[BioC] Rgraphviz: Edge attributes not displaying

[Kasper Daniel Hansen]

Ok, the fixes are incorporated in Rgraphviz 1.13.25, which have been  
committed (and which hopefully works on the other platforms). It may  
take a while for it to appear on the website. You should just install  
this version to fix the edge label problem.

Kasper

On Feb 15, 2007, at 9:03 PM, Kasper Daniel Hansen wrote:

> I believe I have been a bit quick. I should be able to include the
> fix in the autoconfigure script of Rgraphviz, so don't go and apply
> the stuff below, unless you have a problem with command-line Graphviz
> or other applications using Graphviz. Hopefully this will be nailed
> down tonight.
>
> Kasper
>
> On Feb 15, 2007, at 7:56 PM, Kasper Daniel Hansen wrote:
>
>> A fix has been found to the problem reported by Jarrett: the fact
>> that edge labels are not showing up on Mac (and possibly 64bit Linux
>> as well as reported by Li).
>>
>> Unfortunately the fix is distinctively not nice :) I have only tested
>> this on Graphviz 2.12 on a Mac G4. You need to modify the Graphviz
>> header files which usually (if you have a default installation)
>> resides in
>>    /usr/local/include/graphviz
>> The file in question is called
>>    logic.h
>>
>> At the start of the file, just below the lines
>>
>> #ifndef GV_LOGIC_H
>> #define GV_LOGIC_H
>>
>> (which are at lines 17 and 18 in my installation), add the two lines
>>
>> #define HAVE_BOOL 1
>> #define HAVE_STDBOOL_H 1
>>
>> (you will probably need to have superuser privileges to do so, on a
>> Mac do
>> # sudo pico logic.h
>> )
>>
>> And reinstall Rgraphviz from source (you do not need to recompile
>> Graphviz, but you need to recompile Rgraphviz).
>>
>> I am very curious if this works with
>> 1) Simon's Graphviz-2.8 binary from r.research.att.com
>> 2) 64bit Linux
>> 3) Intel Mac (not sure if there was a problem to begin with on that
>> platform)
>> so please send me an email if you try this.
>>
>> For background, read the post by Emden R. Gansner on the Graphviz-
>> interest email-list. Apparently they were being a bit too smart
>> regarding the use of bool, which on Apple's machines have sizeof
>> (bool) = 4.
>>
>> Kasper
>>
>> On Feb 5, 2007, at 9:28 AM, Kasper Daniel Hansen wrote:
>>
>>>
>>> On Feb 5, 2007, at 9:22 AM, Li.Long at isb-sib.ch wrote:
>>>
>>>>> Nope, I get something very different
>>>>>
>>>>>>
>>>>> character(0)
>>>>>> AgEdge(g2)[[10]]@txtLabel at labelText
>>>>> character(0)
>>>>>
>>>>> Given what I saw looking at the edgeAttrs of the Ragraph object
>>>>> itself, (namely, Null), I'm guessing that the problem is there.
>>>>> This
>>>>> may also be why edge style (solid v. dashed) wasn't getting picked
>>>>
>>>> The problem with "lty" is different from this, we didn't even try
>>>> to set
>>>> that entry.  Here we do try, but don't get it right.
>>>>
>>>>> up.  Why it is different on linux instead of a mac, I am  
>>>>> uncertain,
>>>>> unless there are different binaries in the Bioconductor archive.
>>>>
>>>> Kasper,
>>>>
>>>> I see this problem on a 64-bit Linux machine as well.  So this
>>>> might be a
>>>> 64-bit vs. 32-bit issue.
>>>>
>>>> The size of a pointer is different on 64-bit machine vs. 32-bit
>>>> machine,
>>>> I'd pay some attention to that, since we are looking at the  
>>>> pointers
>>>> here...
>>>
>>> There is also the endian issue on the PPC (I am on a 32 bit machine)
>>>
>>>> I'll take a closer look at it tomorrow.
>>>
>>> It is rather bewildering. I have quite a lot of experience of  
>>> looking
>>> at how _node_ labels are handled in graphviz' C structures, and in
>>> this case the edge labels are certainly behaving differently. Of
>>> course, I guess edge labels are not used as much, so it could be a
>>> bug somewhere.
>>>
>>> The fact you see it on 64 bit Linux is at least a bit  
>>> comforting :) I
>>> guess it is using Graphviz 2.12?
>>>
>>> Like I just wrote: I'll follow up on the Graphviz list later today.
>>>
>>> Kasper
>>>
>>>
>>>> Li
>>>>
>>>
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>>
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>
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