Re: [ccp4bb] compiling problems ccp4-6.0.2 and gcc-4.1.2

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: heavyatom soaking problem
From: Melanie Adams madams {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-28

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Subject: Re: heavyatom soaking problem
From: verdino {- at -} SCRIPPS {- dot -} EDU verdino {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-28

Subject: Re: compiling problems ccp4-6.0.2 and gcc-4.1.2
From: Tim Grune tim {- dot -} grune {- at -} SYNCHROTRON {- dot -} VIC {- dot -} GOV {- dot -} AU
Date: 2007-06-28

Hi,

according to this page
(http://www.xastir.org/wiki/index.php/HowTo:Ubuntu_6.10) the problem arises
due to a wrong ld option ('ld -shared' rather than 'gcc -shared'). How did
you run configure ? Are you trying to build shared libraries?

ccp4 works fine with Debian lenny, gcc-4.1.2 with just running
FC=g77 F77=g77 ./configure linux
(you should use g77 rather than gfortran. The programs compile but do not work
properly, especially with mosflm in Harry Powell's experience).

Tim

On Thursday 28 June 2007 20:32, Miguel Ortiz-LombardÃa wrote:
> Dear all,
>
> Has anyone succeeded at compiling the latest release of CCP4 with gcc-4.1.2
> This is the compiler version in Ubuntu 7.04 (Feisty Fawn)
>
> At the very beginning (ccif lib compilation), I get this error:
>
> /usr/bin/ld: final link failed: Nonrepresentable section on output
>
> I looked around and found that:
>
> export CC="gcc -fno-stack-protector"
>
> might help. It did help, and the compilation proceeded... to the program
> solomon, where I get again:
>
> eval gcc -fno-stack-protector ${pdbhtf_FLAGS-"-O -DGFORTRAN -DPROTOTYPE
> -fPIC"} -o pdbhtf pdbhtf.o -Wl,-rpath,/home/miguel/Desktop/ccp4-build/ccp4-
> 6.0.2/lib -lm && rm -f pdbhtf.o
> /home/miguel/Desktop/ccp4-build/ccp4-6.0.2/src/solomon_/cmap_io.c: In
> function 'WriteMap':
> /home/miguel/Desktop/ccp4-build/ccp4-6.0.2/src/solomon_/cmap_io.c:356:
> warning: passing arg 3 of 'mat4_to_symop' from incompatible pointer
> /usr/bin/ld: solomon: hidden symbol `__stack_chk_fail_local' in
> /usr/lib/libc_nonshared.a(stack_chk_fail_local.oS) is referenced by DSO
> /usr/bin/ld: final link failed: Nonrepresentable section on output
>
> Any clues anyone?
> Thanks a lot!
>
>
>
> Miguel

--
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: heavyatom soaking problem
From: Melanie Adams madams {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-28

Next message:
Subject: Re: heavyatom soaking problem
From: verdino {- at -} SCRIPPS {- dot -} EDU verdino {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-28