[BioC] iFlow/flowCore installation problem

[Gabriel Nathan Kaufman, Mr]

 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?



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 at fhcrc.org]

Sent: March 13, 2011 4:37 PM

To: Gabriel Nathan Kaufman, Mr

Cc: bioconductor at 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