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
>

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