[EMBOSS] X11 version requirement for EMBOSS 3.0.0?

Thu May 18 14:21:24 UTC 2006

If you do a:

 setenv CFLAGS "-D__amd64__"   (4 underscores in all!)

before configuring then that will stop the segfaulting on
opterons.

You should at least 'make clean' before configuring again.
The above will not be required in the next release of EMBOSS.

Alan

> Hi again,
>
> the machine is an HP DL385 med 2xOpteron 2.8GHz CPUs ...
> and yes, I've checked for the 64bit libraries, too.
>
> To add to my woes, configuring "--without-x" (thanks Mark
> for the pointer!) and compiling (w/o warnings but for two
> incompatible pointers in ajfmt.c) gives binaries that segfault
> immediately. The config.log has some more
>
> 	'/usr/bin/ld: skipping incompatible' library,
>
> but now for libz, libm and libc in the conftest for inflateEnd
> in -lz ... So I tried turning configuring w/o the pngdriver, but
> still get segfault'ing binaries.
>
> So I'm at a bit of a loss about what to do right
> now - except force our IS/IT dept to upgrade RedHat ...
>
> If anyone want to see the output from configure and/or make you're
> welcome (but no sniffing around ;-)
>
> cheers /staffan
>
> -----Original Message-----
> From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk]
> Sent: 18 May 2006 15:17
> To: Staffan.X.Bergh at astrazeneca.com
> Subject: RE: [EMBOSS] X11 version requirement for EMBOSS 3.0.0?
>
>
> Hi Staffan,
>
> Oh dear. Is it an AMD64 or EM64T by any chance as that error might make
> sense
> if it was trying to combine 32bit and 64 bit libraries. Noone has
> reported it before though - but I expect few of our users have
> RHES. If it is a 64bit m/c you will, of course, have checked that
> both 32bit and 64bit libs/devel files have been installed.
>
> Also, as you're corporate, there is patently no chance of a sniff
> around from this end.
>
> It looks like an X11 upgrade might be worth a try.
>
> Cheers
> Alan
>
>
>
>
>
>
>
>
>> Hi Alan,
>>
>> I do have the devel package installed ...
>>
>>> $ rpm -q -f /usr/X11R6/lib/libX11.a -i
>>> Name        : XFree86-devel                Relocations: (not
>>> relocatable)
>>> Version     : 4.3.0                             Vendor: Red Hat, Inc.
>>> Release     : 68.EL                         Build Date: Sun 22 Aug 2004
>> 04:22:47 PM CEST
>>> Install Date: Sun 25 Sep 2005 01:05:22 AM CEST      Build Host:
>> tweety.build.redhat.com
>>> Group       : Development/Libraries         Source RPM:
>> XFree86-4.3.0-68.EL.src.rpm
>>> Size        : 13528038                         License:
>> MIT/X11/XFree86/many others
>>> Signature   : DSA/SHA1, Mon 23 Aug 2004 07:58:10 PM CEST, Key ID
>> 219180cddb42a60e
>>> Packager    : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
>>> URL         : http://www.xfree86.org
>>> Summary     : X11R6 static libraries, headers and programming man
>>> pages.
>>> Description :
>>> XFree86-devel includes the libraries, header files and documentation
>>> needed for developing applications for the X window system.
>>
>> and it verifies OK, so it's not broken in some mysterious way ...
>>
>> cheers /staffan
>>
>> -----Original Message-----
>> From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk]
>> Sent: 18 May 2006 13:26
>> To: Staffan.X.Bergh at astrazeneca.com
>> Cc: emboss-bug at emboss.open-bio.org
>> Subject: Re: [EMBOSS] X11 version requirement for EMBOSS 3.0.0?
>>
>>
>> Hi Staffan,
>>
>> First check that you have the XFree86-devel RPM installed.
>> If not, then install it, do a make clean and then configure
>> again.
>>
>> Let us know whether that solves it. I've never seen that error
>> in quite that form before but the XFree86-devel RPM is essential.
>>
>> Alan Bleasby
>> EBI
>>
>> PS: CCing to the rest of the developers
>>
>>
>>> Hi, I'm trying to compile/install EMBOSS 3.0.0 on a linux box with
>>> RedHat
>>> Enterprise Server 3 (not
>>> the latest, I know, but corporate standards, etc, etc, ...)
>>>
>>> The error message from make/ld is:
>>>
>>>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when
>>>> searching
>>> for -lX11
>>>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when
>>>> searching
>>> for -lX11
>>>> /usr/bin/ld: cannot find -lX11
>>>
>>> The X version that RHES3 ships with is 4.3.0
>>>
>>>> $ X -version
>>>> XFree86 Version 4.3.0 (Red Hat Enterprise Linux 3 release:
>>>> 4.3.0-68.EL)
>>>> Release Date: 15 August 2003
>>>> (and a lot more, deleted by the RSSPBW [Royal Swedish Society for the
>>> Preservation of BandWidth]).
>>>
>>> I couldn't find answer to this in the docs, nor in the mail archives,
>>> and
>>> I
>>> guess that I'll end up having to
>>> upgrade X, but it would be nice if someone could confirm that that
>>> would
>>> solve the problem before I try?
>>> Or is this something else?
>>>
>>> cheers /staffan
>>> _____________________________________________________________
>>> Staffan Bergh, PhD
>>> Informatics and Logistics, Molecular Pharmacology, AstraZeneca R&D
>>> B209:537, SE-151 81 Södertälje, Sweden
>>> Tel: +46 8 553 215 72
>>> staffan.x.bergh at astrazeneca.com
>>>
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>>
>>
>>
>>
>
>