[EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11

[Robin Colgrove]

Thanks again for everyone's helpful suggestions.
I will try to get back to this later today.

I have to be careful, since I am unfamiliar with large-scale  
programming (mostly a bench virologist, my own sequence analysis  
programs are usually only a few pages of code, with text as the only  
input and output) and I cannot afford to break my existing system. In  
particular, I am using phred/phrap/consed for several important  
sequencing projects and it is -after a good deal of struggle- working  
fine with my existing X11 from the Apple SDK (about which I know  
nothing except at the user level). I am hesitant to mess with this. I  
may try again to compile without X11 (this failed before but may have  
been because of something else I was working on at the time). If this  
works, can one go back and add X11 later, once the kinks have been  
worked out? For now, I would be happy with just text-based sequence  
manipulation.

thanks again
robin



On Mar 31, 2005, at 6:40 AM, Koen van der Drift wrote:

>
> On Mar 30, 2005, at 9:23 PM, Robin Colgrove wrote:
>
>> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
>> This package refuses to overwrite these. Remove them, then tell Fink  
>> to
>> install xfree86 again. (The package won't be recompiled.) If you want
>> to keep your X11 installation, install system-xfree86 resp.  
>> system-xtools
>> instead to make this known to Fink's package system.
>>
>
> Sorry that fink is giving you so much problems. It can indeed be  
> frustrating for new users, especially with all the X11 options. If I  
> understand it correctly, you are building xfree86 from fink, but you  
> already have it installed by yourself. I suggest you remove (or  
> better, move it to a temp folder so you can always move it back) the  
> /usr/X11R6 and /etc/X11 directories, and try the fink package again.  
> You have to make sure that you install everyting from the same  
> package, don't mix and match your xfree86 with apple's X11, or fink's  
> xorg. See also this entry in the fink FAQ:
>
> http://fink.sourceforge.net/faq/usage-general.php?phpLang=en#x-options
>
>> dpkg: error processing  
>> /sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
>> xfree86_4.4.0-13_darwin-powerpc.deb (--install):
>
> I see that you are using the stable tree from fink. Emboss 2.10 is so  
> far only available in the unstable tree. This doesn't mean that it is  
> not working, it means that there hasn't been feedback from users that  
> it is working with or without problems. Please keep me informed if you  
> got it to work, since I am the maintainer of the emboss package in  
> fink. If you give me positive feeedback, I can move it to the stable  
> tree.
>
> http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable
>
>
> Finally, if everything went fine, I can highly recommend the  
> emboss-kaptain package from fink which will give you a very nice GUI  
> in X11.
>
> good luck,
>
> - Koen.
>