Re: [Fink-beginners] Emboss on OSX 10.6

[Shae P. <Shae.Padrick@UTSouthwestern.edu>]

To my eye there are a few line break differences, and the substitution of /sw32 for /sw everywhere.  Otherwise identical to my eye.  

I get:

$ fink dumpinfo -fconfigureparams -fcompilescript emboss
Information about 9947 packages read in 1 seconds.
configureparams: --prefix=/sw  --with-java=${java_home} \ --with-javaos=${java_home}/include \ --enable-dependency-tracking --disable-static \ --includedir=/sw/lib/EMBOSS/include --libdir=/sw/lib/EMBOSS/lib \ --docdir=/sw/share/EMBOSS \ --enable-systemlibs --with-postgresql=/sw/opt/postgresql-8.4/bin/pg_config
compilescript:
 #!/bin/sh -ev
 	/sw/bin/autoreconf -fi
 	if [ -x /usr/libexec/java_home ]; then
 		export java_home=`/usr/libexec/java_home`
 	else
 		export java_home=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
 	fi 
 	./configure --prefix=/sw  --with-java=${java_home} \
  --with-javaos=${java_home}/include \
  --enable-dependency-tracking --disable-static \
  --includedir=/sw/lib/EMBOSS/include --libdir=/sw/lib/EMBOSS/lib \
  --docdir=/sw/share/EMBOSS \
  --enable-systemlibs --with-postgresql=/sw/opt/postgresql-8.4/bin/pg_config
 	make
 	fink-package-precedence \
 		--prohibit-bdep=emboss-libajax6-dev,emboss-libnucleus6-dev \
 		--prohibit-bdep=emboss-ajax6-dev,emboss-nucleus6-dev,emboss-plplot3-dev,emboss-plplot6-dev \
 		.


and:
$ /usr/libexec/java_home
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

And I think I mentioned this before (this is as provided by Apple):
$ ls /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
bin	bundle	lib	man
$ ls /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/
Classes		Headers		Info.plist	MacOS		include
Commands	Home		Libraries	Resources	version.plist

which seems consistent with the error I was getting.

Shae


________________________________________
From: Alexander Hansen [ale...@gm...]
Sent: Friday, January 28, 2011 11:25 AM
To: Shae Padrick
Cc: fin...@li... >> fink beginners mailing list
Subject: Re: [Fink-beginners] Emboss on OSX 10.6

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On 1/28/11 11:36 AM, Shae Padrick wrote:
> Thanks Alexander.
>
> BTW- I've been subscribed to the mailing list for a while and I can tell you put a ton of time into this, thanks for all the effort.
>
> Back to my problem.
>
>> so I suspect that you may not actually be using the unstable package
>> description.  You can confirm this by running
>
>> fink dumpinfo -finfofile emboss
>
> I'm really a newbie here, so no I'm not sure I'm running the unstable tree.  I gather I want to be using the unstable distribution here.  I'm a science user and many packages I'm interested in only show up there, so that was my original motivation on turning them on.
>
> Running the above command I get:
>
> infofile: /sw/fink/dists/unstable/main/finkinfo/sci/emboss.info
>
> Shae
>
>
> ________________________________
>
> UT Southwestern Medical Center
> The future of medicine, today.
>

Yeah, there was a problem with emboss after Apple changed the structure
of their Java, and the package was ostensibly fixed in unstable but not
yet in stable.  It works for me on 10.6/32-bit anyway, and I'm in the
middle of trying 64-bit for completeness.

It looks like you are indeed using the unstable tree version.  Let's
make sure it's current.  Run

$ fink dumpinfo -fconfigureparams -fcompilescript emboss

I get the following (your Fink root will differ):

=====
$ fink dumpinfo -fconfigureparams -fcompilescript emboss
Information about 9955 packages read in 1 seconds.
configureparams: --prefix=/sw32  --with-java=${java_home} \
- --with-javaos=${java_home}/include \ --enable-dependency-tracking
- --disable-static \ --includedir=/sw32/lib/EMBOSS/include
- --libdir=/sw32/lib/EMBOSS/lib \ --docdir=/sw32/share/EMBOSS \
- --enable-systemlibs
--with-postgresql=/sw32/opt/postgresql-8.4/bin/pg_config
compilescript:
 #!/bin/sh -ev
        /sw32/bin/autoreconf -fi
        if [ -x /usr/libexec/java_home ]; then
                export java_home=`/usr/libexec/java_home`
        else
                export
java_home=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
        fi
        ./configure --prefix=/sw32  --with-java=${java_home} \
  --with-javaos=${java_home}/include \
  --enable-dependency-tracking --disable-static \
  --includedir=/sw32/lib/EMBOSS/include --libdir=/sw32/lib/EMBOSS/lib \
  --docdir=/sw32/share/EMBOSS \
  --enable-systemlibs
- --with-postgresql=/sw32/opt/postgresql-8.4/bin/pg_config
        make
        fink-package-precedence \
                --prohibit-bdep=emboss-libajax6-dev,emboss-libnucleus6-dev \

-
--prohibit-bdep=emboss-ajax6-dev,emboss-nucleus6-dev,emboss-plplot3-dev,emboss-plplot6-dev
\
                .

=====
And also, what do you get if you run "/usr/libexec/java_home" ?
- --
Alexander Hansen, Ph.D.
Fink User Liaison
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