From schristley at mac.com  Mon Aug  1 18:12:54 2011
From: schristley at mac.com (Scott Christley)
Date: Mon, 01 Aug 2011 17:12:54 -0500
Subject: [Biococoa-dev] BCSequenceView binding problem
In-Reply-To: <93A83614-0EDF-4403-A993-B1A5DA303A17@st-andrews.ac.uk>
References: <C12B691C-096E-4099-9153-22F95724EBE4@st-andrews.ac.uk>
	<107B1C0D-D85F-431A-9FB3-7020E34D7031@mac.com>
	<93A83614-0EDF-4403-A993-B1A5DA303A17@st-andrews.ac.uk>
Message-ID: <05F59FB8-8621-47CB-B32E-184FCEBF580E@mac.com>

Hello Gregor,

That helps.  What is curious is line 8 where it indicates a category (NSSharing) added to NSTextView.  I cannot find that category in my Xcode 3 documentation, but I don't have Lion.  Is this something that is part of your framework, or maybe something new added in Lion?  Maybe there has been a change to the NSText system such that the way NCSequenceView is using it is no longer correct.

Are you able to run the Peptides demo app on Lion?  That is a working demo of BCSequenceView.

Scott

On Aug 1, 2011, at 8:22 AM, Gregor Hageluken wrote:

> Hi Scott,
> 
> thanks for your reply! I guess it is something like this that you want to see:
> <Proteins2 - -[NSTextView insertText_]_disassembly_0x00007fff8b686d75.s.jpg>
> Unfortunately I have no idea, how to export that to a text file. Does this give you any clue?
> 
> Cheers,
> Gregor
> On 1 Aug 2011, at 01:44, Scott Christley wrote:
> 
>> Hi Gregor,
>> 
>> Are you able to get a stack trace so we can see the loop and what is calling setString?
>> 
>> Scot
>> 
>> On Jul 31, 2011, at 4:22 PM, Gregor Hageluken wrote:
>> 
>>> Hi,
>>> 
>>> I am trying to bind the 'value' property of a BCSequenceView to a TreeController that is again bound to my CoreData model. When I start my app it gets stuck in an infinite loop in the setString: method of BCSequenceView.
>>> 
>>> I did not change anything in the code of the class.
>>> 
>>> The app works fine when I remove this binding or when I bind it to a normal TextView instead.
>>> 
>>> Any idea what's wrong? I am not using the whole BioCocoa framework by the way, just the BCSequenceView class and the BCAppKitDefines.h file.
>>> 
>>> Also I get a couple of compiler warnings for this line of code:
>>> id <BCSequenceViewDelegate> delegate = [self delegate];
>>> The warning is: 
>>> Semantic Issue: Initializing 'id<BCSequenceViewDelegate>' with an expression of incompatible type 'id<NSTextViewDelegate>'
>>> Can I do something about that?
>>> 
>>> I am using Xcode 4.1 on OSX Lion.
>>> 
>>> 
>>> Thanks,
>>> Gregor
>>> 
>>> 
>>> 
>>> 
>>> -----
>>> Gregor Hagelueken
>>> Postdoctoral Research Fellow, Naismith Group
>>> Biomedical Sciences Research Complex
>>> University of St Andrews
>>> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
>>> Email: gh50 at st-andrews.ac.uk
>>> Tel: 
>>> +44 1334 467247
>>> -----
>>> 
>>> _______________________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>> 
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
> 
> -----
> Gregor Hagelueken
> Postdoctoral Research Fellow, Naismith Group
> Biomedical Sciences Research Complex
> University of St Andrews
> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
> Email: gh50 at st-andrews.ac.uk
> Tel: 
> +44 1334 467247
> -----
> 

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From schristley at mac.com  Tue Aug  2 18:15:39 2011
From: schristley at mac.com (Scott Christley)
Date: Tue, 02 Aug 2011 17:15:39 -0500
Subject: [Biococoa-dev] warning
In-Reply-To: <09D4A5DC-AD75-4C04-9F79-A12E71CF3396@st-andrews.ac.uk>
References: <4DAC1A0A-C2DC-4C83-B566-DA3107851EE6@st-andrews.ac.uk>
	<550371CF-898E-459F-97AC-D414A06EA9B6@mac.com>
	<09D4A5DC-AD75-4C04-9F79-A12E71CF3396@st-andrews.ac.uk>
Message-ID: <3436BBA1-36C4-4C03-9016-8A1D1FE2D60E@mac.com>

Hi Gregor,

Somebody mentioned this not too long ago on the mailing list, but I forgot what the solution was though, maybe they will chime in.  I tend to always copy BioCocoa.framework into /Library/Frameworks, so you can see if that works, otherwise it is something like deleting and re-adding the framework into the xcode project or something like that.

Scott

On Aug 2, 2011, at 4:55 PM, Gregor Hageluken wrote:

> Hi Scott,
> 
> I am trying to compile the Peptides app, but I am having problems with linking the framework to it. I always get the error below. Before that, I compiled the framework and added it to the Biococoa samples Xcode project via 'Link Binaries with library' and I also added a 'copy bundle resources' build phase. That is why I only added the BCSequenceView class to my app. I couldn't get the whole Framework linked to it.
> 
> However, I tried if the EnzymeX app still works on Lion because I think it also uses BCSequenceView. And that works without any problems.
> 
> Here is the error when I try to compile the Peptides.app:
> 
> GNU gdb 6.3.50-20050815 (Apple version gdb-1705) (Fri Jul  1 10:50:06 UTC 2011)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.  Type "show warranty" for details.
> This GDB was configured as "x86_64-apple-darwin".tty /dev/ttys000
> warning: Unable to read symbols for @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa (file not found).
> warning: Unable to read symbols from "BioCocoa" (not yet mapped into memory).
> [Switching to process 40114 thread 0x0]
> dyld: Library not loaded: @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>   Referenced from: /Users/gha/Library/Developer/Xcode/DerivedData/BioCocoaDemos-edqepdxbqxxpskctncdqmziaeyjr/Build/Products/Debug/Peptides.app/Contents/MacOS/Peptides
>   Reason: image not found
> sharedlibrary apply-load-rules all
> (gdb) 
> 
> Cheers,
> Gregor
> 
> On 2 Aug 2011, at 00:57, Scott Christley wrote:
> 
>> Nope, I highly doubt it as that is a simple casting warning about a protocol and shouldn't affect runtime behavior.
>> 
>> Scott
>> 
>> On Aug 1, 2011, at 5:50 PM, Gregor Hageluken wrote:
>> 
>>> Hi Scott,
>>> 
>>> I will let you know if the peptides app works. In the meantime, could it have anything to do with this warning that I get:
>>> 
>>> <Proteins2 - BCSequenceView.m.jpg>
>>> 
>>> it appears at several places in the BCSequenceView class.
>>> 
>>> Cheers,
>>> Gregor
>>> 
>>> -----
>>> Gregor Hagelueken
>>> Postdoctoral Research Fellow, Naismith Group
>>> Biomedical Sciences Research Complex
>>> University of St Andrews
>>> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
>>> Email: gh50 at st-andrews.ac.uk
>>> Tel: 
>>> +44 1334 467247
>>> -----
>>> 
>> 
> 
> -----
> Gregor Hagelueken
> Postdoctoral Research Fellow, Naismith Group
> Biomedical Sciences Research Complex
> University of St Andrews
> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
> Email: gh50 at st-andrews.ac.uk
> Tel: 
> +44 1334 467247
> -----
> 

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From koenvanderdrift at gmail.com  Wed Aug  3 10:53:53 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Wed, 3 Aug 2011 10:53:53 -0400
Subject: [Biococoa-dev] warning
In-Reply-To: <3436BBA1-36C4-4C03-9016-8A1D1FE2D60E@mac.com>
References: <4DAC1A0A-C2DC-4C83-B566-DA3107851EE6@st-andrews.ac.uk>
	<550371CF-898E-459F-97AC-D414A06EA9B6@mac.com>
	<09D4A5DC-AD75-4C04-9F79-A12E71CF3396@st-andrews.ac.uk>
	<3436BBA1-36C4-4C03-9016-8A1D1FE2D60E@mac.com>
Message-ID: <CAF8z=Hdk4HSiSE8Y526nLyKeYua3kmoiXFHbV6TdcfW3mZ-wng@mail.gmail.com>

To me, adding frameworks in Xcode sucks...  It is not very intuitive,
and takes several steps.  I will try to build the Peptides app tonight
with Xcode 4/Lion and see how it works.

Cheers,

- Koen.

ps, Gregor, when you reply could you reply to the list and not just to
Scott, so we can all see your posts? Thanks :)


On Tue, Aug 2, 2011 at 6:15 PM, Scott Christley <schristley at mac.com> wrote:
> Hi Gregor,
> Somebody mentioned this not too long ago on the mailing list, but I forgot
> what the solution was though, maybe they will chime in. ?I tend to always
> copy BioCocoa.framework into /Library/Frameworks, so you can see if that
> works, otherwise it is something like deleting and re-adding the framework
> into the xcode project or something like that.
> Scott
> On Aug 2, 2011, at 4:55 PM, Gregor Hageluken wrote:
>
> Hi Scott,
> I am trying to compile the Peptides app, but I am having problems with
> linking the framework to it. I always get the error below. Before that, I
> compiled the framework and added it to the Biococoa samples Xcode project
> via 'Link Binaries with library' and I also added a 'copy bundle resources'
> build phase. That is why I only added the BCSequenceView class to my app. I
> couldn't get the whole Framework linked to it.
> However, I tried if the EnzymeX app still works on Lion because I think it
> also uses BCSequenceView. And that works without any problems.
> Here is the error when I try to compile the Peptides.app:
> GNU gdb 6.3.50-20050815 (Apple version gdb-1705) (Fri Jul? 1 10:50:06 UTC
> 2011)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.? Type "show warranty" for details.
> This GDB was configured as "x86_64-apple-darwin".tty /dev/ttys000
> warning: Unable to read symbols for
> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa (file
> not found).
> warning: Unable to read symbols from "BioCocoa" (not yet mapped into
> memory).
> [Switching to process 40114 thread 0x0]
> dyld: Library not loaded:
> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
> ? Referenced from:
> /Users/gha/Library/Developer/Xcode/DerivedData/BioCocoaDemos-edqepdxbqxxpskctncdqmziaeyjr/Build/Products/Debug/Peptides.app/Contents/MacOS/Peptides
> ? Reason: image not found
> sharedlibrary apply-load-rules all
> (gdb)
> Cheers,
> Gregor
> On 2 Aug 2011, at 00:57, Scott Christley wrote:
>
> Nope, I highly doubt it as that is a simple casting warning about a protocol
> and shouldn't affect runtime behavior.
> Scott
> On Aug 1, 2011, at 5:50 PM, Gregor Hageluken wrote:
>
> Hi Scott,
> I will let you know if the peptides app works. In the meantime, could it
> have anything to do with this warning that I get:
> <Proteins2 - BCSequenceView.m.jpg>
>
> it appears at several places in the BCSequenceView class.
> Cheers,
> Gregor
> -----
> Gregor Hagelueken
> Postdoctoral Research Fellow,?Naismith Group
> Biomedical Sciences Research Complex
> University of St Andrews
> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
> Email: gh50 at st-andrews.ac.uk
> Tel:? +44?1334 467247
> -----
>
>
> -----
> Gregor Hagelueken
> Postdoctoral Research Fellow,?Naismith Group
> Biomedical Sciences Research Complex
> University of St Andrews
> Purdie Building, North Haugh, St Andrews, Fife, KY16 9ST
> Email: gh50 at st-andrews.ac.uk
> Tel:? +44?1334 467247
> -----
>
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>
>