with mni_n3
In-Reply-To: <400528B5.60707@sghms.ac.uk>
Message-ID: <Pine.LNX.4.44.0401141014190.24369-100000@hydra.bic.mni.mcgill.ca>

Hi Asim,

which version of N3 you are using? If I am not wrong, to install N3 you 
need first to install "netCDF", "minc", "EBTKS", "BLAS" or "LAPACK" and 
"Perl5". Also, in which system are you installing the N3?

Andre Matos
amatos@mrs.mni.mcgill.ca


On Wed, 14 Jan 2004, Asim Khan wrote:

> Dear mni_n3 support,
> 
> I have a make build problem:
> 
>   env NETCDF_INCLUDE=/usr/local/netcdf-3.5.0/include/ 
> MINC_INCLUDE=/usr/local/mni/include MINC_LIB=/usr/local/mni/lib 
> VOLUMEIO_INCLUDE=/usr/local/mni/include VOLUMEIO_LIB=/usr/local/mni/lib 
> MNI_DATAPATH=/usr/local/mni/data ./configure --prefix=/usr/local/n3
> 
> and get this error at the end :
> 
> make[3]: *** [volumeStats.o] Error 1
> make[3]: Leaving directory `/space/N3/src/VolumeStats'
> umask 022;
> make[2]: Leaving directory `/space/N3/src'
> make[1]: Leaving directory `/space/N3/src'
> 
> and
> 
> even make test fails,eg
> MNI_DATAPATH=/usr/local/mni/data with all the files,ie
> 
> 
>   ls -l /usr/local/mni/data/N3
> total 126
> -rw-r--r--   1 root     other      64270 Jan  8 15:30 
> average_305_mask_1mm.mnc.gz
>   ls -l /usr/local/mni/data/testing/
> total 126
> -rw-r--r--   1 root     other      64270 Jan  8 16:22 
> average_305_mask_1mm.mnc.gz
> 
> make test
> (cd testing; ./do_test test.log )
> 
> ---------------------------------------------------------------------
>   Testing MNI N3 software package
> 
> ---------------------------------------------------------------------
> 
> do_test: couldn't find program "field2imp"
> do_test: couldn't find program "imp2field"
> do_test: couldn't find program "sharpen_volume"
> do_test: couldn't find program "nu_estimate_np_and_em"
> do_test: couldn't find program "nu_evaluate"
> do_test: couldn't find program "nu_evaluate"
> do_test: couldn't find program "nu_estimate"
> do_test: couldn't find program "evaluate_field"
> do_test: couldn't find program "extracttag"
> do_test: couldn't find program "sharpen_hist"
> do_test: couldn't find program "spline_smooth"
> do_test: couldn't find program "volume_hist"
> do_test: couldn't find program "volume_stats"
> Cannot find the file N3/testing/average_305_mask_1mm.mnc.gz.  The data 
> for the test suite
> does not appear to be installed correctly.
> make: *** [test] Error 1
> 
> 
> ..help would be much appreciated ..!
> 

-- 
Andre Matos
amatos@mrs.mni.mcgill.ca



From minc-users@bic.mni.mcgill.ca  Wed Jan 14 16:56:06 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Wed, 14 Jan 2004 16:56:06 +0000
Subject: [MINC-users] make build problem with mni_n3
References: <Pine.LNX.4.44.0401141014190.24369-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <400574A6.3030706@sghms.ac.uk>

Hi Andre,

I have version 1.05 of N3 and the following are installed :

mni_perllib-0.05 the Perl -v is  5.005_03 on solaris 2.8
netcdf-3.5.0 binaries for solaris 2.8 from unidata
minc-1.2 installed in /usr/local/mni

the 'Building and installating N3 from source code' page from URL:
http://www.bic.mni.mcgill.ca/software/N3/node5.html
does not mention  "EBTKS", "BLAS" or "LAPACK" ..?


Andre MATOS wrote:
> Hi Asim,
> 
> which version of N3 you are using? If I am not wrong, to install N3 you 
> need first to install "netCDF", "minc", "EBTKS", "BLAS" or "LAPACK" and 
> "Perl5". Also, in which system are you installing the N3?
> 
> Andre Matos
> amatos@mrs.mni.mcgill.ca
> 
> 
> On Wed, 14 Jan 2004, Asim Khan wrote:
> 
> 
>>Dear mni_n3 support,
>>
>>I have a make build problem:
>>
>>  env NETCDF_INCLUDE=/usr/local/netcdf-3.5.0/include/ 
>>MINC_INCLUDE=/usr/local/mni/include MINC_LIB=/usr/local/mni/lib 
>>VOLUMEIO_INCLUDE=/usr/local/mni/include VOLUMEIO_LIB=/usr/local/mni/lib 
>>MNI_DATAPATH=/usr/local/mni/data ./configure --prefix=/usr/local/n3
>>
>>and get this error at the end :
>>
>>make[3]: *** [volumeStats.o] Error 1
>>make[3]: Leaving directory `/space/N3/src/VolumeStats'
>>umask 022;
>>make[2]: Leaving directory `/space/N3/src'
>>make[1]: Leaving directory `/space/N3/src'
>>
>>and
>>
>>even make test fails,eg
>>MNI_DATAPATH=/usr/local/mni/data with all the files,ie
>>
>>
>>  ls -l /usr/local/mni/data/N3
>>total 126
>>-rw-r--r--   1 root     other      64270 Jan  8 15:30 
>>average_305_mask_1mm.mnc.gz
>>  ls -l /usr/local/mni/data/testing/
>>total 126
>>-rw-r--r--   1 root     other      64270 Jan  8 16:22 
>>average_305_mask_1mm.mnc.gz
>>
>>make test
>>(cd testing; ./do_test test.log )
>>
>>---------------------------------------------------------------------
>>  Testing MNI N3 software package
>>
>>---------------------------------------------------------------------
>>
>>do_test: couldn't find program "field2imp"
>>do_test: couldn't find program "imp2field"
>>do_test: couldn't find program "sharpen_volume"
>>do_test: couldn't find program "nu_estimate_np_and_em"
>>do_test: couldn't find program "nu_evaluate"
>>do_test: couldn't find program "nu_evaluate"
>>do_test: couldn't find program "nu_estimate"
>>do_test: couldn't find program "evaluate_field"
>>do_test: couldn't find program "extracttag"
>>do_test: couldn't find program "sharpen_hist"
>>do_test: couldn't find program "spline_smooth"
>>do_test: couldn't find program "volume_hist"
>>do_test: couldn't find program "volume_stats"
>>Cannot find the file N3/testing/average_305_mask_1mm.mnc.gz.  The data 
>>for the test suite
>>does not appear to be installed correctly.
>>make: *** [test] Error 1
>>
>>
>>..help would be much appreciated ..!
>>
> 
> 


-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



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dangerous content by MailScanner, and is
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From minc-users@bic.mni.mcgill.ca  Wed Jan 14 17:09:45 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 14 Jan 2004 12:09:45 -0500
Subject: [MINC-users] make build problem with mni_n3
In-Reply-To: <400574A6.3030706@sghms.ac.uk>
References: <Pine.LNX.4.44.0401141014190.24369-100000@hydra.bic.mni.mcgill.ca> <400574A6.3030706@sghms.ac.uk>
Message-ID: <73D2AD5C-46B4-11D8-8CD7-000A95DBBFD8@bic.mni.mcgill.ca>

On Jan 14, 2004, at 11:56 AM, Asim Khan wrote:

> Hi Andre,
>
> I have version 1.05 of N3 and the following are installed :
>
> mni_perllib-0.05 the Perl -v is  5.005_03 on solaris 2.8
> netcdf-3.5.0 binaries for solaris 2.8 from unidata
> minc-1.2 installed in /usr/local/mni
>
> the 'Building and installating N3 from source code' page from URL:
> http://www.bic.mni.mcgill.ca/software/N3/node5.html
> does not mention  "EBTKS", "BLAS" or "LAPACK" ..?

That page is unfortunately out of date. If you check the readme file 
that comes with the N3 package (which you should obtain from 
http://www.bic.mni.mcgill.ca/software/distribution) it should mention 
all the required packages and where to get them.

Cheers,

Jason


>
>
> Andre MATOS wrote:
>> Hi Asim,
>> which version of N3 you are using? If I am not wrong, to install N3 
>> you need first to install "netCDF", "minc", "EBTKS", "BLAS" or 
>> "LAPACK" and "Perl5". Also, in which system are you installing the 
>> N3?
>> Andre Matos
>> amatos@mrs.mni.mcgill.ca
>> On Wed, 14 Jan 2004, Asim Khan wrote:
>>> Dear mni_n3 support,
>>>
>>> I have a make build problem:
>>>
>>>  env NETCDF_INCLUDE=/usr/local/netcdf-3.5.0/include/ 
>>> MINC_INCLUDE=/usr/local/mni/include MINC_LIB=/usr/local/mni/lib 
>>> VOLUMEIO_INCLUDE=/usr/local/mni/include 
>>> VOLUMEIO_LIB=/usr/local/mni/lib MNI_DATAPATH=/usr/local/mni/data 
>>> ./configure --prefix=/usr/local/n3
>>>
>>> and get this error at the end :
>>>
>>> make[3]: *** [volumeStats.o] Error 1
>>> make[3]: Leaving directory `/space/N3/src/VolumeStats'
>>> umask 022;
>>> make[2]: Leaving directory `/space/N3/src'
>>> make[1]: Leaving directory `/space/N3/src'
>>>
>>> and
>>>
>>> even make test fails,eg
>>> MNI_DATAPATH=/usr/local/mni/data with all the files,ie
>>>
>>>
>>>  ls -l /usr/local/mni/data/N3
>>> total 126
>>> -rw-r--r--   1 root     other      64270 Jan  8 15:30 
>>> average_305_mask_1mm.mnc.gz
>>>  ls -l /usr/local/mni/data/testing/
>>> total 126
>>> -rw-r--r--   1 root     other      64270 Jan  8 16:22 
>>> average_305_mask_1mm.mnc.gz
>>>
>>> make test
>>> (cd testing; ./do_test test.log )
>>>
>>> ---------------------------------------------------------------------
>>>  Testing MNI N3 software package
>>>
>>> ---------------------------------------------------------------------
>>>
>>> do_test: couldn't find program "field2imp"
>>> do_test: couldn't find program "imp2field"
>>> do_test: couldn't find program "sharpen_volume"
>>> do_test: couldn't find program "nu_estimate_np_and_em"
>>> do_test: couldn't find program "nu_evaluate"
>>> do_test: couldn't find program "nu_evaluate"
>>> do_test: couldn't find program "nu_estimate"
>>> do_test: couldn't find program "evaluate_field"
>>> do_test: couldn't find program "extracttag"
>>> do_test: couldn't find program "sharpen_hist"
>>> do_test: couldn't find program "spline_smooth"
>>> do_test: couldn't find program "volume_hist"
>>> do_test: couldn't find program "volume_stats"
>>> Cannot find the file N3/testing/average_305_mask_1mm.mnc.gz.  The 
>>> data for the test suite
>>> does not appear to be installed correctly.
>>> make: *** [test] Error 1
>>>
>>>
>>> ..help would be much appreciated ..!
>>>
>
>
> -- 
> ------------------------------------
> Asim Khan
> Unix Systems Administrator
> St George's Hospital Medical School
> www.sghms.ac.uk
> ------------------------------------
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Wed Jan 14 17:14:32 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Wed, 14 Jan 2004 17:14:32 +0000
Subject: [MINC-users] make build problem with mni_n3
References: <Pine.LNX.4.44.0401141014190.24369-100000@hydra.bic.mni.mcgill.ca>
 <400574A6.3030706@sghms.ac.uk>
 <73D2AD5C-46B4-11D8-8CD7-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <400578F8.7000807@sghms.ac.uk>

Okay and thanks

..I'll try and install using the following page:

http://www.bic.mni.mcgill.ca/software/distribution

and install the extra packages..

Jason Lerch wrote:
> 
> On Jan 14, 2004, at 11:56 AM, Asim Khan wrote:
> 
>> Hi Andre,
>>
>> I have version 1.05 of N3 and the following are installed :
>>
>> mni_perllib-0.05 the Perl -v is  5.005_03 on solaris 2.8
>> netcdf-3.5.0 binaries for solaris 2.8 from unidata
>> minc-1.2 installed in /usr/local/mni
>>
>> the 'Building and installating N3 from source code' page from URL:
>> http://www.bic.mni.mcgill.ca/software/N3/node5.html
>> does not mention  "EBTKS", "BLAS" or "LAPACK" ..?
> 
> 
> That page is unfortunately out of date. If you check the readme file 
> that comes with the N3 package (which you should obtain from 
> http://www.bic.mni.mcgill.ca/software/distribution) it should mention 
> all the required packages and where to get them.
> 
> Cheers,
> 
> Jason
> 
> 
>>
>>
>> Andre MATOS wrote:
>>
>>> Hi Asim,
>>> which version of N3 you are using? If I am not wrong, to install N3 
>>> you need first to install "netCDF", "minc", "EBTKS", "BLAS" or 
>>> "LAPACK" and "Perl5". Also, in which system are you installing the N3?
>>> Andre Matos
>>> amatos@mrs.mni.mcgill.ca
>>> On Wed, 14 Jan 2004, Asim Khan wrote:
>>>
>>>> Dear mni_n3 support,
>>>>
>>>> I have a make build problem:
>>>>
>>>>  env NETCDF_INCLUDE=/usr/local/netcdf-3.5.0/include/ 
>>>> MINC_INCLUDE=/usr/local/mni/include MINC_LIB=/usr/local/mni/lib 
>>>> VOLUMEIO_INCLUDE=/usr/local/mni/include 
>>>> VOLUMEIO_LIB=/usr/local/mni/lib MNI_DATAPATH=/usr/local/mni/data 
>>>> ./configure --prefix=/usr/local/n3
>>>>
>>>> and get this error at the end :
>>>>
>>>> make[3]: *** [volumeStats.o] Error 1
>>>> make[3]: Leaving directory `/space/N3/src/VolumeStats'
>>>> umask 022;
>>>> make[2]: Leaving directory `/space/N3/src'
>>>> make[1]: Leaving directory `/space/N3/src'
>>>>
>>>> and
>>>>
>>>> even make test fails,eg
>>>> MNI_DATAPATH=/usr/local/mni/data with all the files,ie
>>>>
>>>>
>>>>  ls -l /usr/local/mni/data/N3
>>>> total 126
>>>> -rw-r--r--   1 root     other      64270 Jan  8 15:30 
>>>> average_305_mask_1mm.mnc.gz
>>>>  ls -l /usr/local/mni/data/testing/
>>>> total 126
>>>> -rw-r--r--   1 root     other      64270 Jan  8 16:22 
>>>> average_305_mask_1mm.mnc.gz
>>>>
>>>> make test
>>>> (cd testing; ./do_test test.log )
>>>>
>>>> ---------------------------------------------------------------------
>>>>  Testing MNI N3 software package
>>>>
>>>> ---------------------------------------------------------------------
>>>>
>>>> do_test: couldn't find program "field2imp"
>>>> do_test: couldn't find program "imp2field"
>>>> do_test: couldn't find program "sharpen_volume"
>>>> do_test: couldn't find program "nu_estimate_np_and_em"
>>>> do_test: couldn't find program "nu_evaluate"
>>>> do_test: couldn't find program "nu_evaluate"
>>>> do_test: couldn't find program "nu_estimate"
>>>> do_test: couldn't find program "evaluate_field"
>>>> do_test: couldn't find program "extracttag"
>>>> do_test: couldn't find program "sharpen_hist"
>>>> do_test: couldn't find program "spline_smooth"
>>>> do_test: couldn't find program "volume_hist"
>>>> do_test: couldn't find program "volume_stats"
>>>> Cannot find the file N3/testing/average_305_mask_1mm.mnc.gz.  The 
>>>> data for the test suite
>>>> does not appear to be installed correctly.
>>>> make: *** [test] Error 1
>>>>
>>>>
>>>> ..help would be much appreciated ..!
>>>>
>>
>>
>> -- 
>> ------------------------------------
>> Asim Khan
>> Unix Systems Administrator
>> St George's Hospital Medical School
>> www.sghms.ac.uk
>> ------------------------------------
>>
>>
>>
>> -- 
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>> _______________________________________________
>> MINC-users@bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



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From minc-users@bic.mni.mcgill.ca  Mon Jan 19 15:00:40 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Mon, 19 Jan 2004 15:00:40 +0000
Subject: [MINC-users] EBTKS fails on make
Message-ID: <400BF118.60906@sghms.ac.uk>

Dear All,

My configure works but make gives an error - see below ?

./configure --prefix=/opt/N3/EBTKS CC=gcc

checking for a BSD-compatible install... ./install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ./install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for a sed that does not truncate output... /usr/local/bin/sed
checking for egrep... egrep
checking for ld used by gcc... /usr/local/sparc-sun-solaris2.8/bin/ld
checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
ld... yes
checking for /usr/local/sparc-sun-solaris2.8/bin/ld option to reload 
object files... -r
checking for BSD-compatible nm... /usr/local/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... no
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking the maximum length of command line arguments... 262144
checking command to parse /usr/local/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc static flag  works... yes
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
supports shared libraries... yes
checking dynamic linker characteristics... solaris2.8 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/local/sparc-sun-solaris2.8/bin/ld
checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
ld... yes
checking whether the g++ linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
supports shared libraries... yes
checking dynamic linker characteristics... solaris2.8 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
supports shared libraries... yes
checking dynamic linker characteristics... solaris2.8 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for finite... yes
checking for isfinite... no
checking for mkstemp... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands


  make

make[1]: *** [Matrix.lo] Error 1
make[1]: Leaving directory `/opt/N3/EBTKS-1.1'
make: *** [all] Error 2

-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


From minc-users@bic.mni.mcgill.ca  Mon Jan 19 15:14:47 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Mon, 19 Jan 2004 10:14:47 -0500
Subject: [MINC-users] EBTKS fails on make
In-Reply-To: <400BF118.60906@sghms.ac.uk>
References: <400BF118.60906@sghms.ac.uk>
Message-ID: <3831DB6C-4A92-11D8-8757-000A95DBBFD8@bic.mni.mcgill.ca>

Greetings,

not a very easy to decipher error - any chance you could give some more 
details. Especially the config.log could be useful.

Cheers,

Jason

On Jan 19, 2004, at 10:00 AM, Asim Khan wrote:

> Dear All,
>
> My configure works but make gives an error - see below ?
>
> ./configure --prefix=/opt/N3/EBTKS CC=gcc
>
> checking for a BSD-compatible install... ./install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ./install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc... gcc
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for a sed that does not truncate output... /usr/local/bin/sed
> checking for egrep... egrep
> checking for ld used by gcc... /usr/local/sparc-sun-solaris2.8/bin/ld
> checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
> ld... yes
> checking for /usr/local/sparc-sun-solaris2.8/bin/ld option to reload 
> object files... -r
> checking for BSD-compatible nm... /usr/local/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking how to run the C preprocessor... gcc -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... no
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for g77... g77
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether g77 accepts -g... yes
> checking the maximum length of command line arguments... 262144
> checking command to parse /usr/local/bin/nm -B output from gcc 
> object... ok
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking if gcc static flag  works... yes
> checking if gcc supports -fno-rtti -fno-exceptions... yes
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc supports -c -o file.o... yes
> checking whether the gcc linker 
> (/usr/local/sparc-sun-solaris2.8/bin/ld) supports shared libraries... 
> yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> checking for ld used by g++... /usr/local/sparc-sun-solaris2.8/bin/ld
> checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
> ld... yes
> checking whether the g++ linker 
> (/usr/local/sparc-sun-solaris2.8/bin/ld) supports shared libraries... 
> yes
> checking for g++ option to produce PIC... -fPIC
> checking if g++ PIC flag -fPIC works... yes
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker 
> (/usr/local/sparc-sun-solaris2.8/bin/ld) supports shared libraries... 
> yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> appending configuration tag "F77" to libtool
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for g77 option to produce PIC... -fPIC
> checking if g77 PIC flag -fPIC works... yes
> checking if g77 supports -c -o file.o... yes
> checking whether the g77 linker 
> (/usr/local/sparc-sun-solaris2.8/bin/ld) supports shared libraries... 
> yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking for finite... yes
> checking for isfinite... no
> checking for mkstemp... yes
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: executing depfiles commands
>
>
>  make
>
> make[1]: *** [Matrix.lo] Error 1
> make[1]: Leaving directory `/opt/N3/EBTKS-1.1'
> make: *** [all] Error 2
>
> -- 
> ------------------------------------
> Asim Khan
> Unix Systems Administrator
> St George's Hospital Medical School
> www.sghms.ac.uk
> ------------------------------------
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Mon Jan 19 15:31:26 2004
From: minc-users@bic.mni.mcgill.ca (Andre MATOS)
Date: Mon, 19 Jan 2004 10:31:26 -0500 (EST)
Subject: [MINC-users] EBTKS fails on make
In-Reply-To: <400BF118.60906@sghms.ac.uk>
Message-ID: <Pine.LNX.4.44.0401191029110.20564-100000@hydra.bic.mni.mcgill.ca>

May be it's missing the parameter 

"--with-build-path=..."


Andre Matos
amatos@mrs.mni.mcgill.ca


On Mon, 19 Jan 2004, Asim Khan wrote:

> Dear All,
> 
> My configure works but make gives an error - see below ?
> 
> ./configure --prefix=/opt/N3/EBTKS CC=gcc
> 
> checking for a BSD-compatible install... ./install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ./install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc... gcc
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for a sed that does not truncate output... /usr/local/bin/sed
> checking for egrep... egrep
> checking for ld used by gcc... /usr/local/sparc-sun-solaris2.8/bin/ld
> checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
> ld... yes
> checking for /usr/local/sparc-sun-solaris2.8/bin/ld option to reload 
> object files... -r
> checking for BSD-compatible nm... /usr/local/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking how to run the C preprocessor... gcc -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... no
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for g77... g77
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether g77 accepts -g... yes
> checking the maximum length of command line arguments... 262144
> checking command to parse /usr/local/bin/nm -B output from gcc object... ok
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking if gcc static flag  works... yes
> checking if gcc supports -fno-rtti -fno-exceptions... yes
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc supports -c -o file.o... yes
> checking whether the gcc linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
> supports shared libraries... yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> checking for ld used by g++... /usr/local/sparc-sun-solaris2.8/bin/ld
> checking if the linker (/usr/local/sparc-sun-solaris2.8/bin/ld) is GNU 
> ld... yes
> checking whether the g++ linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
> supports shared libraries... yes
> checking for g++ option to produce PIC... -fPIC
> checking if g++ PIC flag -fPIC works... yes
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
> supports shared libraries... yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> appending configuration tag "F77" to libtool
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for g77 option to produce PIC... -fPIC
> checking if g77 PIC flag -fPIC works... yes
> checking if g77 supports -c -o file.o... yes
> checking whether the g77 linker (/usr/local/sparc-sun-solaris2.8/bin/ld) 
> supports shared libraries... yes
> checking dynamic linker characteristics... solaris2.8 ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking for finite... yes
> checking for isfinite... no
> checking for mkstemp... yes
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: executing depfiles commands
> 
> 
>   make
> 
> make[1]: *** [Matrix.lo] Error 1
> make[1]: Leaving directory `/opt/N3/EBTKS-1.1'
> make: *** [all] Error 2
> 
> 

-- 
Andre Matos
amatos@mrs.mni.mcgill.ca



From minc-users@bic.mni.mcgill.ca  Tue Jan 20 01:42:15 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Mon, 19 Jan 2004 20:42:15 -0500
Subject: [MINC-users] EBTKS fails on make
In-Reply-To: <400BF118.60906@sghms.ac.uk>; from akhan@sghms.ac.uk on Mon, Jan 19, 2004 at 03:00:40PM +0000
References: <400BF118.60906@sghms.ac.uk>
Message-ID: <20040119204215.A1284903@shadow.bic.mni.mcgill.ca>

On Mon, Jan 19, 2004 at 03:00:40PM +0000, Asim Khan wrote:
> Dear All,
> 
> My configure works but make gives an error - see below ?
 
>   make
> 
> make[1]: *** [Matrix.lo] Error 1
> make[1]: Leaving directory `/opt/N3/EBTKS-1.1'
> make: *** [all] Error 2
 
Surely there's a bit of output between "make" and the error message
you quote.  For example, was there no diagnostic from the compiler?


-S 


From minc-users@bic.mni.mcgill.ca  Tue Jan 20 16:35:46 2004
From: minc-users@bic.mni.mcgill.ca (Sven Joubert)
Date: Tue, 20 Jan 2004 11:35:46 -0500
Subject: [MINC-users] (no subject)
Message-ID: <BAY1-F20JZGT9KP4vtA0000141f@hotmail.com>

Hello,

Could you please remove me from your mailing list (svenjoubert@hotmail.com)? 
Many thanks in advance,

Sven Joubert

_________________________________________________________________
STOP MORE SPAM with the new MSN 8 and get 2 months FREE*   
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From minc-users@bic.mni.mcgill.ca  Tue Jan 20 19:26:55 2004
From: minc-users@bic.mni.mcgill.ca (Nugent, Allison C. (NIH/NIMH))
Date: Tue, 20 Jan 2004 14:26:55 -0500
Subject: [MINC-users] (no subject)
Message-ID: <5F9DE1C25708B04EAD634A1AE3D9113001E51E6A@nihexchange20.nih.gov>

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01C3DF8B.5D8DAC40
Content-Type: text/plain

Hello,

            I'm having a frustrating problem with the N3 package, running on
solaris.  Version 1.0 had previously worked fine on my machine, then one
day, it stopped.  It would crash at nu_evaluate, leaving .imp files, but not
creating my n3 corrected .mnc files.  It would give errors saying things
like the temporary files had different image dimensions than my input file.
So, instead of fixing it, I decided it was time for an upgrade.  I bogged
down somewhere in getting the fortran gcc libraries, and turned things over
to my system administrator.  He's still working on the upgraded version of
N3, but just recompiled N3 1.0.  Here's the message I get when it quits:

 

[nu_evaluate]
[allison@kismet:/mnt/v1280/raid1/mood/users/allison/struct_workspace/allison
_nugent] [2004-01-20 14:20:29] /usr/local/bin/evaluate_field -clobber
-verbose -like /tmp//template.mnc test.imp /tmp//field_volume.mnc

Error: MINC file has only 0 dims, volume requires 3.

Failed to read volume: /tmp//template.mnc.

nu_evaluate: crashed while running evaluate_field (termination status=256)

nu_correct: crashed while running nu_evaluate (termination status=256)

 

mincinfo on the temporary file template.mnc crashes

mincheader complains, but writes the header.  The values for xspace, yspace,
and zspace are given, but the full definition of the structures is missing. 

 

It seems that the problem is in the writing of these temporary images.  I've
tried specifying a different tmp directory, but that didn't' help.  

 

Can anyone please help? I'm at my wit's end with this!!

 

Allison C. Nugent, PhD

MRI Physicist

Mood and Anxiety Disorders Program

(301)451-8863 

 


------_=_NextPart_001_01C3DF8B.5D8DAC40
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<div class=Section1>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hello,</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I'm
having a frustrating problem with the N3 package, running on solaris.&nbsp;
Version 1.0 had previously worked fine on my machine, then one day, it
stopped.&nbsp; It would crash at nu_evaluate, leaving .imp files, but not
creating my n3 corrected .mnc files.&nbsp; It would give errors saying things
like the temporary files had different image dimensions than my input
file.&nbsp; So, instead of fixing it, I decided it was time for an upgrade.&nbsp;
I bogged down somewhere in getting the fortran gcc libraries, and turned things
over to my system administrator.&nbsp; He's still working on the upgraded
version of N3, but just recompiled N3 1.0.&nbsp; Here's the message I get
when it quits:</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[nu_evaluate]
[allison@kismet:/mnt/v1280/raid1/mood/users/allison/struct_workspace/allison_nugent]
[2004-01-20 </span></font><font size=2 face=Arial><span style='font-size:10.0pt;
 font-family:Arial'>14:20:29</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>] /usr/local/bin/evaluate_field
-clobber -verbose -like /tmp//template.mnc test.imp /tmp//field_volume.mnc</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Error: MINC file has only 0 dims, volume requires 3.</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Failed to read volume: /tmp//template.mnc.</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nu_evaluate: crashed while running evaluate_field
(termination status=256)</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nu_correct: crashed while running nu_evaluate (termination
status=256)</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>mincinfo on the temporary file template.mnc crashes</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>mincheader complains, but writes the header.&nbsp; The
values for xspace, yspace, and zspace are given, but the full definition of the
structures is missing. </span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>It seems that the problem is in the writing of these
temporary images.&nbsp; I've tried specifying a different tmp directory,
but that didn't' help.&nbsp; </span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Can anyone please help? I'm at my wit's end with
this!!</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Allison C. Nugent, PhD</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>MRI Physicist</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Mood and Anxiety Disorders Program</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>(301)451-8863 </span></font></p>

<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>&nbsp;</span></font></p>

</div>

</body>

</html>

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From minc-users@bic.mni.mcgill.ca  Wed Jan 21 14:37:26 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 21 Jan 2004 09:37:26 -0500
Subject: [MINC-users] (no subject)
In-Reply-To: <5F9DE1C25708B04EAD634A1AE3D9113001E51E6A@nihexchange20.nih.gov>
References: <5F9DE1C25708B04EAD634A1AE3D9113001E51E6A@nihexchange20.nih.gov>
Message-ID: <556282A4-4C1F-11D8-B516-000A95DBBFD8@bic.mni.mcgill.ca>

--Apple-Mail-1--248117349
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=ISO-8859-1;
	delsp=yes;
	format=flowed

Greetings,

I think that your problem relates to the headers in your MINC files. N3 =20=

is unfortunately a bit brain-dead at the moment about how it handles =20
those headers, and if they are too large, it will crash. This has =20
become a problem only recently since newer scanners have started adding =20=

a lot of DICOM information to their headers.

To see if this is your problem, try editing out the DICOM stuff from =20
your minc-headers. Create a script that looks something like this =20
(modified where necessary):

=3D=3D=3D begin script =3D=3D=3D

#!/usr/local/bin/perl5 -w

open IN, "$ARGV[0]";
open OUT, ">/tmp/mincedittmp_$$.txt";

while (<IN>) {
     if ($_ =3D~ /dicom_0x.+/) {
         # do nothing
     }
     else {
         print OUT $_;
     }
}

close IN;
close OUT;

system("mv /tmp/mincedittmp_$$.txt $ARGV[0]");

=3D=3D=3D end script =3D=3D=3D=3D

And use that script like so:

mincedit file.mnc script.pl

That should leave you with the same minc file you had before with the =20=

DICOM headers removed. Afterwards run N3 as you would have before and =20=

see if it works.

Then again, this might not be your problem after all ...

Jason


On Jan 20, 2004, at 2:26 PM, Nugent, Allison C. (NIH/NIMH) wrote:

> Hello,
>
> =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I'm having a frustrating problem =
with the N3 package, =20
> running on solaris.=A0 Version 1.0 had previously worked fine on my =20=

> machine, then one day, it stopped.=A0 It would crash at nu_evaluate, =20=

> leaving .imp files, but not creating my n3 corrected .mnc files.=A0 It =
=20
> would give errors saying things like the temporary files had different =
=20
> image dimensions than my input file.=A0 So, instead of fixing it, I =20=

> decided it was time for an upgrade.=A0 I bogged down somewhere in =20
> getting the fortran gcc libraries, and turned things over to my system =
=20
> administrator.=A0 He's still working on the upgraded version of N3, =
but =20
> just recompiled N3 1.0.=A0 Here's the message I get when it quits:
>
> =A0
>
> [nu_evaluate] =20
> [allison@kismet:/mnt/v1280/raid1/mood/users/allison/struct_workspace/=20=

> allison_nugent] [2004-01-2014:20:29] /usr/local/bin/evaluate_field =20
> -clobber -verbose -like /tmp//template.mnc test.imp =20
> /tmp//field_volume.mnc
>
> Error: MINC file has only 0 dims, volume requires 3.
>
> Failed to read volume: /tmp//template.mnc.
>
> nu_evaluate: crashed while running evaluate_field (termination =20
> status=3D256)
>
> nu_correct: crashed while running nu_evaluate (termination status=3D256)=

>
> =A0
>
> mincinfo on the temporary file template.mnc crashes
>
> mincheader complains, but writes the header.=A0 The values for xspace, =
=20
> yspace, and zspace are given, but the full definition of the =20
> structures is missing.
>
> =A0
>
> It seems that the problem is in the writing of these temporary =20
> images.=A0 I've tried specifying a different tmp directory, but that =20=

> didn't' help.=A0
>
> =A0
>
> Can anyone please help? I'm at my wit's end with this!!
>
> =A0
>
> Allison C. Nugent, PhD
>
> MRI Physicist
>
> Mood and Anxiety Disorders Program
>
> (301)451-8863
>
> =A0

--Apple-Mail-1--248117349
Content-Transfer-Encoding: quoted-printable
Content-Type: text/enriched;
	charset=ISO-8859-1

Greetings,


I think that your problem relates to the headers in your MINC files.
N3 is unfortunately a bit brain-dead at the moment about how it
handles those headers, and if they are too large, it will crash. This
has become a problem only recently since newer scanners have started
adding a lot of DICOM information to their headers.=20


To see if this is your problem, try editing out the DICOM stuff from
your minc-headers. Create a script that looks something like this
(modified where necessary):


=3D=3D=3D begin script =3D=3D=3D


#!/usr/local/bin/perl5 -w


open IN, "$ARGV[0]";

open OUT, ">/tmp/mincedittmp_$$.txt";


while (<<IN>) {

    if ($_ =3D~ /dicom_0x.+/) {

        # do nothing

    }

    else {

        print OUT $_;

    }

}


close IN;

close OUT;


system("mv /tmp/mincedittmp_$$.txt $ARGV[0]");


=3D=3D=3D end script =3D=3D=3D=3D


And use that script like so:


mincedit file.mnc script.pl


That should leave you with the same minc file you had before with the
DICOM headers removed. Afterwards run N3 as you would have before and
see if it works.


Then again, this might not be your problem after all ...


Jason



On Jan 20, 2004, at 2:26 PM, Nugent, Allison C. (NIH/NIMH) wrote:


=
<excerpt><fontfamily><param>Arial</param><x-tad-bigger>Hello,</x-tad-bigge=
r></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0 I'm having a
frustrating problem with the N3 package, running on solaris.=A0 Version
1.0 had previously worked fine on my machine, then one day, it
stopped.=A0 It would crash at nu_evaluate, leaving .imp files, but not
creating my n3 corrected .mnc files.=A0 It would give errors saying
things like the temporary files had different image dimensions than my
input file.=A0 So, instead of fixing it, I decided it was time for an
upgrade.=A0 I bogged down somewhere in getting the fortran gcc
libraries, and turned things over to my system administrator.=A0 He's
still working on the upgraded version of N3, but just recompiled N3
1.0.=A0 Here's the message I get when it =
quits:</x-tad-bigger></fontfamily>


=
<fontfamily><param>Arial</param><x-tad-bigger>=A0</x-tad-bigger></fontfami=
ly>


<fontfamily><param>Arial</param><x-tad-bigger>[nu_evaluate]
=
[allison@kismet:/mnt/v1280/raid1/mood/users/allison/struct_workspace/allis=
on_nugent]
[2004-01-2014:20:29] /usr/local/bin/evaluate_field -clobber -verbose
-like /tmp//template.mnc test.imp =
/tmp//field_volume.mnc</x-tad-bigger></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>Error: MINC file has
only 0 dims, volume requires 3.</x-tad-bigger></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>Failed to read volume:
/tmp//template.mnc.</x-tad-bigger></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>nu_evaluate: crashed
while running evaluate_field (termination =
status=3D256)</x-tad-bigger></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>nu_correct: crashed
while running nu_evaluate (termination =
status=3D256)</x-tad-bigger></fontfamily>


=
<fontfamily><param>Arial</param><x-tad-bigger>=A0</x-tad-bigger></fontfami=
ly>


<fontfamily><param>Arial</param><x-tad-bigger>mincinfo on the
temporary file template.mnc crashes</x-tad-bigger></fontfamily>


<fontfamily><param>Arial</param><x-tad-bigger>mincheader complains,
but writes the header.=A0 The values for xspace, yspace, and zspace are
given, but the full definition of the structures is =
missing.</x-tad-bigger></fontfamily>


=
<fontfamily><param>Arial</param><x-tad-bigger>=A0</x-tad-bigger></fontfami=
ly>


<fontfamily><param>Arial</param><x-tad-bigger>It seems that the
problem is in the writing of these temporary images.=A0 I've tried
specifying a different tmp directory, but that didn't' =
help.=A0</x-tad-bigger></fontfamily>


=
<fontfamily><param>Arial</param><x-tad-bigger>=A0</x-tad-bigger></fontfami=
ly>


<fontfamily><param>Arial</param><x-tad-bigger>Can anyone please help?
I'm at my wit's end with this!!</x-tad-bigger></fontfamily>


=
<fontfamily><param>Arial</param><x-tad-bigger>=A0</x-tad-bigger></fontfami=
ly>


<fontfamily><param>Arial</param><bigger><bigger>Allison C. Nugent, =
PhD</bigger></bigger></fontfamily>


<fontfamily><param>Arial</param><bigger><bigger>MRI =
Physicist</bigger></bigger></fontfamily>


<fontfamily><param>Arial</param><bigger><bigger>Mood and Anxiety
Disorders Program</bigger></bigger></fontfamily>


=
<fontfamily><param>Arial</param><bigger><bigger>(301)451-8863</bigger></bi=
gger></fontfamily>


<fontfamily><param>Times New =
Roman</param><bigger><bigger>=A0</bigger></bigger></fontfamily>

</excerpt>=

--Apple-Mail-1--248117349--


From minc-users@bic.mni.mcgill.ca  Thu Jan 22 14:56:24 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Thu, 22 Jan 2004 14:56:24 +0000
Subject: [MINC-users] EBTKS lib problems
Message-ID: <400FE498.2000601@sghms.ac.uk>

Bert,

Still cannot find EBTKS even when in /usr/local ,eg

[root@eclipse EBTKS-1.1]#> make check
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT version.lo -MD -MP -MF ".deps/version.Tpo" \
   -c -o version.lo `test -f 'version.cc' || echo './'`version.cc; \
then mv -f ".deps/version.Tpo" ".deps/version.Plo"; \
else rm -f ".deps/version.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT version.lo -MD -MP 
-MF .deps/version.Tpo -c version.cc -o version.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT FileIO.lo -MD -MP -MF ".deps/FileIO.Tpo" \
   -c -o FileIO.lo `test -f 'src/FileIO.cc' || echo './'`src/FileIO.cc; \
then mv -f ".deps/FileIO.Tpo" ".deps/FileIO.Plo"; \
else rm -f ".deps/FileIO.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT FileIO.lo -MD -MP 
-MF .deps/FileIO.Tpo -c src/FileIO.cc -o FileIO.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Histogram.lo -MD -MP -MF ".deps/Histogram.Tpo" \
   -c -o Histogram.lo `test -f 'src/Histogram.cc' || echo 
'./'`src/Histogram.cc; \
then mv -f ".deps/Histogram.Tpo" ".deps/Histogram.Plo"; \
else rm -f ".deps/Histogram.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Histogram.lo -MD 
-MP -MF .deps/Histogram.Tpo -c src/Histogram.cc -o Histogram.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT MPoint.lo -MD -MP -MF ".deps/MPoint.Tpo" \
   -c -o MPoint.lo `test -f 'src/MPoint.cc' || echo './'`src/MPoint.cc; \
then mv -f ".deps/MPoint.Tpo" ".deps/MPoint.Plo"; \
else rm -f ".deps/MPoint.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT MPoint.lo -MD -MP 
-MF .deps/MPoint.Tpo -c src/MPoint.cc -o MPoint.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT MString.lo -MD -MP -MF ".deps/MString.Tpo" \
   -c -o MString.lo `test -f 'src/MString.cc' || echo './'`src/MString.cc; \
then mv -f ".deps/MString.Tpo" ".deps/MString.Plo"; \
else rm -f ".deps/MString.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT MString.lo -MD -MP 
-MF .deps/MString.Tpo -c src/MString.cc -o MString.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT OpTimer.lo -MD -MP -MF ".deps/OpTimer.Tpo" \
   -c -o OpTimer.lo `test -f 'src/OpTimer.cc' || echo './'`src/OpTimer.cc; \
then mv -f ".deps/OpTimer.Tpo" ".deps/OpTimer.Plo"; \
else rm -f ".deps/OpTimer.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT OpTimer.lo -MD -MP 
-MF .deps/OpTimer.Tpo -c src/OpTimer.cc -o OpTimer.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT OrderedCltn.lo -MD -MP -MF ".deps/OrderedCltn.Tpo" \
   -c -o OrderedCltn.lo `test -f 'src/OrderedCltn.cc' || echo 
'./'`src/OrderedCltn.cc; \
then mv -f ".deps/OrderedCltn.Tpo" ".deps/OrderedCltn.Plo"; \
else rm -f ".deps/OrderedCltn.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT OrderedCltn.lo -MD 
-MP -MF .deps/OrderedCltn.Tpo -c src/OrderedCltn.cc -o OrderedCltn.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Path.lo -MD -MP -MF ".deps/Path.Tpo" \
   -c -o Path.lo `test -f 'src/Path.cc' || echo './'`src/Path.cc; \
then mv -f ".deps/Path.Tpo" ".deps/Path.Plo"; \
else rm -f ".deps/Path.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Path.lo -MD -MP 
-MF .deps/Path.Tpo -c src/Path.cc -o Path.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Polynomial.lo -MD -MP -MF ".deps/Polynomial.Tpo" \
   -c -o Polynomial.lo `test -f 'src/Polynomial.cc' || echo 
'./'`src/Polynomial.cc; \
then mv -f ".deps/Polynomial.Tpo" ".deps/Polynomial.Plo"; \
else rm -f ".deps/Polynomial.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Polynomial.lo -MD 
-MP -MF .deps/Polynomial.Tpo -c src/Polynomial.cc -o Polynomial.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Spline.lo -MD -MP -MF ".deps/Spline.Tpo" \
   -c -o Spline.lo `test -f 'src/Spline.cc' || echo './'`src/Spline.cc; \
then mv -f ".deps/Spline.Tpo" ".deps/Spline.Plo"; \
else rm -f ".deps/Spline.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Spline.lo -MD -MP 
-MF .deps/Spline.Tpo -c src/Spline.cc -o Spline.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT TBSpline.lo -MD -MP -MF ".deps/TBSpline.Tpo" \
   -c -o TBSpline.lo `test -f 'src/TBSpline.cc' || echo 
'./'`src/TBSpline.cc; \
then mv -f ".deps/TBSpline.Tpo" ".deps/TBSpline.Plo"; \
else rm -f ".deps/TBSpline.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT TBSpline.lo -MD 
-MP -MF .deps/TBSpline.Tpo -c src/TBSpline.cc -o TBSpline.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT TrainingSet.lo -MD -MP -MF ".deps/TrainingSet.Tpo" \
   -c -o TrainingSet.lo `test -f 'src/TrainingSet.cc' || echo 
'./'`src/TrainingSet.cc; \
then mv -f ".deps/TrainingSet.Tpo" ".deps/TrainingSet.Plo"; \
else rm -f ".deps/TrainingSet.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT TrainingSet.lo -MD 
-MP -MF .deps/TrainingSet.Tpo -c src/TrainingSet.cc -o TrainingSet.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT amoeba.lo -MD -MP -MF ".deps/amoeba.Tpo" \
   -c -o amoeba.lo `test -f 'src/amoeba.cc' || echo './'`src/amoeba.cc; \
then mv -f ".deps/amoeba.Tpo" ".deps/amoeba.Plo"; \
else rm -f ".deps/amoeba.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT amoeba.lo -MD -MP 
-MF .deps/amoeba.Tpo -c src/amoeba.cc -o amoeba.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT backProp.lo -MD -MP -MF ".deps/backProp.Tpo" \
   -c -o backProp.lo `test -f 'src/backProp.cc' || echo 
'./'`src/backProp.cc; \
then mv -f ".deps/backProp.Tpo" ".deps/backProp.Plo"; \
else rm -f ".deps/backProp.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT backProp.lo -MD 
-MP -MF .deps/backProp.Tpo -c src/backProp.cc -o backProp.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT fcomplex.lo -MD -MP -MF ".deps/fcomplex.Tpo" \
   -c -o fcomplex.lo `test -f 'src/fcomplex.cc' || echo 
'./'`src/fcomplex.cc; \
then mv -f ".deps/fcomplex.Tpo" ".deps/fcomplex.Plo"; \
else rm -f ".deps/fcomplex.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT fcomplex.lo -MD 
-MP -MF .deps/fcomplex.Tpo -c src/fcomplex.cc -o fcomplex.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT dcomplex.lo -MD -MP -MF ".deps/dcomplex.Tpo" \
   -c -o dcomplex.lo `test -f 'src/dcomplex.cc' || echo 
'./'`src/dcomplex.cc; \
then mv -f ".deps/dcomplex.Tpo" ".deps/dcomplex.Plo"; \
else rm -f ".deps/dcomplex.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT dcomplex.lo -MD 
-MP -MF .deps/dcomplex.Tpo -c src/dcomplex.cc -o dcomplex.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Array.lo -MD -MP -MF ".deps/Array.Tpo" \
   -c -o Array.lo `test -f 'templates/Array.cc' || echo 
'./'`templates/Array.cc; \
then mv -f ".deps/Array.Tpo" ".deps/Array.Plo"; \
else rm -f ".deps/Array.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Array.lo -MD -MP 
-MF .deps/Array.Tpo -c templates/Array.cc -o Array.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT CachedArray.lo -MD -MP -MF ".deps/CachedArray.Tpo" \
   -c -o CachedArray.lo `test -f 'templates/CachedArray.cc' || echo 
'./'`templates/CachedArray.cc; \
then mv -f ".deps/CachedArray.Tpo" ".deps/CachedArray.Plo"; \
else rm -f ".deps/CachedArray.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT CachedArray.lo -MD 
-MP -MF .deps/CachedArray.Tpo -c templates/CachedArray.cc -o CachedArray.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Dictionary.lo -MD -MP -MF ".deps/Dictionary.Tpo" \
   -c -o Dictionary.lo `test -f 'templates/Dictionary.cc' || echo 
'./'`templates/Dictionary.cc; \
then mv -f ".deps/Dictionary.Tpo" ".deps/Dictionary.Plo"; \
else rm -f ".deps/Dictionary.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Dictionary.lo -MD 
-MP -MF .deps/Dictionary.Tpo -c templates/Dictionary.cc -o Dictionary.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Matrix.lo -MD -MP -MF ".deps/Matrix.Tpo" \
   -c -o Matrix.lo `test -f 'templates/Matrix.cc' || echo 
'./'`templates/Matrix.cc; \
then mv -f ".deps/Matrix.Tpo" ".deps/Matrix.Plo"; \
else rm -f ".deps/Matrix.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Matrix.lo -MD -MP 
-MF .deps/Matrix.Tpo -c templates/Matrix.cc -o Matrix.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT MatrixSupport.lo -MD -MP -MF ".deps/MatrixSupport.Tpo" \
   -c -o MatrixSupport.lo `test -f 'templates/MatrixSupport.cc' || echo 
'./'`templates/MatrixSupport.cc; \
then mv -f ".deps/MatrixSupport.Tpo" ".deps/MatrixSupport.Plo"; \
else rm -f ".deps/MatrixSupport.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT MatrixSupport.lo 
-MD -MP -MF .deps/MatrixSupport.Tpo -c templates/MatrixSupport.cc -o 
MatrixSupport.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT Pool.lo -MD -MP -MF ".deps/Pool.Tpo" \
   -c -o Pool.lo `test -f 'templates/Pool.cc' || echo 
'./'`templates/Pool.cc; \
then mv -f ".deps/Pool.Tpo" ".deps/Pool.Plo"; \
else rm -f ".deps/Pool.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT Pool.lo -MD -MP 
-MF .deps/Pool.Tpo -c templates/Pool.cc -o Pool.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT SimpleArray.lo -MD -MP -MF ".deps/SimpleArray.Tpo" \
   -c -o SimpleArray.lo `test -f 'templates/SimpleArray.cc' || echo 
'./'`templates/SimpleArray.cc; \
then mv -f ".deps/SimpleArray.Tpo" ".deps/SimpleArray.Plo"; \
else rm -f ".deps/SimpleArray.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT SimpleArray.lo -MD 
-MP -MF .deps/SimpleArray.Tpo -c templates/SimpleArray.cc -o SimpleArray.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT ValueMap.lo -MD -MP -MF ".deps/ValueMap.Tpo" \
   -c -o ValueMap.lo `test -f 'templates/ValueMap.cc' || echo 
'./'`templates/ValueMap.cc; \
then mv -f ".deps/ValueMap.Tpo" ".deps/ValueMap.Plo"; \
else rm -f ".deps/ValueMap.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT ValueMap.lo -MD 
-MP -MF .deps/ValueMap.Tpo -c templates/ValueMap.cc -o ValueMap.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT miscTemplateFunc.lo -MD -MP -MF ".deps/miscTemplateFunc.Tpo" \
   -c -o miscTemplateFunc.lo `test -f 'templates/miscTemplateFunc.cc' || 
echo './'`templates/miscTemplateFunc.cc; \
then mv -f ".deps/miscTemplateFunc.Tpo" ".deps/miscTemplateFunc.Plo"; \
else rm -f ".deps/miscTemplateFunc.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT 
miscTemplateFunc.lo -MD -MP -MF .deps/miscTemplateFunc.Tpo -c 
templates/miscTemplateFunc.cc -o miscTemplateFunc.o
if /bin/bash ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. 
-I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS  -g 
-O2 -MT MatrixConv.lo -MD -MP -MF ".deps/MatrixConv.Tpo" \
   -c -o MatrixConv.lo `test -f 'templates/MatrixConv.cc' || echo 
'./'`templates/MatrixConv.cc; \
then mv -f ".deps/MatrixConv.Tpo" ".deps/MatrixConv.Plo"; \
else rm -f ".deps/MatrixConv.Tpo"; exit 1; \
fi
  g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates 
-DUSE_COMPMAT -DUSE_DBLMAT -I/opt/N3/EBTKS -g -O2 -MT MatrixConv.lo -MD 
-MP -MF .deps/MatrixConv.Tpo -c templates/MatrixConv.cc -o MatrixConv.o
/bin/bash ./libtool --mode=link g++  -g -O2   -o libEBTKS.la -rpath 
/usr/local/lib  version.lo FileIO.lo Histogram.lo MPoint.lo MString.lo 
OpTimer.lo OrderedCltn.lo Path.lo Polynomial.lo Spline.lo TBSpline.lo 
TrainingSet.lo amoeba.lo backProp.lo fcomplex.lo dcomplex.lo Array.lo 
CachedArray.lo Dictionary.lo Matrix.lo MatrixSupport.lo Pool.lo 
SimpleArray.lo ValueMap.lo miscTemplateFunc.lo MatrixConv.lo
mkdir .libs
ar cru .libs/libEBTKS.a  version.o FileIO.o Histogram.o MPoint.o 
MString.o OpTimer.o OrderedCltn.o Path.o Polynomial.o Spline.o 
TBSpline.o TrainingSet.o amoeba.o backProp.o fcomplex.o dcomplex.o 
Array.o CachedArray.o Dictionary.o Matrix.o MatrixSupport.o Pool.o 
SimpleArray.o ValueMap.o miscTemplateFunc.o MatrixConv.o
ranlib .libs/libEBTKS.a
creating libEBTKS.la
(cd .libs && rm -f libEBTKS.la && ln -s ../libEBTKS.la libEBTKS.la)
[root@eclipse EBTKS-1.1]#> make
make  all-am
make[1]: Entering directory `/opt/N3/EBTKS-1.1'
make[1]: Leaving directory `/opt/N3/EBTKS-1.1'
[root@eclipse EBTKS-1.1]#> make install
make[1]: Entering directory `/opt/N3/EBTKS-1.1'
/bin/bash ./mkinstalldirs /usr/local/lib
  /bin/bash ./libtool --mode=install ./install-sh -c  libEBTKS.la 
/usr/local/lib/libEBTKS.la
./install-sh -c .libs/libEBTKS.lai /usr/local/lib/libEBTKS.la
./install-sh -c .libs/libEBTKS.a /usr/local/lib/libEBTKS.a
ranlib /usr/local/lib/libEBTKS.a
chmod 644 /usr/local/lib/libEBTKS.a
----------------------------------------------------------------------
Libraries have been installed in:
    /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
      during execution
    - use the `-RLIBDIR' linker flag

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/bash ./mkinstalldirs /usr/local/include/EBTKS
mkdir -p -- /usr/local/include/EBTKS
  ./install-sh -c -m 644 include/amoeba.h /usr/local/include/EBTKS/amoeba.h
  ./install-sh -c -m 644 include/assert.h /usr/local/include/EBTKS/assert.h
  ./install-sh -c -m 644 include/backProp.h 
/usr/local/include/EBTKS/backProp.h
  ./install-sh -c -m 644 include/Complex.h 
/usr/local/include/EBTKS/Complex.h
  ./install-sh -c -m 644 include/dcomplex.h 
/usr/local/include/EBTKS/dcomplex.h
  ./install-sh -c -m 644 include/fcomplex.h 
/usr/local/include/EBTKS/fcomplex.h
  ./install-sh -c -m 644 include/FileIO.h /usr/local/include/EBTKS/FileIO.h
  ./install-sh -c -m 644 include/Histogram.h 
/usr/local/include/EBTKS/Histogram.h
  ./install-sh -c -m 644 include/matlabSupport.h 
/usr/local/include/EBTKS/matlabSupport.h
  ./install-sh -c -m 644 include/Minc.h /usr/local/include/EBTKS/Minc.h
  ./install-sh -c -m 644 include/MPoint.h /usr/local/include/EBTKS/MPoint.h
  ./install-sh -c -m 644 include/MString.h 
/usr/local/include/EBTKS/MString.h
  ./install-sh -c -m 644 include/MTypes.h /usr/local/include/EBTKS/MTypes.h
  ./install-sh -c -m 644 include/OpTimer.h 
/usr/local/include/EBTKS/OpTimer.h
  ./install-sh -c -m 644 include/OrderedCltn.h 
/usr/local/include/EBTKS/OrderedCltn.h
  ./install-sh -c -m 644 include/Path.h /usr/local/include/EBTKS/Path.h
  ./install-sh -c -m 644 include/Polynomial.h 
/usr/local/include/EBTKS/Polynomial.h
  ./install-sh -c -m 644 include/popen.h /usr/local/include/EBTKS/popen.h
  ./install-sh -c -m 644 include/Spline.h /usr/local/include/EBTKS/Spline.h
  ./install-sh -c -m 644 include/TBSpline.h 
/usr/local/include/EBTKS/TBSpline.h
  ./install-sh -c -m 644 include/TrainingSet.h 
/usr/local/include/EBTKS/TrainingSet.h
  ./install-sh -c -m 644 include/trivials.h 
/usr/local/include/EBTKS/trivials.h
  ./install-sh -c -m 644 templates/Array.h /usr/local/include/EBTKS/Array.h
  ./install-sh -c -m 644 templates/CachedArray.h 
/usr/local/include/EBTKS/CachedArray.h
  ./install-sh -c -m 644 templates/Dictionary.h 
/usr/local/include/EBTKS/Dictionary.h
  ./install-sh -c -m 644 templates/Matrix3D.h 
/usr/local/include/EBTKS/Matrix3D.h
  ./install-sh -c -m 644 templates/Matrix.h 
/usr/local/include/EBTKS/Matrix.h
  ./install-sh -c -m 644 templates/MatrixSupport.h 
/usr/local/include/EBTKS/MatrixSupport.h
  ./install-sh -c -m 644 templates/MatrixTest.h 
/usr/local/include/EBTKS/MatrixTest.h
  ./install-sh -c -m 644 templates/miscTemplateFunc.h 
/usr/local/include/EBTKS/miscTemplateFunc.h
  ./install-sh -c -m 644 templates/Pool.h /usr/local/include/EBTKS/Pool.h
  ./install-sh -c -m 644 templates/SimpleArray.h 
/usr/local/include/EBTKS/SimpleArray.h
  ./install-sh -c -m 644 templates/Stack.h /usr/local/include/EBTKS/Stack.h
  ./install-sh -c -m 644 templates/ValueMap.h 
/usr/local/include/EBTKS/ValueMap.h
make[1]: Leaving directory `/opt/N3/EBTKS-1.1'sti



[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
make=/opt/SUNWspro/bin/maketool
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... /opt/SUNWspro/bin/c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none needed
checking dependency style of /opt/SUNWspro/bin/c89... none
checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
together... yes
checking whether we are using the GNU C++ compiler... no
checking whether /opt/SUNWspro/bin/CC accepts -g... yes
checking dependency style of /opt/SUNWspro/bin/CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
checking how to get verbose linking output from /opt/SUNWspro/bin/f77... -v
checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
-R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
-L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS
[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... /opt/SUNWspro/bin/c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none needed
checking dependency style of /opt/SUNWspro/bin/c89... none
checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
together... yes
checking whether we are using the GNU C++ compiler... no
checking whether /opt/SUNWspro/bin/CC accepts -g... yes
checking dependency style of /opt/SUNWspro/bin/CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
checking how to get verbose linking output from /opt/SUNWspro/bin/f77... -v
checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
-L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib 
-L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 
-lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS

-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



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This message has been scanned for viruses and
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From minc-users@bic.mni.mcgill.ca  Thu Jan 22 15:03:38 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Thu, 22 Jan 2004 15:03:38 +0000
Subject: [MINC-users] EBTKS not found when configuring N3
Message-ID: <400FE64A.40702@sghms.ac.uk>

configure:6762: error: cannot find required library EBTKS
LIBS='-lEBTKS -lm '

./configure --prefix=/opt/N3/mni CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" 
CXXFLAGS=-O CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
make=/opt/SUNWspro/bin/maketool
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... /opt/SUNWspro/bin/c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none needed
checking dependency style of /opt/SUNWspro/bin/c89... none
checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
together... yes
checking whether we are using the GNU C++ compiler... no
checking whether /opt/SUNWspro/bin/CC accepts -g... yes
checking dependency style of /opt/SUNWspro/bin/CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
checking how to get verbose linking output from /opt/SUNWspro/bin/f77... -v
checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
-R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
-L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS
[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... /opt/SUNWspro/bin/c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none needed
checking dependency style of /opt/SUNWspro/bin/c89... none
checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
together... yes
checking whether we are using the GNU C++ compiler... no
checking whether /opt/SUNWspro/bin/CC accepts -g... yes
checking dependency style of /opt/SUNWspro/bin/CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
checking how to get verbose linking output from /opt/SUNWspro/bin/f77... -v
checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
-L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib 
-L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 
-lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS

-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


From minc-users@bic.mni.mcgill.ca  Thu Jan 22 15:23:13 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 22 Jan 2004 10:23:13 -0500
Subject: [MINC-users] EBTKS not found when configuring N3
In-Reply-To: <400FE64A.40702@sghms.ac.uk>
References: <400FE64A.40702@sghms.ac.uk>
Message-ID: <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>

You never specify where the library should be found. Try this instead

./configure --prefix=/opt/N3/mni 
--with-build-path=/path/to/libraries:/path/to/other/libs

or set the LDFLAGS environment along with the ones that you have set 
below.

Jason

On Jan 22, 2004, at 10:03 AM, Asim Khan wrote:

> configure:6762: error: cannot find required library EBTKS
> LIBS='-lEBTKS -lm '
>
> ./configure --prefix=/opt/N3/mni CC=/opt/SUNWspro/bin/c89 FFLAGS="-O 
> -w" CXXFLAGS=-O CPPFLAGS="-I/usr/local/include" 
> CXX=/opt/SUNWspro/bin/CC F90=/opt/SUNWspro/bin/f90 
> F77=/opt/SUNWspro/bin/f77 make=/opt/SUNWspro/bin/maketool
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for style of include used by make... GNU
> checking for gcc... /opt/SUNWspro/bin/c89
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... no
> checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
> checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none 
> needed
> checking dependency style of /opt/SUNWspro/bin/c89... none
> checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
> together... yes
> checking whether we are using the GNU C++ compiler... no
> checking whether /opt/SUNWspro/bin/CC accepts -g... yes
> checking dependency style of /opt/SUNWspro/bin/CC... none
> checking for ranlib... ranlib
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for library m... yes
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
> checking how to get verbose linking output from 
> /opt/SUNWspro/bin/f77... -v
> checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
> -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
> -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, 
> no extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -framework vecLib... no
> checking for sgemm_ in -lblas... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for acosp in -lsunmath... yes
> checking for sgemm_ in -lsunperf... yes
> checking for cheev_... yes
> checking for library EBTKS... no
> configure: error: cannot find required library EBTKS
> [root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
> CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
> CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
> F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
> make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for style of include used by make... GNU
> checking for gcc... /opt/SUNWspro/bin/c89
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... no
> checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
> checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none 
> needed
> checking dependency style of /opt/SUNWspro/bin/c89... none
> checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
> together... yes
> checking whether we are using the GNU C++ compiler... no
> checking whether /opt/SUNWspro/bin/CC accepts -g... yes
> checking dependency style of /opt/SUNWspro/bin/CC... none
> checking for ranlib... ranlib
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for library m... yes
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
> checking how to get verbose linking output from 
> /opt/SUNWspro/bin/f77... -v
> checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
> -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib 
> -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 
> -lsunmath -lcx
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, 
> no extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -framework vecLib... no
> checking for sgemm_ in -lblas... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for acosp in -lsunmath... yes
> checking for sgemm_ in -lsunperf... yes
> checking for cheev_... yes
> checking for library EBTKS... no
> configure: error: cannot find required library EBTKS
>
> -- 
> ------------------------------------
> Asim Khan
> Unix Systems Administrator
> St George's Hospital Medical School
> www.sghms.ac.uk
> ------------------------------------
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Thu Jan 22 15:23:53 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 22 Jan 2004 10:23:53 -0500
Subject: [MINC-users] EBTKS not found when configuring N3
In-Reply-To: <400FE64A.40702@sghms.ac.uk>
References: <400FE64A.40702@sghms.ac.uk>
Message-ID: <FD136887-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>

P.S. It is always most useful if you could send the config.log along as 
well (or even better, just the relevant parts of that file) in order to 
help us debug your problems.

Jason

On Jan 22, 2004, at 10:03 AM, Asim Khan wrote:

> configure:6762: error: cannot find required library EBTKS
> LIBS='-lEBTKS -lm '
>
> ./configure --prefix=/opt/N3/mni CC=/opt/SUNWspro/bin/c89 FFLAGS="-O 
> -w" CXXFLAGS=-O CPPFLAGS="-I/usr/local/include" 
> CXX=/opt/SUNWspro/bin/CC F90=/opt/SUNWspro/bin/f90 
> F77=/opt/SUNWspro/bin/f77 make=/opt/SUNWspro/bin/maketool
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for style of include used by make... GNU
> checking for gcc... /opt/SUNWspro/bin/c89
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... no
> checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
> checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none 
> needed
> checking dependency style of /opt/SUNWspro/bin/c89... none
> checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
> together... yes
> checking whether we are using the GNU C++ compiler... no
> checking whether /opt/SUNWspro/bin/CC accepts -g... yes
> checking dependency style of /opt/SUNWspro/bin/CC... none
> checking for ranlib... ranlib
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for library m... yes
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
> checking how to get verbose linking output from 
> /opt/SUNWspro/bin/f77... -v
> checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
> -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
> -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, 
> no extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -framework vecLib... no
> checking for sgemm_ in -lblas... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for acosp in -lsunmath... yes
> checking for sgemm_ in -lsunperf... yes
> checking for cheev_... yes
> checking for library EBTKS... no
> configure: error: cannot find required library EBTKS
> [root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
> CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
> CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
> F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
> make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether build environment is sane... yes
> checking for gawk... no
> checking for mawk... no
> checking for nawk... nawk
> checking whether make sets $(MAKE)... yes
> checking for a BSD-compatible install... ac_config_aux/install-sh -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for style of include used by make... GNU
> checking for gcc... /opt/SUNWspro/bin/c89
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... no
> checking whether /opt/SUNWspro/bin/c89 accepts -g... yes
> checking for /opt/SUNWspro/bin/c89 option to accept ANSI C... none 
> needed
> checking dependency style of /opt/SUNWspro/bin/c89... none
> checking whether /opt/SUNWspro/bin/c89 and cc understand -c and -o 
> together... yes
> checking whether we are using the GNU C++ compiler... no
> checking whether /opt/SUNWspro/bin/CC accepts -g... yes
> checking dependency style of /opt/SUNWspro/bin/CC... none
> checking for ranlib... ranlib
> checking build system type... sparc-sun-solaris2.8
> checking host system type... sparc-sun-solaris2.8
> checking for library m... yes
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether /opt/SUNWspro/bin/f77 accepts -g... yes
> checking how to get verbose linking output from 
> /opt/SUNWspro/bin/f77... -v
> checking for Fortran libraries of /opt/SUNWspro/bin/f77... 
> -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib 
> -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 
> -lsunmath -lcx
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, 
> no extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -framework vecLib... no
> checking for sgemm_ in -lblas... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for acosp in -lsunmath... yes
> checking for sgemm_ in -lsunperf... yes
> checking for cheev_... yes
> checking for library EBTKS... no
> configure: error: cannot find required library EBTKS
>
> -- 
> ------------------------------------
> Asim Khan
> Unix Systems Administrator
> St George's Hospital Medical School
> www.sghms.ac.uk
> ------------------------------------
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Fri Jan 23 00:42:20 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Thu, 22 Jan 2004 19:42:20 -0500
Subject: [MINC-users] EBTKS not found when configuring N3
In-Reply-To: <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>; from jason@bic.mni.mcgill.ca on Thu, Jan 22, 2004 at 10:23:13AM -0500
References: <400FE64A.40702@sghms.ac.uk> <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <20040122194220.C114951@shadow.bic.mni.mcgill.ca>

On Thu, Jan 22, 2004 at 10:23:13AM -0500, Jason Lerch wrote:
> You never specify where the library should be found. Try this instead
> 
> ./configure --prefix=/opt/N3/mni 
> --with-build-path=/path/to/libraries:/path/to/other/libs


To be precise, use
                                                                                
        --with-build-path=/usr/local
                                                                                
since you installed EBTKS into /usr/local/{lib,include} according
to one of your previous mails.  As a bonus: if you do this, you no longer
need to set CPPFLAGS for configure.
                                                                                
 
> or set the LDFLAGS environment along with the ones that you have set 
> below.

Err, but this ought to have worked:
 
> > [root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
> > CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
> > CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
> > F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
> > make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"

You need to check config.log.  If it doesn't point you to the cause,
send that file to me off-list.

-S


From minc-users@bic.mni.mcgill.ca  Tue Jan 27 12:33:33 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Tue, 27 Jan 2004 12:33:33 +0000
Subject: ****RejectedAttachment**** Re: [MINC-users] EBTKS not found when configuring N3
References: <400FE64A.40702@sghms.ac.uk>
 <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>
 <20040122194220.C114951@shadow.bic.mni.mcgill.ca>
Message-ID: <40165A9D.8060104@sghms.ac.uk>

This is a multi-part message in MIME format.

--Boundary_(ID_/nmY59mw39DBDuBYhtO9aA)
Content-type: text/plain; charset=us-ascii; format=flowed
Content-transfer-encoding: 7BIT

Warning: This message has had one or more attachments removed
Warning: (config.log.tar).
Warning: Please read the "VirusWarning.txt" attachment(s) for more information.

Steve,

Thanks for your suggestion but I'm completely dumbfounded as to why it 
doesn't work.


[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
--with-build-path=/usr/local CXX=CC CC=c89 F90=f90 F77=f77 make=maketool
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether c89 accepts -g... yes
checking for c89 option to accept ANSI C... none needed
checking dependency style of c89... none
checking whether c89 and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... no
checking whether CC accepts -g... yes
checking dependency style of CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether f77 accepts -g... yes
checking how to get verbose linking output from f77... -v
checking for Fortran libraries of f77...  -L/usr/local/lib 
-R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
-L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS

Please find attached the config.log.tar and the enviroment and path to 
libraries is shown below:


[root@eclipse N3-1.07]#> env
PWD=/opt/N3/N3-1.07
TZ=GB
HZ=100
HOSTNAME=eclipse
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/include:/opt/SUNWspro/lib:/opt/SUNWspro/include
MANPATH=:/usr/local/man:/usr/share/man
MACHTYPE=sparc-sun-solaris
OLDPWD=/opt/N3
LOGNAME=root
SHLVL=1
SHELL=/sbin/sh
HOSTTYPE=sparc
OSTYPE=solaris
HOME=/
TERM=vt100
PATH=/usr/bin:/bin:/usr/sbin:/usr/local:/usr/local/bin:/usr/ccs/bin:/usr/dt/bin:/usr/openwin/bin:/usr/bin/nsr:/usr/ucb:/opt/SUNWspro/bin/
_=/usr/bin/env

[root@eclipse N3-1.07]#> ls -l /usr/local/lib/libE*
-rw-r--r--   1 bin      bin      9600780 Jan 22 14:44 
/usr/local/lib/libEBTKS.a
-rwxr-xr-x   1 bin      bin         1056 Jan 22 14:44 
/usr/local/lib/libEBTKS.la

ls -l /usr/local/include/EBTKS/
total 488
-rw-r--r--   1 bin      bin         7562 Jan 22 14:44 Array.h
-rw-r--r--   1 bin      bin         9781 Jan 22 14:44 CachedArray.h
-rw-r--r--   1 bin      bin         1935 Jan 22 14:44 Complex.h
-rw-r--r--   1 bin      bin         4640 Jan 22 14:44 Dictionary.h
-rw-r--r--   1 bin      bin         3627 Jan 22 14:44 FileIO.h
-rw-r--r--   1 bin      bin         4313 Jan 22 14:44 Histogram.h
-rw-r--r--   1 bin      bin         7698 Jan 22 14:44 MPoint.h
-rw-r--r--   1 bin      bin         6426 Jan 22 14:44 MString.h
-rw-r--r--   1 bin      bin         2640 Jan 22 14:44 MTypes.h
-rw-r--r--   1 bin      bin        50789 Jan 22 14:44 Matrix.h
-rw-r--r--   1 bin      bin        30004 Jan 22 14:44 Matrix3D.h
-rw-r--r--   1 bin      bin         8790 Jan 22 14:44 MatrixSupport.h
-rw-r--r--   1 bin      bin         4444 Jan 22 14:44 MatrixTest.h
-rw-r--r--   1 bin      bin         1528 Jan 22 14:44 Minc.h
-rw-r--r--   1 bin      bin         2835 Jan 22 14:44 OpTimer.h
-rw-r--r--   1 bin      bin         6705 Jan 22 14:44 OrderedCltn.h
-rw-r--r--   1 bin      bin         2962 Jan 22 14:44 Path.h
-rw-r--r--   1 bin      bin         4411 Jan 22 14:44 Polynomial.h
-rw-r--r--   1 bin      bin         2147 Jan 22 14:44 Pool.h
-rw-r--r--   1 bin      bin        14634 Jan 22 14:44 SimpleArray.h
-rw-r--r--   1 bin      bin         7215 Jan 22 14:44 Spline.h
-rw-r--r--   1 bin      bin         1515 Jan 22 14:44 Stack.h
-rw-r--r--   1 bin      bin         9668 Jan 22 14:44 TBSpline.h
-rw-r--r--   1 bin      bin         3816 Jan 22 14:44 TrainingSet.h
-rw-r--r--   1 bin      bin         5644 Jan 22 14:44 ValueMap.h
-rw-r--r--   1 bin      bin         3001 Jan 22 14:44 amoeba.h
-rw-r--r--   1 bin      bin         1444 Jan 22 14:44 assert.h
-rw-r--r--   1 bin      bin         4613 Jan 22 14:44 backProp.h
-rw-r--r--   1 bin      bin         1437 Jan 22 14:44 dcomplex.h
-rw-r--r--   1 bin      bin         4843 Jan 22 14:44 fcomplex.h
-rw-r--r--   1 bin      bin         3064 Jan 22 14:44 matlabSupport.h
-rw-r--r--   1 bin      bin         4419 Jan 22 14:44 miscTemplateFunc.h
-rw-r--r--   1 bin      bin         2037 Jan 22 14:44 popen.h
-rw-r--r--   1 bin      bin         2399 Jan 22 14:44 trivials.h




Steve ROBBINS wrote:
> On Thu, Jan 22, 2004 at 10:23:13AM -0500, Jason Lerch wrote:
> 
>>You never specify where the library should be found. Try this instead
>>
>>./configure --prefix=/opt/N3/mni 
>>--with-build-path=/path/to/libraries:/path/to/other/libs
> 
> 
> 
> To be precise, use
>                                                                                 
>         --with-build-path=/usr/local
>                                                                                 
> since you installed EBTKS into /usr/local/{lib,include} according
> to one of your previous mails.  As a bonus: if you do this, you no longer
> need to set CPPFLAGS for configure.
>                                                                                 
>  
> 
>>or set the LDFLAGS environment along with the ones that you have set 
>>below.
> 
> 
> Err, but this ought to have worked:
>  
> 
>>>[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
>>>CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
>>>CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
>>>F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
>>>make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
>>
> 
> You need to check config.log.  If it doesn't point you to the cause,
> send that file to me off-list.
> 
> -S
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------


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From minc-users@bic.mni.mcgill.ca  Tue Jan 27 12:36:23 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Tue, 27 Jan 2004 12:36:23 +0000
Subject: [MINC-users] EBTKS not found when configuring N3
References: <400FE64A.40702@sghms.ac.uk>
 <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>
 <20040122194220.C114951@shadow.bic.mni.mcgill.ca>
Message-ID: <40165B47.7000103@sghms.ac.uk>

This is a multi-part message in MIME format.

--Boundary_(ID_I2lNbVmJf0AEwlQyfkSRKw)
Content-type: text/plain; charset=us-ascii; format=flowed
Content-transfer-encoding: 7BIT

Steve,

Thanks for your suggestion but I'm completely dumbfounded as to why it 
doesn't work ?


[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
--with-build-path=/usr/local CXX=CC CC=c89 F90=f90 F77=f77 make=maketool
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... ac_config_aux/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... c89
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether c89 accepts -g... yes
checking for c89 option to accept ANSI C... none needed
checking dependency style of c89... none
checking whether c89 and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... no
checking whether CC accepts -g... yes
checking dependency style of CC... none
checking for ranlib... ranlib
checking build system type... sparc-sun-solaris2.8
checking host system type... sparc-sun-solaris2.8
checking for library m... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether f77 accepts -g... yes
checking how to get verbose linking output from f77... -v
checking for Fortran libraries of f77...  -L/usr/local/lib 
-R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib 
-L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for acosp in -lsunmath... yes
checking for sgemm_ in -lsunperf... yes
checking for cheev_... yes
checking for library EBTKS... no
configure: error: cannot find required library EBTKS

Please find attached the config.log and the enviroment and path to 
libraries is shown below:


[root@eclipse N3-1.07]#> env
PWD=/opt/N3/N3-1.07
TZ=GB
HZ=100
HOSTNAME=eclipse
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/include:/opt/SUNWspro/lib:/opt/SUNWspro/include
MANPATH=:/usr/local/man:/usr/share/man
MACHTYPE=sparc-sun-solaris
OLDPWD=/opt/N3
LOGNAME=root
SHLVL=1
SHELL=/sbin/sh
HOSTTYPE=sparc
OSTYPE=solaris
HOME=/
TERM=vt100
PATH=/usr/bin:/bin:/usr/sbin:/usr/local:/usr/local/bin:/usr/ccs/bin:/usr/dt/bin:/usr/openwin/bin:/usr/bin/nsr:/usr/ucb:/opt/SUNWspro/bin/
_=/usr/bin/env

[root@eclipse N3-1.07]#> ls -l /usr/local/lib/libE*
-rw-r--r--   1 bin      bin      9600780 Jan 22 14:44 
/usr/local/lib/libEBTKS.a
-rwxr-xr-x   1 bin      bin         1056 Jan 22 14:44 
/usr/local/lib/libEBTKS.la

ls -l /usr/local/include/EBTKS/
total 488
-rw-r--r--   1 bin      bin         7562 Jan 22 14:44 Array.h
-rw-r--r--   1 bin      bin         9781 Jan 22 14:44 CachedArray.h
-rw-r--r--   1 bin      bin         1935 Jan 22 14:44 Complex.h
-rw-r--r--   1 bin      bin         4640 Jan 22 14:44 Dictionary.h
-rw-r--r--   1 bin      bin         3627 Jan 22 14:44 FileIO.h
-rw-r--r--   1 bin      bin         4313 Jan 22 14:44 Histogram.h
-rw-r--r--   1 bin      bin         7698 Jan 22 14:44 MPoint.h
-rw-r--r--   1 bin      bin         6426 Jan 22 14:44 MString.h
-rw-r--r--   1 bin      bin         2640 Jan 22 14:44 MTypes.h
-rw-r--r--   1 bin      bin        50789 Jan 22 14:44 Matrix.h
-rw-r--r--   1 bin      bin        30004 Jan 22 14:44 Matrix3D.h
-rw-r--r--   1 bin      bin         8790 Jan 22 14:44 MatrixSupport.h
-rw-r--r--   1 bin      bin         4444 Jan 22 14:44 MatrixTest.h
-rw-r--r--   1 bin      bin         1528 Jan 22 14:44 Minc.h
-rw-r--r--   1 bin      bin         2835 Jan 22 14:44 OpTimer.h
-rw-r--r--   1 bin      bin         6705 Jan 22 14:44 OrderedCltn.h
-rw-r--r--   1 bin      bin         2962 Jan 22 14:44 Path.h
-rw-r--r--   1 bin      bin         4411 Jan 22 14:44 Polynomial.h
-rw-r--r--   1 bin      bin         2147 Jan 22 14:44 Pool.h
-rw-r--r--   1 bin      bin        14634 Jan 22 14:44 SimpleArray.h
-rw-r--r--   1 bin      bin         7215 Jan 22 14:44 Spline.h
-rw-r--r--   1 bin      bin         1515 Jan 22 14:44 Stack.h
-rw-r--r--   1 bin      bin         9668 Jan 22 14:44 TBSpline.h
-rw-r--r--   1 bin      bin         3816 Jan 22 14:44 TrainingSet.h
-rw-r--r--   1 bin      bin         5644 Jan 22 14:44 ValueMap.h
-rw-r--r--   1 bin      bin         3001 Jan 22 14:44 amoeba.h
-rw-r--r--   1 bin      bin         1444 Jan 22 14:44 assert.h
-rw-r--r--   1 bin      bin         4613 Jan 22 14:44 backProp.h
-rw-r--r--   1 bin      bin         1437 Jan 22 14:44 dcomplex.h
-rw-r--r--   1 bin      bin         4843 Jan 22 14:44 fcomplex.h
-rw-r--r--   1 bin      bin         3064 Jan 22 14:44 matlabSupport.h
-rw-r--r--   1 bin      bin         4419 Jan 22 14:44 miscTemplateFunc.h
-rw-r--r--   1 bin      bin         2037 Jan 22 14:44 popen.h
-rw-r--r--   1 bin      bin         2399 Jan 22 14:44 trivials.h

Steve ROBBINS wrote:
> On Thu, Jan 22, 2004 at 10:23:13AM -0500, Jason Lerch wrote:
> 
>>You never specify where the library should be found. Try this instead
>>
>>./configure --prefix=/opt/N3/mni 
>>--with-build-path=/path/to/libraries:/path/to/other/libs
> 
> 
> 
> To be precise, use
>                                                                                 
>         --with-build-path=/usr/local
>                                                                                 
> since you installed EBTKS into /usr/local/{lib,include} according
> to one of your previous mails.  As a bonus: if you do this, you no longer
> need to set CPPFLAGS for configure.
>                                                                                 
>  
> 
>>or set the LDFLAGS environment along with the ones that you have set 
>>below.
> 
> 
> Err, but this ought to have worked:
>  
> 
>>>[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
>>>CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
>>>CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
>>>F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
>>>make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
>>
> 
> You need to check config.log.  If it doesn't point you to the cause,
> send that file to me off-list.
> 
> -S
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------


-- 
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--Boundary_(ID_I2lNbVmJf0AEwlQyfkSRKw)
Content-type: text/plain; name=config.log
Content-transfer-encoding: 7BIT
Content-disposition: inline; filename=config.log

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.58.  Invocation command line was

  $ ./configure --prefix=/opt/N3/mni --with-build-path=/usr/local CXX=CC CC=c89 F90=f90 F77=f77 make=maketool

## --------- ##
## Platform. ##
## --------- ##

hostname = eclipse
uname -m = sun4u
uname -r = 5.8
uname -s = SunOS
uname -v = Generic_108528-24

/usr/bin/uname -p = sparc
/bin/uname -X     = System = SunOS
Node = eclipse
Release = 5.8
KernelID = Generic_108528-24
Machine = sun4u
BusType = <unknown>
Serial = <unknown>
Users = <unknown>
OEM# = 0
Origin# = 1
NumCPU = 4

/bin/arch              = sun4
/usr/bin/arch -k       = sun4u
/usr/convex/getsysinfo = unknown
hostinfo               = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /usr/local
PATH: /usr/local/bin
PATH: /usr/ccs/bin
PATH: /usr/dt/bin
PATH: /usr/openwin/bin
PATH: /usr/bin/nsr
PATH: /usr/ucb
PATH: /opt/SUNWspro/bin/


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1326: checking for a BSD-compatible install
configure:1381: result: ac_config_aux/install-sh -c
configure:1392: checking whether build environment is sane
configure:1435: result: yes
configure:1468: checking for gawk
configure:1497: result: no
configure:1468: checking for mawk
configure:1497: result: no
configure:1468: checking for nawk
configure:1484: found /usr/bin/nawk
configure:1494: result: nawk
configure:1504: checking whether make sets $(MAKE)
configure:1524: result: yes
configure:1706: checking for a BSD-compatible install
configure:1761: result: ac_config_aux/install-sh -c
configure:1772: checking whether ln -s works
configure:1776: result: yes
configure:1783: checking whether make sets $(MAKE)
configure:1803: result: yes
configure:1825: checking for style of include used by make
configure:1853: result: GNU
configure:1924: checking for gcc
configure:1950: result: c89
configure:2194: checking for C compiler version
configure:2197: c89 --version </dev/null >&5
cc: Warning: option -- passed to ld
usage: c89 [ options] files.  Use 'c89 -flags' for details
configure:2200: $? = 1
configure:2202: c89 -v </dev/null >&5
usage: c89 [ options] files.  Use 'c89 -flags' for details
configure:2205: $? = 1
configure:2207: c89 -V </dev/null >&5
cc: WorkShop Compilers 5.0 98/12/15 C 5.0
usage: c89 [ options] files.  Use 'c89 -flags' for details
configure:2210: $? = 1
configure:2233: checking for C compiler default output file name
configure:2236: c89    conftest.c  >&5
configure:2239: $? = 0
configure:2285: result: a.out
configure:2290: checking whether the C compiler works
configure:2296: ./a.out
configure:2299: $? = 0
configure:2316: result: yes
configure:2323: checking whether we are cross compiling
configure:2325: result: no
configure:2328: checking for suffix of executables
configure:2330: c89 -o conftest    conftest.c  >&5
configure:2333: $? = 0
configure:2358: result: 
configure:2364: checking for suffix of object files
configure:2385: c89 -c   conftest.c >&5
configure:2388: $? = 0
configure:2410: result: o
configure:2414: checking whether we are using the GNU C compiler
configure:2438: c89 -c   conftest.c >&5
"conftest.c", line 16: undefined symbol: choke
"conftest.c", line 16: syntax error before or at: me
c89: acomp failed for conftest.c
configure:2444: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| #ifndef __GNUC__
|        choke me
| #endif
| 
|   ;
|   return 0;
| }
configure:2469: result: no
configure:2475: checking whether c89 accepts -g
configure:2496: c89 -c -g  conftest.c >&5
configure:2502: $? = 0
configure:2505: test -z 			 || test ! -s conftest.err
configure:2508: $? = 0
configure:2511: test -s conftest.o
configure:2514: $? = 0
configure:2525: result: yes
configure:2542: checking for c89 option to accept ANSI C
configure:2612: c89  -c -g  conftest.c >&5
"conftest.c", line 54: warning: statement not reached
configure:2618: $? = 0
configure:2621: test -z 			 || test ! -s conftest.err
configure:2624: $? = 0
configure:2627: test -s conftest.o
configure:2630: $? = 0
configure:2648: result: none needed
configure:2666: c89 -c -g  conftest.c >&5
"conftest.c", line 2: undefined or not a type: choke
"conftest.c", line 2: syntax error before or at: me
"conftest.c", line 4: undefined or not a type: me
c89: acomp failed for conftest.c
configure:2672: $? = 2
configure: failed program was:
| #ifndef __cplusplus
|   choke me
| #endif
configure:2804: checking dependency style of c89
configure:2887: result: none
configure:2905: checking whether c89 and cc understand -c and -o together
configure:2935: c89 -c conftest.c -o conftest.o >&5
configure:2938: $? = 0
configure:2940: c89 -c conftest.c -o conftest.o >&5
configure:2943: $? = 0
configure:2950: cc -c conftest.c >&5
/usr/ucb/cc:  language optional software package not installed
configure:2953: $? = 1
configure:2982: result: yes
configure:3101: checking for C++ compiler version
configure:3104: CC --version </dev/null >&5
CC: Warning: Option --version passed to ld, if ld is invoked, ignored otherwise
configure:3107: $? = 0
configure:3109: CC -v </dev/null >&5
### CC: Note: LM_LICENSE_FILE = (null)
### CC: Note: NLSPATH = /opt/SUNWspro/bin//../SC5.0/bin/../lib/locale/%L/LC_MESSAGES/%N.cat:/opt/SUNWspro/bin//../SC5.0/bin/../../lib/locale/%L/LC_MESSAGES/%N.cat
configure:3112: $? = 0
configure:3114: CC -V </dev/null >&5
CC: WorkShop Compilers 5.0 98/12/15 C++ 5.0
configure:3117: $? = 0
configure:3120: checking whether we are using the GNU C++ compiler
configure:3144: CC -c   conftest.cc >&5
"conftest.cc", line 16: Error: choke is not defined.
1 Error(s) detected.
configure:3150: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| #ifndef __GNUC__
|        choke me
| #endif
| 
|   ;
|   return 0;
| }
configure:3175: result: no
configure:3181: checking whether CC accepts -g
configure:3202: CC -c -g  conftest.cc >&5
configure:3208: $? = 0
configure:3211: test -z 			 || test ! -s conftest.err
configure:3214: $? = 0
configure:3217: test -s conftest.o
configure:3220: $? = 0
configure:3231: result: yes
configure:3273: CC -c -g  conftest.cc >&5
configure:3279: $? = 0
configure:3282: test -z 			 || test ! -s conftest.err
configure:3285: $? = 0
configure:3288: test -s conftest.o
configure:3291: $? = 0
configure:3317: CC -c -g  conftest.cc >&5
"conftest.cc", line 15: Error: The function "exit" must have a prototype.
1 Error(s) detected.
configure:3323: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3273: CC -c -g  conftest.cc >&5
"conftest.cc", line 11: Error: The class member exit(int) cannot be declared outside the class.
"conftest.cc", line 11: Error: exit is not a member of std.
2 Error(s) detected.
configure:3279: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| /* end confdefs.h.  */
| extern "C" void std::exit (int) throw (); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3273: CC -c -g  conftest.cc >&5
"conftest.cc", line 11: Error: The class member exit(int) cannot be declared outside the class.
"conftest.cc", line 11: Error: exit is not a member of std.
2 Error(s) detected.
configure:3279: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| /* end confdefs.h.  */
| extern "C" void std::exit (int); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3273: CC -c -g  conftest.cc >&5
configure:3279: $? = 0
configure:3282: test -z 			 || test ! -s conftest.err
configure:3285: $? = 0
configure:3288: test -s conftest.o
configure:3291: $? = 0
configure:3317: CC -c -g  conftest.cc >&5
configure:3323: $? = 0
configure:3326: test -z 			 || test ! -s conftest.err
configure:3329: $? = 0
configure:3332: test -s conftest.o
configure:3335: $? = 0
configure:3360: checking dependency style of CC
configure:3443: result: none
configure:3501: checking for ranlib
configure:3517: found /usr/local/bin/ranlib
configure:3528: result: ranlib
configure:3564: checking build system type
configure:3582: result: sparc-sun-solaris2.8
configure:3590: checking host system type
configure:3604: result: sparc-sun-solaris2.8
configure:3643: checking for library m
configure:3662: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lm  >&5
configure:3668: $? = 0
configure:3671: test -z 			 || test ! -s conftest.err
configure:3674: $? = 0
configure:3677: test -s conftest
configure:3680: $? = 0
configure:3691: result: yes
configure:3802: checking for Fortran 77 compiler version
configure:3805: f77 --version </dev/null >&5
f77: Warning: Option --version passed to ld, if ld is invoked, ignored otherwise
Usage: f77 [ options ] files.  Use 'f77 -flags' for details
configure:3808: $? = 0
configure:3810: f77 -v </dev/null >&5
Usage: f77 [ options ] files.  Use 'f77 -flags' for details
configure:3813: $? = 0
configure:3815: f77 -V </dev/null >&5
f77: WorkShop Compilers 5.0 98/12/15 FORTRAN 77 5.0
Usage: f77 [ options ] files.  Use 'f77 -flags' for details
configure:3818: $? = 0
configure:3826: checking whether we are using the GNU Fortran 77 compiler
configure:3840: f77 -c  conftest.F >&5
/tmp/fpp.27297.0.f:
 MAIN main:
"conftest.F", line 3: Error: unclassifiable statement
configure:3846: $? = 1
configure: failed program was:
|       program main
| #ifndef __GNUC__
|        choke me
| #endif
| 
|       end
configure:3871: result: no
configure:3877: checking whether f77 accepts -g
configure:3889: f77 -c -g conftest.f >&5
conftest.f:
 MAIN main:
configure:3895: $? = 0
configure:3898: test -z 			 || test ! -s conftest.err
configure:3901: $? = 0
configure:3904: test -s conftest.o
configure:3907: $? = 0
configure:3919: result: yes
configure:3949: checking how to get verbose linking output from f77
configure:3960: f77 -c -g conftest.f >&5
conftest.f:
 MAIN main:
configure:3966: $? = 0
configure:3969: test -z 			 || test ! -s conftest.err
configure:3972: $? = 0
configure:3975: test -s conftest.o
configure:3978: $? = 0
configure:3995: f77 -o conftest -g -v  -L/usr/local/lib conftest.f -lm  >&5
### f77: Note: LM_LICENSE_FILE = (null)
### f77: Note: NLSPATH = /opt/SUNWspro/bin//../SC5.0/bin/../lib/locale/%L/LC_MESSAGES/%N.cat:/opt/SUNWspro/bin//../SC5.0/bin/../../lib/locale/%L/LC_MESSAGES/%N.cat
/opt/SUNWspro/bin//../SC5.0/bin/f77pass1 -y-o -yconftest.o -y-fbe -y/opt/SUNWspro/bin//../SC5.0/bin/fbe -y-xarch=v7 -y-s -ptk "-g -v -L/usr/local/lib " -xcache=64/32/1 -I/opt/SUNWspro/SC5.0/include/f77 -verbose -y-verbose -g -y-g conftest.f /tmp/f77pass1.27345.s.0.s conftest.o /tmp/f77pass1.27345.d.1.s
conftest.f:
 MAIN main:
rm /tmp/f77pass1.27345.s.0.s
rm /tmp/f77pass1.27345.d.1.s
### f77: Note: LD_LIBRARY_PATH = /usr/local/lib:/usr/local/include:/opt/SUNWspro/lib:/opt/SUNWspro/include
### f77: Note: LD_RUN_PATH     = (null)
### f77: Note: LD_OPTIONS = (null)
/usr/ccs/bin/ld -t -L/usr/local/lib -R/opt/SUNWspro/lib -o conftest /opt/SUNWspro/SC5.0/lib/crti.o /opt/SUNWspro/SC5.0/lib/crt1.o /opt/SUNWspro/SC5.0/lib/values-xi.o -Y P,/opt/SUNWspro/lib:/opt/SUNWspro/SC5.0/lib:/usr/ccs/lib:/usr/lib conftest.o -lm -lF77 -lM77 -lsunmath -lm -lcx -lc /opt/SUNWspro/SC5.0/lib/crtn.o
rm conftest.o
configure:4050: result: -v
configure:4052: checking for Fortran libraries of f77
configure:4073: f77 -o conftest -g -v  -L/usr/local/lib conftest.f -lm  >&5
### f77: Note: LM_LICENSE_FILE = (null)
### f77: Note: NLSPATH = /opt/SUNWspro/bin//../SC5.0/bin/../lib/locale/%L/LC_MESSAGES/%N.cat:/opt/SUNWspro/bin//../SC5.0/bin/../../lib/locale/%L/LC_MESSAGES/%N.cat
/opt/SUNWspro/bin//../SC5.0/bin/f77pass1 -y-o -yconftest.o -y-fbe -y/opt/SUNWspro/bin//../SC5.0/bin/fbe -y-xarch=v7 -y-s -ptk "-g -v -L/usr/local/lib " -xcache=64/32/1 -I/opt/SUNWspro/SC5.0/include/f77 -verbose -y-verbose -g -y-g conftest.f /tmp/f77pass1.27359.s.0.s conftest.o /tmp/f77pass1.27359.d.1.s
conftest.f:
 MAIN main:
rm /tmp/f77pass1.27359.s.0.s
rm /tmp/f77pass1.27359.d.1.s
### f77: Note: LD_LIBRARY_PATH = /usr/local/lib:/usr/local/include:/opt/SUNWspro/lib:/opt/SUNWspro/include
### f77: Note: LD_RUN_PATH     = (null)
### f77: Note: LD_OPTIONS = (null)
/usr/ccs/bin/ld -t -L/usr/local/lib -R/opt/SUNWspro/lib -o conftest /opt/SUNWspro/SC5.0/lib/crti.o /opt/SUNWspro/SC5.0/lib/crt1.o /opt/SUNWspro/SC5.0/lib/values-xi.o -Y P,/opt/SUNWspro/lib:/opt/SUNWspro/SC5.0/lib:/usr/ccs/lib:/usr/lib conftest.o -lm -lF77 -lM77 -lsunmath -lm -lcx -lc /opt/SUNWspro/SC5.0/lib/crtn.o
rm conftest.o
configure:4234: result:  -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx
configure:4250: checking for dummy main to link with Fortran libraries
configure:4289: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
configure:4295: $? = 0
configure:4298: test -z 			 || test ! -s conftest.err
configure:4301: $? = 0
configure:4304: test -s conftest
configure:4307: $? = 0
configure:4384: result: none
configure:4421: checking for Fortran name-mangling scheme
configure:4435: f77 -c -g conftest.f >&5
conftest.f:
	foobar:
	foo_bar:
configure:4441: $? = 0
configure:4444: test -z 			 || test ! -s conftest.err
configure:4447: $? = 0
configure:4450: test -s conftest.o
configure:4453: $? = 0
configure:4500: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c cfortran_test.o -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
Undefined			first referenced
 symbol  			    in file
foobar                              conftest.o
ld: fatal: Symbol referencing errors. No output written to conftest
configure:4506: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char foobar ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| foobar ();
|   ;
|   return 0;
| }
configure:4500: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c cfortran_test.o -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
configure:4506: $? = 0
configure:4509: test -z 			 || test ! -s conftest.err
configure:4512: $? = 0
configure:4515: test -s conftest
configure:4518: $? = 0
configure:4586: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c cfortran_test.o -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
configure:4592: $? = 0
configure:4595: test -z 			 || test ! -s conftest.err
configure:4598: $? = 0
configure:4601: test -s conftest
configure:4604: $? = 0
configure:4654: result: lower case, underscore, no extra underscore
configure:4800: checking for sgemm_
configure:4865: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
"conftest.c", line 64: warning: statement not reached
Undefined			first referenced
 symbol  			    in file
sgemm_                              conftest.o
ld: fatal: Symbol referencing errors. No output written to conftest
configure:4871: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| /* Define sgemm_ to an innocuous variant, in case <limits.h> declares sgemm_.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define sgemm_ innocuous_sgemm_
| 
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char sgemm_ (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| 
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| 
| #undef sgemm_
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| {
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char sgemm_ ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined (__stub_sgemm_) || defined (__stub___sgemm_)
| choke me
| #else
| char (*f) () = sgemm_;
| #endif
| #ifdef __cplusplus
| }
| #endif
| 
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| return f != sgemm_;
|   ;
|   return 0;
| }
configure:4895: result: no
configure:4906: checking for ATL_xerbla in -latlas
configure:4944: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -latlas  -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
ld: fatal: library -latlas: not found
ld: fatal: File processing errors. No output written to conftest
configure:4950: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char ATL_xerbla ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| ATL_xerbla ();
|   ;
|   return 0;
| }
configure:4975: result: no
configure:5137: checking for sgemm_ in -framework vecLib
configure:5170: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -framework vecLib -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
cc: Warning: illegal option -framework
ld: fatal: file vecLib: open failed: No such file or directory
ld: fatal: File processing errors. No output written to conftest
configure:5176: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char sgemm_ ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| sgemm_ ();
|   ;
|   return 0;
| }
configure:5199: result: no
configure:5207: checking for sgemm_ in -lblas
configure:5245: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lblas  -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
ld: fatal: library -lblas: not found
ld: fatal: File processing errors. No output written to conftest
configure:5251: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char sgemm_ ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| sgemm_ ();
|   ;
|   return 0;
| }
configure:5276: result: no
configure:5437: checking for sgemm_ in -lcxml
configure:5475: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lcxml  -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
ld: fatal: library -lcxml: not found
ld: fatal: File processing errors. No output written to conftest
configure:5481: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char sgemm_ ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| sgemm_ ();
|   ;
|   return 0;
| }
configure:5506: result: no
configure:5517: checking for sgemm_ in -ldxml
configure:5555: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -ldxml  -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
ld: fatal: library -ldxml: not found
ld: fatal: File processing errors. No output written to conftest
configure:5561: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char sgemm_ ();
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| sgemm_ ();
|   ;
|   return 0;
| }
configure:5586: result: no
configure:5597: checking for acosp in -lsunmath
configure:5635: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lsunmath  -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
configure:5641: $? = 0
configure:5644: test -z 			 || test ! -s conftest.err
configure:5647: $? = 0
configure:5650: test -s conftest
configure:5653: $? = 0
configure:5666: result: yes
configure:5670: checking for sgemm_ in -lsunperf
configure:5708: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lsunperf -lsunmath -lm   -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
configure:5714: $? = 0
configure:5717: test -z 			 || test ! -s conftest.err
configure:5720: $? = 0
configure:5723: test -s conftest
configure:5726: $? = 0
configure:5739: result: yes
configure:6283: checking for cheev_
configure:6348: c89 -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.c -lm  -xlic_lib=sunperf -lsunmath  -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx >&5
"conftest.c", line 65: warning: statement not reached
configure:6354: $? = 0
configure:6357: test -z 			 || test ! -s conftest.err
configure:6360: $? = 0
configure:6363: test -s conftest
configure:6366: $? = 0
configure:6378: result: yes
configure:6703: checking for library EBTKS
configure:6730: CC -o conftest -g  -I/usr/local/include  -L/usr/local/lib conftest.cc -lEBTKS -lm  >&5
"/usr/include/iso/wchar_iso.h", line 100: Error: Multiple declaration for mbstate_t.
"/opt/SUNWspro/SC5.0/include/CC/./iosfwd", line 51: Error: The name mbstate_t is ambiguous, std::mbstate_t and std::mbstate_t.
"/opt/SUNWspro/SC5.0/include/CC/./iosfwd", line 78: Error: The name mbstate_t is ambiguous, std::mbstate_t and std::mbstate_t.
"/opt/SUNWspro/SC5.0/include/CC/rw/iotraits", line 56: Error: The name mbstate_t is ambiguous, std::mbstate_t and std::mbstate_t.
4 Error(s) detected.
configure:6736: $? = 4
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "N3"
| #define VERSION "1.07"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| #define HAVE_BLAS 1
| #define HAVE_LAPACK 1
| /* end confdefs.h.  */
| #include <EBTKS/Path.h>
| #ifdef F77_DUMMY_MAIN
| 
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
| 
| #endif
| int
| main ()
| {
| Path path;
|   ;
|   return 0;
| }
configure:6759: result: no
configure:6762: error: cannot find required library EBTKS

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=sparc-sun-solaris2.8
ac_cv_build_alias=sparc-sun-solaris2.8
ac_cv_c_compiler_gnu=no
ac_cv_cxx_compiler_gnu=no
ac_cv_env_CC_set=set
ac_cv_env_CC_value=c89
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=CC
ac_cv_env_F77_set=set
ac_cv_env_F77_value=f77
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_f77_compiler_gnu=no
ac_cv_f77_dummy_main=none
ac_cv_f77_libs=' -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx'
ac_cv_f77_mangling='lower case, underscore, no extra underscore'
ac_cv_fortran_dummy_main=none
ac_cv_func_cheev_=yes
ac_cv_func_sgemm_=no
ac_cv_host=sparc-sun-solaris2.8
ac_cv_host_alias=sparc-sun-solaris2.8
ac_cv_lib_atlas_ATL_xerbla=no
ac_cv_lib_blas_sgemm_=no
ac_cv_lib_cxml_sgemm_=no
ac_cv_lib_dxml_sgemm_=no
ac_cv_lib_sunmath_acosp=yes
ac_cv_lib_sunperf_sgemm_=yes
ac_cv_objext=o
ac_cv_prog_AWK=nawk
ac_cv_prog_ac_ct_CC=c89
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89_c_o=yes
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=yes
ac_cv_prog_f77_g=yes
ac_cv_prog_f77_v=-v
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run aclocal-1.7'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run tar'
AUTOCONF='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run autoconf'
AUTOHEADER='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run autoheader'
AUTOMAKE='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run automake-1.7'
AWK='nawk'
BLAS_LIBS='-xlic_lib=sunperf -lsunmath'
CC='c89'
CCDEPMODE='depmode=none'
CFLAGS='-g'
CPPFLAGS=' -I/usr/local/include'
CXX='CC'
CXXDEPMODE='depmode=none'
CXXFLAGS='-g'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EXEEXT=''
F77='f77'
FFLAGS='-g'
FLIBS=' -L/usr/local/lib -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC5.0/lib -L/usr/ccs/lib -L/usr/lib -lm -lF77 -lM77 -lsunmath -lcx'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LAPACK_LIBS=''
LDFLAGS=' -L/usr/local/lib'
LIBOBJS=''
LIBS='-lEBTKS -lm '
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /opt/N3/N3-1.07/ac_config_aux/missing --run makeinfo'
OBJEXT='o'
PACKAGE='N3'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
PERL=''
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='1.07'
ac_ct_CC='c89'
ac_ct_CXX=''
ac_ct_F77=''
ac_ct_RANLIB='ranlib'
ac_ct_STRIP=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE='#'
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__leading_dot='.'
am__quote=''
bindir='${exec_prefix}/bin'
build='sparc-sun-solaris2.8'
build_alias=''
build_cpu='sparc'
build_os='solaris2.8'
build_vendor='sun'
datadir='${prefix}/share'
date='2004-01-27'
exec_prefix='NONE'
host='sparc-sun-solaris2.8'
host_alias=''
host_cpu='sparc'
host_os='solaris2.8'
host_vendor='sun'
includedir='${prefix}/include'
infodir='${prefix}/info'
install_sh='/opt/N3/N3-1.07/ac_config_aux/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
long_version='Package MNI N3, version 1.07, compiled by admin@eclipse (sparc-sun-solaris2.8) on 2004-01-27 at 12:31:26'
machine='eclipse'
mandir='${prefix}/man'
modeldir=''
oldincludedir='/usr/include'
prefix='/opt/N3/mni'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
time='12:31:26'
user='admin'
version='1.07'

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define HAVE_BLAS 1
#define HAVE_LAPACK 1
#define PACKAGE "N3"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME ""
#define PACKAGE_STRING ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define VERSION "1.07"
#endif
#ifdef __cplusplus
extern "C" void exit (int) throw ();

configure: exit 1

--Boundary_(ID_I2lNbVmJf0AEwlQyfkSRKw)--

From minc-users@bic.mni.mcgill.ca  Tue Jan 27 12:52:45 2004
From: minc-users@bic.mni.mcgill.ca (Asim Khan)
Date: Tue, 27 Jan 2004 12:52:45 +0000
Subject: [MINC-users] EBTKS not found when configuring N3
References: <400FE64A.40702@sghms.ac.uk>
 <E4FD51C6-4CEE-11D8-9C3C-000A95DBBFD8@bic.mni.mcgill.ca>
 <20040122194220.C114951@shadow.bic.mni.mcgill.ca>
Message-ID: <40165F1D.4090608@sghms.ac.uk>

Steve,

I tried this aswell:

[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
--with-build-path=/usr/local:/opt/N3 CXX=CC CC=c89 F90=f90 F77=f77 
make=maketool

Steve ROBBINS wrote:
> On Thu, Jan 22, 2004 at 10:23:13AM -0500, Jason Lerch wrote:
> 
>>You never specify where the library should be found. Try this instead
>>
>>./configure --prefix=/opt/N3/mni 
>>--with-build-path=/path/to/libraries:/path/to/other/libs
> 
> 
> 
> To be precise, use
>                                                                                 
>         --with-build-path=/usr/local
>                                                                                 
> since you installed EBTKS into /usr/local/{lib,include} according
> to one of your previous mails.  As a bonus: if you do this, you no longer
> need to set CPPFLAGS for configure.
>                                                                                 
>  
> 
>>or set the LDFLAGS environment along with the ones that you have set 
>>below.
> 
> 
> Err, but this ought to have worked:
>  
> 
>>>[root@eclipse N3-1.07]#> ./configure --prefix=/opt/N3/mni 
>>>CC=/opt/SUNWspro/bin/c89 FFLAGS="-O -w" CXXFLAGS=-O 
>>>CPPFLAGS="-I/usr/local/include" CXX=/opt/SUNWspro/bin/CC 
>>>F90=/opt/SUNWspro/bin/f90 F77=/opt/SUNWspro/bin/f77 
>>>make=/opt/SUNWspro/bin/maketool  LDFLAGS="-L/usr/local/lib"
>>
> 
> You need to check config.log.  If it doesn't point you to the cause,
> send that file to me off-list.
> 
> -S
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
------------------------------------
Asim Khan
Unix Systems Administrator
St George's Hospital Medical School
www.sghms.ac.uk
------------------------------------



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


From minc-users@bic.mni.mcgill.ca  Wed Jan 28 10:19:01 2004
From: minc-users@bic.mni.mcgill.ca (Roger Luechinger)
Date: Wed, 28 Jan 2004 11:19:01 +0100
Subject: [MINC-users] Convert Philips REC/PAR-Files zu minc-format
Message-ID: <40178C95.8000705@biomed.ee.ethz.ch>

Hi minc-users,

Up to now we used in Zurich the dicom-server from the mni-project to get 
the data from our Philips scanners to the minc format. However with each 
release change we (or better say Gerard Crelier) had to adaped the 
dicomserver.
The last time ~3 year ago we had huge problems to find a suitable old 
Linux installation to compile it (it worked only on a Suse ~6.x), but now 
we do no longer have such an old system. Together with other problems 
concerning the dicom transfer and the lake of knowledge about that 
dicomserver we are thinking to change the way to create the minc-files.

And for that purpose I need some tips and infos.

Over the last few year Philips create for offline postprocessing a new 
file format (REC and PAR-Files) which are usd in our lab for all purposes...
The REC-File contains all images from a scans in a binary format 
(integers) without any header, the PAR-Files contains all the infos for 
the scan and also for each image in an ASCII format.
Converter for REC/PAR to analyze we wrote by ourself, and now I would like 
to do the same for the minc format. However I could not find infos which 
parameter and image infos have to be stored in a minc-file.

Preferable I'd like to write it with perl. Mainly do to portability and 
prior knowlegde reason. The initial implementation will be under Linux.

Can you gave me any links, documents, software-templates which would be 
useful for such a project. Perhaps there are other users which would be 
interested in such a project.

Regards

Roger
-- 
                               ^   ^
                               o   o
------------------------OOO----(_)----OOO---------------------
Dr. Roger Luechinger    E-Mail: luechinger@biomed.ee.ethz.ch
Universitaetsspital
MR-Zentrum VMR30      www/PGP: http://www.mr.ethz.ch/~rluchin/
8091 Zuerich
Tel: ++41 1 255 30 64     Fax: ++41 1 255 45 06
-------------------------oooO-------Oooo----------------------


From minc-users@bic.mni.mcgill.ca  Wed Jan 28 21:34:09 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 28 Jan 2004 16:34:09 -0500
Subject: [MINC-users] New OS X binaries released
Message-ID: <B55DC29C-51D9-11D8-940D-000A95DBBFD8@bic.mni.mcgill.ca>

Greetings all and apologies for cross-posting,

I've just uploaded a new release of the OS 10.3 binaries to our 
web-site:

http://www.bic.mni.mcgill.ca/software/distribution/osx.html

The package should solve most outstanding issues, such as the broken 
N3, the lack of support for gzipped files, etc. The Register problem is 
still unresolved, though a workaround has been posted.

The new package contains the following:

This binary distribution contains the following packages:
NetCDF		3.5.0
MINC			1.3 from CVS
BICPL			1.4.0-1
Register		1.3.4
Display		1.3.8
Conglomerate	1.3 from CVS with some still uncommitted patches
mni_autoreg		0.98k
mni_perllib		0.07
Getopt-Tabular	0.3
mni_autoreg_model 1.03
ray_trace		1.0
EBTKS		from CVS with still uncommitted patches
classify		from CVS
N3			1.0.6 with ugly compile time hacks
mincmorph		1.1
mincblob		1.1
cortical_surface	1.0 from CVS
ana2mnc		from CVS

Please let me know of any issues that might arise. The ReadMe file 
should contain all the instructions necessary for using this 
distribution.

Cheers,

Jason


From minc-users@bic.mni.mcgill.ca  Thu Jan 29 16:02:01 2004
From: minc-users@bic.mni.mcgill.ca (Marc D. Migge)
Date: Thu, 29 Jan 2004 17:02:01 +0100
Subject: [MINC-users] Convert Philips REC/PAR-Files zu minc-format
In-Reply-To: <40178C95.8000705@biomed.ee.ethz.ch>
References: <40178C95.8000705@biomed.ee.ethz.ch>
Message-ID: <40192E79.6000801@pet.mpin-koeln.mpg.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi,

if you want to stick to perl you might want to try
http://www.unidata.ucar.edu/packages/netcdf-perl/ . But it's not quite
up to date. It supports only NetCDF 3.3 (the current version is 3.5.0).
Plus you will have to be very careful to follow the document structure
as outlined in the MINC-Documentation.

If you use the C/C++ you could make use of the libraries from the
MINC-package. With little extra work you can compile these under Windows
as well. You could then use volume_io to create a basic MINC file and
write the image-data. To set the image-attributes use the MINC-or
NetCDF-library directly.

Best regards,
Marc Migge


Roger Luechinger wrote:
| Hi minc-users,
|
| Up to now we used in Zurich the dicom-server from the mni-project to get
| the data from our Philips scanners to the minc format. However with each
| release change we (or better say Gerard Crelier) had to adaped the
| dicomserver.
| The last time ~3 year ago we had huge problems to find a suitable old
| Linux installation to compile it (it worked only on a Suse ~6.x), but
| now we do no longer have such an old system. Together with other
| problems concerning the dicom transfer and the lake of knowledge about
| that dicomserver we are thinking to change the way to create the
| minc-files.
|
| And for that purpose I need some tips and infos.
|
| Over the last few year Philips create for offline postprocessing a new
| file format (REC and PAR-Files) which are usd in our lab for all
| purposes...
| The REC-File contains all images from a scans in a binary format
| (integers) without any header, the PAR-Files contains all the infos for
| the scan and also for each image in an ASCII format.
| Converter for REC/PAR to analyze we wrote by ourself, and now I would
| like to do the same for the minc format. However I could not find infos
| which parameter and image infos have to be stored in a minc-file.
|
| Preferable I'd like to write it with perl. Mainly do to portability and
| prior knowlegde reason. The initial implementation will be under Linux.
|
| Can you gave me any links, documents, software-templates which would be
| useful for such a project. Perhaps there are other users which would be
| interested in such a project.
|
| Regards
|
| Roger

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFAGS55PxXwn5JoIGsRAj+yAJ9Q/aDmpYU6pBKbibeZfaZsgbVDjQCg26B2
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From minc-users@bic.mni.mcgill.ca  Thu Jan 29 16:22:44 2004
From: minc-users@bic.mni.mcgill.ca (Jonathan HARLAP)
Date: Thu, 29 Jan 2004 11:22:44 -0500
Subject: [MINC-users] Convert Philips REC/PAR-Files zu minc-format
In-Reply-To: <40192E79.6000801@pet.mpin-koeln.mpg.de>; from migge@pet.mpin-koeln.mpg.de on Thu, Jan 29, 2004 at 05:02:01PM +0100
References: <40178C95.8000705@biomed.ee.ethz.ch> <40192E79.6000801@pet.mpin-koeln.mpg.de>
Message-ID: <20040129112243.A516431@shadow.bic.mni.mcgill.ca>

Alternately, if you wished to use Perl you could follow a design
similar to dicom_to_minc.  In a nutshell, this means parsing the
header data into a MINC-friendly format and then running rawtominc.

I haven't looked at dicomserver recently, but you might want to get in
touch with Leili Torab (leili@bic.mni.mcgill.ca) who I believe has
been working on dicomserver - perhaps she has a version that runs on
more up-to-date linuxes.

Jon


On Thu, Jan 29, 2004 at 05:02:01PM +0100, Marc D. Migge wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Hi,
> 
> if you want to stick to perl you might want to try
> http://www.unidata.ucar.edu/packages/netcdf-perl/ . But it's not quite
> up to date. It supports only NetCDF 3.3 (the current version is 3.5.0).
> Plus you will have to be very careful to follow the document structure
> as outlined in the MINC-Documentation.
> 
> If you use the C/C++ you could make use of the libraries from the
> MINC-package. With little extra work you can compile these under Windows
> as well. You could then use volume_io to create a basic MINC file and
> write the image-data. To set the image-attributes use the MINC-or
> NetCDF-library directly.
> 
> Best regards,
> Marc Migge
> 
> 
> Roger Luechinger wrote:
> | Hi minc-users,
> |
> | Up to now we used in Zurich the dicom-server from the mni-project to get
> | the data from our Philips scanners to the minc format. However with each
> | release change we (or better say Gerard Crelier) had to adaped the
> | dicomserver.
> | The last time ~3 year ago we had huge problems to find a suitable old
> | Linux installation to compile it (it worked only on a Suse ~6.x), but
> | now we do no longer have such an old system. Together with other
> | problems concerning the dicom transfer and the lake of knowledge about
> | that dicomserver we are thinking to change the way to create the
> | minc-files.
> |
> | And for that purpose I need some tips and infos.
> |
> | Over the last few year Philips create for offline postprocessing a new
> | file format (REC and PAR-Files) which are usd in our lab for all
> | purposes...
> | The REC-File contains all images from a scans in a binary format
> | (integers) without any header, the PAR-Files contains all the infos for
> | the scan and also for each image in an ASCII format.
> | Converter for REC/PAR to analyze we wrote by ourself, and now I would
> | like to do the same for the minc format. However I could not find infos
> | which parameter and image infos have to be stored in a minc-file.
> |
> | Preferable I'd like to write it with perl. Mainly do to portability and
> | prior knowlegde reason. The initial implementation will be under Linux.
> |
> | Can you gave me any links, documents, software-templates which would be
> | useful for such a project. Perhaps there are other users which would be
> | interested in such a project.
> |
> | Regards
> |
> | Roger
> 
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.2.3 (MingW32)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> 
> iD8DBQFAGS55PxXwn5JoIGsRAj+yAJ9Q/aDmpYU6pBKbibeZfaZsgbVDjQCg26B2
> 6GceiuMQ8I1HJFzvsf/P0v0=
> =6Orw
> -----END PGP SIGNATURE-----
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From minc-users@bic.mni.mcgill.ca  Thu Jan 29 16:19:44 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Thu, 29 Jan 2004 11:19:44 -0500
Subject: [MINC-users] Convert Philips REC/PAR-Files zu minc-format
In-Reply-To: <40178C95.8000705@biomed.ee.ethz.ch>
Message-ID: <Pine.SGI.4.44.0401291114470.496446-100000@shadow.bic.mni.mcgill.ca>

On Wed, 28 Jan 2004, Roger Luechinger wrote:

> Over the last few year Philips create for offline postprocessing a new
> file format (REC and PAR-Files) which are usd in our lab for all purposes...
> The REC-File contains all images from a scans in a binary format
> (integers) without any header, the PAR-Files contains all the infos for
> the scan and also for each image in an ASCII format.
> Converter for REC/PAR to analyze we wrote by ourself, and now I would like
> to do the same for the minc format. However I could not find infos which
> parameter and image infos have to be stored in a minc-file.
>
> Preferable I'd like to write it with perl. Mainly do to portability and
> prior knowlegde reason. The initial implementation will be under Linux.

A large number of the existing something->MINC converters are written in Perl
already.  However this may be a bit of a misnomer, typically the conversion of
the header and extraction of the header in written in perl. The creation of the
MINC file itself it usually done via a system call to rawtominc with all the
approriate "bits" filled in.

take a look at ana2mnc (analyze to minc) for an example of how to do this:

   http://www.bic.mni.mcgill.ca/~rotor/src/ana2mnc-1.2.tar.gz

the function "write_minc()" will create a minc file from a %gen_hdr hash.  use
the dump_general_header() function to get an idea of the sorts of things that
are required.

If you need more info, you might be better served to send me an email directly
using the address below


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581


From minc-users@bic.mni.mcgill.ca  Thu Jan 29 21:28:06 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Thu, 29 Jan 2004 13:28:06 -0800
Subject: [MINC-users] New OS X binaries released
In-Reply-To: <B55DC29C-51D9-11D8-940D-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <0736F923-52A2-11D8-A42B-000A958920AA@som.llu.edu>

--Apple-Mail-34-467722550
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Installing the new minc binaries under Jaguar (10.2.8) with the gcc3.3 
compiler completed without error. Trying to run the binaries resulted 
in the following errors:

[enoch:~] jween% Display
dyld: Display can't open library: /sw/lib/libglut.3.dylib  (No such 
file or directory, errno = 2)
Trace/BPT trap
[enoch:~] jween% register
dyld: register can't open library: /sw/lib/libglut.3.dylib  (No such 
file or directory, errno = 2)
Trace/BPT trap


Hopes this helps. I'll continue to use the old versions, which work 
fine.

Jon

Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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On Wednesday, January 28, 2004, at 01:34 PM, Jason Lerch wrote:

> Greetings all and apologies for cross-posting,
>
> I've just uploaded a new release of the OS 10.3 binaries to our 
> web-site:
>
> http://www.bic.mni.mcgill.ca/software/distribution/osx.html
>
> The package should solve most outstanding issues, such as the broken 
> N3, the lack of support for gzipped files, etc. The Register problem 
> is still unresolved, though a workaround has been posted.
>
> The new package contains the following:
>
> This binary distribution contains the following packages:
> NetCDF		3.5.0
> MINC			1.3 from CVS
> BICPL			1.4.0-1
> Register		1.3.4
> Display		1.3.8
> Conglomerate	1.3 from CVS with some still uncommitted patches
> mni_autoreg		0.98k
> mni_perllib		0.07
> Getopt-Tabular	0.3
> mni_autoreg_model 1.03
> ray_trace		1.0
> EBTKS		from CVS with still uncommitted patches
> classify		from CVS
> N3			1.0.6 with ugly compile time hacks
> mincmorph		1.1
> mincblob		1.1
> cortical_surface	1.0 from CVS
> ana2mnc		from CVS
>
> Please let me know of any issues that might arise. The ReadMe file 
> should contain all the instructions necessary for using this 
> distribution.
>
> Cheers,
>
> Jason
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


--Apple-Mail-34-467722550--


From minc-users@bic.mni.mcgill.ca  Thu Jan 29 21:37:17 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 29 Jan 2004 16:37:17 -0500
Subject: [MINC-users] New OS X binaries released
In-Reply-To: <0736F923-52A2-11D8-A42B-000A958920AA@som.llu.edu>
References: <0736F923-52A2-11D8-A42B-000A958920AA@som.llu.edu>
Message-ID: <4FC13F78-52A3-11D8-8320-000A95DBBFD8@bic.mni.mcgill.ca>

You still have to set your environment like so:

setenv DYLD_LIBRARY_PATH /usr/local/mni/external-libs

Let me know if you have the same problem even with that variable set 
and I'll look into it.

Thanks!

Jason

On Jan 29, 2004, at 4:28 PM, Jon Erik Ween wrote:

> Installing the new minc binaries under Jaguar (10.2.8) with the gcc3.3 
> compiler completed without error. Trying to run the binaries resulted 
> in the following errors:
>
> [enoch:~] jween% Display
> dyld: Display can't open library: /sw/lib/libglut.3.dylib  (No such 
> file or directory, errno = 2)
> Trace/BPT trap
> [enoch:~] jween% register
> dyld: register can't open library: /sw/lib/libglut.3.dylib  (No such 
> file or directory, errno = 2)
> Trace/BPT trap
>
>
> Hopes this helps. I'll continue to use the old versions, which work 
> fine.
>
> Jon
>
> Jon Erik Ween, MD, MS
> Assistant Professor
> Cognitive and Cerebrovascular Neurology
> Director, Stroke Program
> Loma Linda University
>
> <ADIlogoFinalSmall.jpg>
>
>
> On Wednesday, January 28, 2004, at 01:34 PM, Jason Lerch wrote:
>
>> Greetings all and apologies for cross-posting,
>>
>> I've just uploaded a new release of the OS 10.3 binaries to our 
>> web-site:
>>
>> http://www.bic.mni.mcgill.ca/software/distribution/osx.html
>>
>> The package should solve most outstanding issues, such as the broken 
>> N3, the lack of support for gzipped files, etc. The Register problem 
>> is still unresolved, though a workaround has been posted.
>>
>> The new package contains the following:
>>
>> This binary distribution contains the following packages:
>> NetCDF		3.5.0
>> MINC			1.3 from CVS
>> BICPL			1.4.0-1
>> Register		1.3.4
>> Display		1.3.8
>> Conglomerate	1.3 from CVS with some still uncommitted patches
>> mni_autoreg		0.98k
>> mni_perllib		0.07
>> Getopt-Tabular	0.3
>> mni_autoreg_model 1.03
>> ray_trace		1.0
>> EBTKS		from CVS with still uncommitted patches
>> classify		from CVS
>> N3			1.0.6 with ugly compile time hacks
>> mincmorph		1.1
>> mincblob		1.1
>> cortical_surface	1.0 from CVS
>> ana2mnc		from CVS
>>
>> Please let me know of any issues that might arise. The ReadMe file 
>> should contain all the instructions necessary for using this 
>> distribution.
>>
>> Cheers,
>>
>> Jason
>>
>> _______________________________________________
>> MINC-users@bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
>


From minc-users@bic.mni.mcgill.ca  Fri Jan 30 15:26:16 2004
From: minc-users@bic.mni.mcgill.ca (Roger Luechinger)
Date: Fri, 30 Jan 2004 16:26:16 +0100
Subject: [MINC-users] Convert Philips REC/PAR-Files zu minc-format
In-Reply-To: <Pine.SGI.4.44.0401291114470.496446-100000@shadow.bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0401291114470.496446-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <401A7798.9090508@biomed.ee.ethz.ch>

Thanks for the different answers.

Andrew Janke wrote:
> A large number of the existing something->MINC converters are written in Perl
> already.  However this may be a bit of a misnomer, typically the conversion of
> the header and extraction of the header in written in perl. The creation of the
> MINC file itself it usually done via a system call to rawtominc with all the
> approriate "bits" filled in.
> 
> take a look at ana2mnc (analyze to minc) for an example of how to do this:
> 
>    http://www.bic.mni.mcgill.ca/~rotor/src/ana2mnc-1.2.tar.gz
> 
> the function "write_minc()" will create a minc file from a %gen_hdr hash.  use
> the dump_general_header() function to get an idea of the sorts of things that
> are required.

The ana2mnc script looks very useful. Thanks.

Roger
-- 
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Dr. Roger Luechinger    E-Mail: luechinger@biomed.ee.ethz.ch
Universitaetsspital
MR-Zentrum VMR30      www/PGP: http://www.mr.ethz.ch/~rluchin/
8091 Zuerich
Tel: ++41 1 255 30 64     Fax: ++41 1 255 45 06
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