[ccp4bb] scala on mac osx - off topic, really

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

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CCP4bb <-- 2008 <-- May 2008 <-- 07 May 2008

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Subject: Re: protein-protein docking programs
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-05-07

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Subject: Re: scala on mac osx - off topic, really
From: Chris Richardson Chris {- dot -} Richardson {- at -} ICR {- dot -} AC {- dot -} UK
Date: 2008-05-07

Subject: scala on mac osx - off topic, really
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2008-05-07

Hey all,

a colleague is running ccp4 6.0.2 on a MacBook with Timid Tiger.
Built-in Scala is 3.2.25. Because of a bug, he wants to upgrade Scala.
Running Scala 3.3.2-beta5 or 3.2.34 (phil's binaries) fails because
gcc shared libraries are missing. Here's the setup:

[dyn1208-14:ttgt/TT/process] duolu% fink list gcc
Information about 2696 packages read in 3 seconds.
avr-gcc 4.2.0-1 GNU GCC for
ATMEL AVR micro controllers
broken-gcc 3.3-1 [virtual
package representing a broken gcc compiler]
gcc2 2.95.2-0 [virtual
package representing the gcc 2.95.2 compiler]
gcc2.95 2.95.2-0 [virtual
package representing the gcc 2.95.2 compiler]
gcc3.1 3.1-0 [virtual
package representing the gcc 3.1 compiler]
i gcc3.3 3.3-1819 [virtual
package representing the gcc 3.3 compiler]
i gcc4.0 4.0.1-5250 [virtual
package representing the gcc 4.0.1 compiler]
gcc42 4.2.2-1000 GNU Compiler
Collection Version 4.2
gcc42-shlibs 4.2.2-1000 Shared
libraries for gcc4

Fink is fully up to date. As you can see, gcc4.0 and gcc3.3 are
installed, but not gcc42 or gcc42-shlibs. Installation of gcc42-shlibs
fails:

[dyn1208-14:ttgt/TT/process] duolu% fink install gcc42-shlibs
Password:
Information about 2696 packages read in 0 seconds.
Can't resolve dependency "cctools (>= 622-1)" for package
"gcc42-4.2.2-1000" (no matching packages/versions found)
Exiting with failure.

cctools are installed in version 590 and are not upgraded further. What
looked like an alternative to me, odcctools version 622, does not
fulfill gcc42's requirements.

[dyn1208-14:ttgt/TT/process] duolu% fink list cctools
Information about 2696 packages read in 0 seconds.
i cctools 590-1 [virtual
package representing the developer tools]
i cctools-extra 1:590.18-1002 Extra software
from cctools
i cctools-single-module 590-1 [virtual
package, your dev tools support -single_module]
i odcctools 622.3-20060925 Darwin cctools
build system/code base to support gcc4
odcctools590 20060608-1 Darwin cctools
build system/code base to support g95

My questions are: Short of upgrading to Lazy Leopard, how do I get
gcc42 and gcc42-shlibs installed on my colleague's laptop? Why are
there no gcc4.0-shlibs? Why are different versions of gcc installed?
Could I safely remove gcc3.3? On my own MacBook Pro (running Lazy
Leopard) gcc4.0, gcc43 and gcc43-shlibs are installed, and I can see
that gcc4-shlibs exist, but my colleague's fink doesn't see them.

It's all mighty confusing to me. From the dark ages I dimly remember
similar nightmares during a major gcc version change on linux. Are the
reported problems somehow related to that?

Thanks.

Andreas

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CCP4bb <-- 2008 <-- May 2008 <-- 07 May 2008

Previous message:
Subject: Re: protein-protein docking programs
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-05-07

Next message:
Subject: Re: scala on mac osx - off topic, really
From: Chris Richardson Chris {- dot -} Richardson {- at -} ICR {- dot -} AC {- dot -} UK
Date: 2008-05-07