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

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: MSGPP cocktails for fragment crystallography
From: Jan Abendroth janabend {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-06-28

Next message:
Subject: Re: heavyatom soaking problem
From: Klaas Decanniere kdecanni {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-06-29

Subject: Re: compiling problems ccp4-6.0.2 and gcc-4.1.2
From: Miguel_Ortiz-Lombardía ibdeno {- at -} GMAIL {- dot -} COM
Date: 2007-06-29

Hi Tim,

Sorry, I forgot to mention that I had also tried that. But if you invoke the
linker through 'gcc', then some options (notably -soname) are not
recognized.

Yes, I was trying to build shared libraries. That gives me the idea that I
could try not to do so, thanks!

The problem is with gcc, anyway. I tried both g77 and gfortran. I know the
issues about gfortran, I found one myself concerning molrep. However, I'm
not sure whether the last version of refmac5 compiles with g77.

Thank you!

Miguel

2007/6/29, Tim Grune :
>
> 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-Lombardía 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
>
>

--
correo-e: ibdeno@gmail.com
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!

Georges Brassens

CCP4bb navigation

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

Previous message:
Subject: MSGPP cocktails for fragment crystallography
From: Jan Abendroth janabend {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-06-28

Next message:
Subject: Re: heavyatom soaking problem
From: Klaas Decanniere kdecanni {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-06-29