On Sun, Mar 13, 2011 at 1:59 PM, Gabriel Nathan Kaufman, Mr < gabriel.kaufman@mail.mcgill.ca> wrote: > I can make it work in Terminal somewhat (the iFlow GUI opens up but seems > to be buggy -might be because of a Gtk deprecation). However, I can't seem > to make it work through the Mac R GUI... > > > What could be causing this? An incompatibility with x64? > > > OK, a few thoughts.... How did you get R-2.13? Did you build from source or get binaries from somewhere, and if so, where? Was the output you sent in your first email from the R GUI? Did you click on R.app or R64.app? By default, if memory serves, the R GUI runs in 32-bit mode (though your initial report showed R running in 64 bit mode) and the command line R runs in 64-bit mode. You got it working by using the command line (console) but you didn't indicate whether you were using the --arch i386. The bioconductor package 'graph' comes with the BioC_graph.so library built for all architectures: tar ztf graph_1.29.3.tgz |grep BioC_graph.so graph/libs/i386/BioC_graph.so graph/libs/ppc/BioC_graph.so graph/libs/x86_64/BioC_graph.so So you may want to try a binary install: biocLite("graph", type="mac.binary.leopard") Dan > > Here is the console output from the Terminal route: > > > library(iFlow) > Loading required package: flowCore > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: rrcov > Loading required package: robustbase > Loading required package: pcaPP > Loading required package: mvtnorm > Scalable Robust Estimators with High Breakdown Point (version 1.1-00) > > Attaching package: 'flowCore' > > The following object(s) are masked from 'package:stats': > > alias, filter > > Loading required package: flowViz > Loading required package: lattice > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Loading required package: flowStats > Loading required package: fda > Loading required package: splines > Loading required package: zoo > Loading required package: mvoutlier > Loading required package: cluster > Warning message: > 'method' is deprecated. > Use ''gtk-enable-tooltips' property on GtkSettings' instead. > See help("Deprecated") and help("RGtk2-deprecated"). > > > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextSetFont: invalid context 0x0 > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextSetFontSize: invalid context 0x0 > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextSetTextMatrix: invalid context 0x0 > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextClearRect: invalid context 0x0 > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextSetRGBFillColor: invalid context 0x0 > Sun Mar 13 16:55:39 web020018.wireless.mcgill.ca R[4349] <error>: > CGContextShowGlyphsAtPoint: invalid context 0x0 > > > sessionInfo() > R version 2.13.0 Under development (unstable) (2011-03-13 r54760) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] iFlow_2.3.4 flowStats_1.9.0 cluster_1.13.3 mvoutlier_1.7 > [5] fda_2.2.5 zoo_1.6-4 flowViz_1.15.0 lattice_0.19-17 > [9] flowCore_1.17.2 rrcov_1.1-00 pcaPP_1.8-3 mvtnorm_0.9-96 > [13] robustbase_0.7-3 Biobase_2.11.10 > > loaded via a namespace (and not attached): > [1] cairoDevice_2.14 feature_1.2.6 graph_1.29.3 > [4] grid_2.13.0 KernSmooth_2.23-4 ks_1.8.1 > [7] latticeExtra_0.6-14 MASS_7.3-12 RColorBrewer_1.0-2 > [10] RGtk2_2.20.8 stats4_2.13.0 tools_2.13.0 > > > ----------------------------------------------------------- > > > From: Dan Tenenbaum [dtenenba@fhcrc.org] > > Sent: March 13, 2011 4:37 PM > > To: Gabriel Nathan Kaufman, Mr > > Cc: bioconductor@r-project.org > > Subject: Re: [BioC] iFlow/flowCore installation problem > > > > > I'm not sure exactly what is going on here. As a workaround, can you try > invoking R as follows? > > R --arch i386 > > And let us know if that works. > > Dan > [[alternative HTML version deleted]]

On Tue, Mar 15, 2011 at 3:00 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Gabriel, > > > > On Tue, Mar 15, 2011 at 2:41 PM, Gabriel Nathan Kaufman, Mr < > gabriel.kaufman@mail.mcgill.ca> wrote: > > > I tried reinstalling the graph package from binary, in both the 32- and > > 64-bit R GUI, and still can't manage to load iFlow properly. I keep > getting > > a flowCore installation error that doesn't seem to go away when I > reinstall > > flowCore in the GUI. > > > > When I run R in Terminal (in both 32- and 64-bit) it loads up fine. Any > > other ideas? > > > > > > The console from my last try in the R.app 64-bit GUI is copied below. > > > > > > Gabriel Kaufman > > McGill University Complex Traits Group > > > > > > ---------------------------------- > > > > > library(iFlow) > > Loading required package: flowCore > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'browseVignettes()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: rrcov > > Loading required package: robustbase > > Loading required package: pcaPP > > Loading required package: mvtnorm > > Scalable Robust Estimators with High Breakdown Point (version 1.1-00) > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object > > > '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/flo wCore/libs/x86_64/flowCore.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/libr ary/flowCore/libs/x86_64/flowCore.so, > > 6): Library not loaded: > > /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib > > Referenced from: > > > /Library/Frameworks/R.framework/Versions/2.13/Resources/library/flow Core/libs/x86_64/flowCore.so > > Reason: image not found > > > > > Whenever you see this type of error it means that a library for a > particular > package (in this case flowCore) and architecture (in this case x86_64) is > missing. > This looks to me like he installed a binary package built for 2.12 but is using R 2.13. But your solution of reinstalling from Bioc should work anyway. > This can happen when you build packages from source. There are ways to > build > packages for all architectures (see > > http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Building- universal-package > ), > however, it's much simpler to download the binary version of the package > that bioconductor supplies. You can do this by always supplying the > type="mac.binary.leopard" argument to biocLite. > > So, reinstall flowCore as follows: > > biocLite("flowCore", type="mac.binary.leopard") > > Then try again to run iFlow and if you get a similar error but referring to > a different package, install that package with the > type="mac.binary.leopard" > argument. > > You probably want to do binary installs by default, so you can put this > line: > > options("pkgType" = "mac.binary.leopard") > > in your ~/.Rprofile file and it will be the default, so you won't have to > supply the "type" argument to biocLite() any more. > > Hope this helps > Dan > > > > > > > Error: package 'flowCore' could not be loaded > > > > > > ________________________________________ > > From: Dan Tenenbaum [dtenenba@fhcrc.org] > > Sent: March 14, 2011 3:30 PM > > To: Gabriel Nathan Kaufman, Mr; > bioconductor@stat.math.ethz.chbioconductor > > Subject: Re: [BioC] iFlow/flowCore installation problem > > > > Thanks! Let me know and keep it on the list as well so we can all > > benefit from what you find out. > > Dan > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]