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 >

Thanks, Byron I got graphviz 2.2 from Sean and the installation of both programs (graphviz and Rgraphviz) went without a hitch. So, Kasper is probably right about less trouble with 2.2 Jane -----Original Message----- From: Kasper Daniel Hansen To: Byron Ellis Cc: Fridlyand, Jane; 'jgentry at jimmy.harvard.edu'; 'bioconductor at stat.math.ethz.ch' Sent: 10/28/2005 7:18 PM Subject: Re: [BioC] Rgraphviz load problem 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 >

If you're new to Mac OS X and don't want to have to deal with compiling or porting software packages, I'd check out Fink (http://fink.sourceforge.net). From the Fink website: "The Fink project wants to bring the full world of Unix Open Source software to Darwin and Mac OS X. We modify Unix software so that it compiles and runs on Mac OS X ("port" it) and make it available for download as a coherent distribution. Fink uses Debian tools like dpkg and apt-get to provide powerful binary package management. You can choose whether you want to download precompiled binary packages or build everything from source." Once you have fink installed, installing graphviz is as simple as typing 'fink install graphviz'. Fink will also take care of dependencies... Todd Jane Fridlyand wrote: > Dear Mac users > > can anyone who successfully installed appropriate version of graphviz > (v>1.12) and was able to install/load Rgraphviz on MAC OSX share the > steps they took with me? I was previously having issues because graphviz > version was older but not I am not quite sure. do i need to compile > graphviz from source or downloading compiled dmg from pixelglow and > placing it into applications is sufficient (does not seem to be but i am > not sure how to obtain the other components). I am new to mac so things > are often unintuitive to me. > > thanks and sorry > > Jane > -- ****************************************** Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc. Email: todd at nimblegen.com Phone: 1-608-218-7651

On 10/27/05 4:00 PM, "Jane Fridlyand" <janef at="" stat.berkeley.edu=""> wrote: > > Dear Mac users > > can anyone who successfully installed appropriate version of graphviz > (v>1.12) and was able to install/load Rgraphviz on MAC OSX share the > steps they took with me? I was previously having issues because graphviz > version was older but not I am not quite sure. do i need to compile > graphviz from source or downloading compiled dmg from pixelglow and > placing it into applications is sufficient (does not seem to be but i am > not sure how to obtain the other components). I am new to mac so things > are often unintuitive to me. Jane, It has been a while since I did this, but it looks like I installed 1.12 from source on macos. Compilation would likely have been with gcc-3.3, so you can do 'sudo gcc_select 3.3' to get that behavior, if I remember. I also noticed that there is a graphviz build available via fink, but I'm not sure if that works for Rgraphviz. I haven't tried the PixelGlow route, but I would tend to agree that it won't be sufficient. Sean