[BioC] Rgraphviz load problem

Sat Oct 29 04:18:04 CEST 2005

Nice Byron. I will try this out later. I thought that the version of  
graphviz required by Rgraphviz was a bit "behind" so you might have  
saved some effort by going with (by memory) 2.2 or so. And I seem to  
recall that the DMG file should not be used.

Kasper
On Oct 28, 2005, at 6:26 PM, Byron Ellis wrote:

> Yeah, there's a version mismatch between the graphviz you can easily
> compile and the graphviz required by Rgraphviz on OS X. In answer to
> your earlier question, which is well timed since I decided I needed
> Rgraphviz back today:
>
>
>
> WARNING: THIS IS A HACK. GRAPHVIZ ON MY SYSTEM IS PROBABLY BROKEN IN
> ALL MANNER OF EXCITING WAYS. DO NOT TRY THIS AT HOME, YOUR COMPUTER
> WILL EXPLODE AND APPLE WON'T FIX IT!
>
>
> How to Build Rgraphviz From Source on OS X
> or
> The Path Of Pain
> or
> Can I Have Those Two Hours Back Now?
>
> A Cautionary Tale
>
>
> Step 1. Start coffee brewing, you WILL need it.
>
> Step 1.5. For minimal (hah!) pain get libjpeg/png/tiff/et al and
> install those. A copy of expat might not hurt either.
>
> Step 2. Get graphviz-2.6.tar.gz and unpack that
>
> Step 3. Configure. Make. Observe that it bombs out on something
> called a "codegen."
>
> Step 4. Check configure. Hey! You can disable codegens
>
> Step 5. ./configure --disable-codegens; make
>
> Step 6. Drink coffee
>
> Step 7. Observe that there are two symbols that can't be resolved.
> Furthermore, they are to be found in xdgen.c. But xdgen.c is disabled
> by the codegen option. *sigh*
>
> Step 8. Add xdgen.lo back into the Makefile. Go to xdgen.c and wrap
> up the codegen_t structure in an #ifdef
>
> Step 9. make
>
> Step 10. Contemplate the utility of including configure options that
> don't actually work.
>
> Step 11. For some reason it will bomb again looking for "environ,"
> which is actually there. I suspect a linking issue but don't care so
> I just comment out its usage in the if statement of pathpath.c
>
> Step 11. The usershape_gd will break for reasons unrelated to
> codegens with undefined symbols. Copy the LIBADD from dotplan or
> something and it'll build. For whatever reason it doesn't link, yet
> uses, calls from the cdt library. Linking in gvc seems to do the trick
>
> Step 12. If you were dumb enough (like me) to install tcl support,
> fix various codegen issues in TclDot. Ditch tkgen completely, its
> only going to cause more pain as its related to codegen.
>
> Step 13. If you're dumb enough not to have libjpeg (like me) be aware
> that diffimage doesn't actually, you know, check config.h. Wrap the
> appropriate statements in #ifdef's in contrib/diffimage/diffimage.c
>
> Step 14. make a few more times to see if you got everything
>
> Step 15. make install
>
> Step 16. Hurrah. You can now install Rgraphviz 1.8 unmolested (just
> make sure Biobase is loaded before you try to use the plotting
> routines because they use listLen.)
>
> fink and darwinports can also build graphviz, but I'm not sure if
> they're using a version new enough to match with Rgraphviz-1.8
>
> Perhaps later I'll try a static build of Rgraphviz, but right now I'm
> just happy it works
>
> On Oct 27, 2005, at 11:43 AM, Fridlyand, Jane wrote:
>
>
>>
>> I am trying to install Rgraphviz under Mac OS X Tiger (10.4.2). I
>> am using
>> the latest R (2.2) and Rgraphviz 1.8 . I downloaded and successfully
>> installed what i think is the most current graphviz dmg for mac
>> (1.10.dmg).
>> It installed in /usr/local/lib/graphviz. I added thje fowllowing
>> to .bashrc:
>>
>>
>> export LD_LIBRARY_PATH=/usr/local/lib/graphviz
>>
>> Now, i am getting the follwoing error when installing and loading  
>> from
>> within R: the package seems to install but not load
>>
>>
>>
>>> getBioC("Rgraphviz")
>>>
>>>
>>
>> Running getBioC version 0.8  with R version  2.2.0
>>
>> Running biocinstall version 1.1  with R version  2.2.0
>> Warning: unable to access index for repository
>> http://www.bioconductor.org/packa
>> ges/data/experiment/1.7/bin/macosx/powerpc/contrib/2.2
>> trying URL
>> 'http://www.bioconductor.org/packages/bioc/1.7/bin/macosx/powerpc/con
>> trib/2.2/Rgraphviz_1.8.0.tgz'
>> Content type 'application/x-gzip' length 1263932 bytes
>> opened URL
>> ==================================================
>> downloaded 1234Kb
>>
>>
>> The downloaded packages are in
>>         /tmp/RtmpwRAbnb/downloaded_packages
>>
>>
>>>
>>> library(Rgraphviz)
>>>
>>>
>> Loading required package: graph
>> Loading required package: cluster
>> Loading required package: Ruuid
>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>         unable to load shared library
>> '/Library/Frameworks/R.framework/Resources
>> /library/Rgraphviz/libs/Rgraphviz.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphviz/
>> libs/Rgra
>> ph
>> viz.so, 6): Symbol not found: _agedgeattr
>>   Referenced from:
>> /Library/Frameworks/R.framework/Resources/library/Rgraphviz/l
>> ibs/Rgraphviz.so
>>   Expected in: flat namespace
>> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'
>>
>>
>>>
>>>
>>>
>>
>> I also tried to install from the local file using R CMD INSTALL but
>> get the
>> follwoing error which i am not sure how to remedy:
>>
>> sparky$ sudo R CMD INSTALL Rgraphviz
>> Password:
>> * Installing *source* package 'Rgraphviz' ...
>> checking for graphviz... checking for dotneato-config...
>> /usr/local/bin/dotneato-config
>> /usr/local/bin/dotneato-config
>> failed
>> configure: error: please specify a valid path to 'dotneato-config'
>> version
>>
>>
>>> = 1.12 using --with-graphviz=DIR
>>>
>>>
>> ERROR: configuration failed for package 'Rgraphviz'
>> ** Removing
>> '/usr/local/lib/R.framework/Versions/2.2/Resources/library/Rgraphviz'
>> ** Restoring previous
>> '/usr/local/lib/R.framework/Versions/2.2/Resources/library/Rgraphviz'
>>
>>
>> I appreciate the advice. I noticed a lot of people were having
>> issue with
>> installation and I looked thru the mailing list but most of the
>> solutions
>> amounted to installing graphviz and exporting path  both of which I
>> have
>> done
>>
>> Thank you again
>>
>> Jane
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>
> ---
> Byron Ellis (ellis at stat.harvard.edu)
> "Oook" -- The Librarian
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>