Re: [Fink-users] failed to install apbs

[William G. S. <wg...@ch...>]

Hi Alan:

It looks like there are multiple problems with this package and I  
think I am going to throw the vile thing into the fire and start over.  
I can't give you my debians because they were built for /sw64 instead  
of /sw.

If you need apbs in a hurry for a pymol plugin, you can grab David  
Gohara's very fast (intel only) pre-compiled version from here:
http://sourceforge.net/projects/apbs/
and redirect pymol to it.

I will try to get the fink package fixed as soon as possible.

Sorry for this.

Bill




On Aug 1, 2009, at 6:11 AM, Alan wrote:

> Hi there,
> Well, I found this:
>
> find /sw/src/fink.build | grep site
> /sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/ 
> @INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
>
> Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly  
> being
> replaced in apbs.info:
> sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
>
> In a test, I commented out in apbs.info any reference to python,  
> including
> the patch and I got apbs deb and working.
>
> Dear William, would be possible to you to send me your apbs.info and
> apbs.patch from sw64/ as well as your apbs deb package?
>
> Many thanks in advance.
>
> Alan
>
> On Fri, Jul 31, 2009 at 19:35, Alexander Hansen <ale...@gm...
>> wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> William Scott wrote:
>>>
>>>> There's something funny going on in the install script.  For one  
>>>> thing,
>>>> it's installing files in
>>>>
>>>> /sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/ 
>>>> apbs-1.1.0-2/
>>>>
>>>> I also found the ordering a bit suspect:
>>>>
>>>> make install DESTDIR=%d
>>>> rm -Rf **/CVS     # fink validate complains if this junk is left  
>>>> behind.
>>>> # rm -Rf **/.svn  # fink validate complains if this junk is left  
>>>> behind.
>>>> mkdir -p %i/share/%n
>>>> mkdir -p %i/lib
>>>>
>>>> I'd have assumed that we'd want to create those directories  
>>>> before 'make
>>>> install'.
>>>> - --
>>>> Alexander Hansen
>>>> Fink User Liaison
>>>> -----BEGIN PGP SIGNATURE-----
>>>> Version: GnuPG v1.4.9 (Darwin)
>>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>>>
>>>> iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu
>>>> zPEAniLUCPlwooATD+lGYN9Fd+2w6cto
>>>> =V8ih
>>>> -----END PGP SIGNATURE-----
>>>>
>>>
>>> I'll be happy to change anything, but in my hands it works, and
>> validates:
>>>
>>> % fink -v validate apbs_1.1.0-2_darwin-x86_64.deb
>>> apbs-dev_1.1.0-2_darwin-x86_64.deb
>>> Validating .deb file apbs_1.1.0-2_darwin-x86_64.deb...
>>> Package looks good!
>>> Validating .deb file
>>>
>>> I'm trying to find if there is a missing dependency.  We have the
>>> identical setup, apart from my /sw64  vs. his /sw.
>>>
>>> (I've emailed him back off-list).
>>>
>>> Bill
>>>
>>>
>>> William G. Scott
>>>
>>> Contact info:
>>> http://chemistry.ucsc.edu/~wgscott/
>>>
>>>
>>
>> It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
>>
>> - --
>> Alexander Hansen
>> Fink User Liaison
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.9 (Darwin)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iEYEARECAAYFAkpzOVcACgkQB8UpO3rKjQ8DhACfbIuQE5rffn1Qn/6lAI0wc5hy
>> cngAoKMDRmgsyg53OZLJ9Kwf3zvGyAhM
>> =350/
>> -----END PGP SIGNATURE-----
>>
>
>
>
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>> http://www.bio.cam.ac.uk/~awd28<<