[cctbxbb] Problems compiling cctbx on OS X (10.8.0)

[William G. Scott]

Hi Richard:

The tar ball isn't versioned, but has an md5sum of 9444c00f3c60ad855896e1032b2c5fd2.  I vaguely recall the date being from about 3 months ago.  This only started because I was trying to figure out why I couldn't get it to compile in ccp4.  (It is the same problem. I am also having trouble compiling the ccp4 programs that rely on this, like phaser, aimless, pointless, even after I apply the previous fix. I haven't had a chance to check why yet, but it is a significant problem within the context the ccp4 6.3.0 released a couple of weeks ago.)

Thanks.

Bill



William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
 

On Aug 3, 2012, at 10:25 AM, Richard Gildea <rgildea at gmail.com> wrote:

> Hi Bill,
> 
> What version of the cctbx sources are you using? As Luc mentioned, the first error from your log was resolved about 2 months ago with svn revision 15462 (http://cctbx.svn.sourceforge.net/viewvc/cctbx?view=revision&revision=15462). If you are using the latest "released" build (about 3 months old), then you should either update to latest nightly builds (http://cci.lbl.gov/builds/) or track the svn. It is known that the cctbx will not fully compile using clang with the older version of boost we currently distribute, however if you use a recent boost release it should be fine (it is also fine using --compiler=gcc). We are currently working on updating to the latest boost (the problem is with compatibility with some of the older platforms we support).
> 
> Hope that helps,
> 
> Richard
> 
> On 3 August 2012 08:53, William G. Scott <wgscott at ucsc.edu> wrote:
> Hi Luc:
> 
> I don't know how to find the version of Boost, but everything else is here:
> 
> http://fennario.ucsc.edu/~wgscott/temp/everything.log
> 
> I've hidden all "third-party" stuff like /usr/local and /sw, so the only (unmodified) python is what comes with 10.8, the only compilers are those supplied with the latest Xcode, and so on.
> 
> This time I used the supplied cctbx_install_script.csh and put a -v in the shell invocation to provide verbose output.
> 
> I invoked this from zsh, from bash, and from tcsh.  Only the first of these has significant customizations, so I don't think it is my shell environment.
> 
> I can't think of anything else.  Since g++ works, I can't see how it could be anything other than clang.
> 
> 
> 
> Bill
> 
> 
> William G. Scott
> Professor
> Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> 228 Sinsheimer Laboratories
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
> 
> 
> 
> On Aug 2, 2012, at 5:26 AM, Luc Bourhis <luc_j_bourhis at mac.com> wrote:
> 
> > Hi William,
> >
> >> I am having the same problem compiling cctbx stand-alone, or within CCP4.  I've posted the error log here:
> >>
> >> http://fennario.ucsc.edu/~wgscott/temp/cctbx_compile_errors.log
> >
> > From the information given in the discussion that followed, you have installed Xcode 4.4 command line tools. So do I but I can't reproduce the problem with the cctbx trunk as of a few minutes ago. From the error log you linked to, the compilation of mmtbx/bulk_solvent/bulk_solvent_ext.cpp fails. Could you copy me the exact compiler invocation? Moreover, although it should not matter considering the compiler errors at hand, could you tell me which version of Boost you used?
> >
> > Finally, a general remark is in order: thou shall never try to work around such problems by playing with --compiler. Instead, please, loudly complain on this forum: the cctbx must compile with the latest Xcode tools and a build directory setup with simply "python configure.py mmtbx".
> >
> > Best wishes,
> >
> > Luc
> >
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