[BioC] flowQ on WinXP: Error in matrix for dimnames

[Karin Breuer]

Hello everybody,

I am trying to get flowQ running on Windows XP 2002 Professional SP3 
(ImageMagic 6.6.3). It's running fine on Linux, but for some reason I 
get the following error when trying to reproduce the code for basic 
functions from the vignette (both for R2.10.1 and R2.11.1) - it does 
create the correct output files, though:


Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = 
list(ft,  :
   length of 'dimnames' [1] not equal to array extent


See below for full output and sessionInfo.

I am quite stuck right now and would appreciate any thoughts on this.
Many thanks!
Karin


PS: Also, is there a way to prevent flowQ to use the default "convert" 
command on a Windows system which hasn't ImageMagic installed? It 
totally tries to reformat the file system.


------------------------------------------------------------
 > library(flowQ)
 > options(width=70)
 > binaryAggregator()
Binary quality score passing the requirements
 > discreteAggregator(2)
Discrete quality score not passing the requirements with state warn
 > factorAggregator(factor("a", levels=letters[1:3]))
Factorized quality score passing the requirements of value=a
 > stringAggregator("test", passed=FALSE)
Textual quality score not passing the requirements of value=test
 > numericAggregator(20)
Numeric quality score passing the requirements of value=20
 > rangeAggregator(10, 0, 100)
Range quality score passing the requirements of value=10
 > aggregatorList(bin=binaryAggregator(FALSE), disc=discreteAggregator(1))
List of 2 aggregators
 > tmp <- tempdir()
 > fn <- file.path(tmp, "test.jpg")
 > jpeg(file=fn)
 > plot(1:3)
 > dev.off()
null device
           1
 > idir <- file.path(tmp, "images")
 > g <- qaGraph(fn, imageDir=idir)
'\\sharename\home\homename'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
Error in matrix(c(dims, newDims), ncol = 2, byrow = TRUE, dimnames = 
list(ft,  :
   length of 'dimnames' [1] not equal to array extent
 > g
Error: object 'g' not found
 > qaGraph(imageDir=idir, empty=TRUE)
QA process image information




 > sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  
methods   base

other attached packages:
  [1] flowQ_1.8.0         latticeExtra_0.6-11 RColorBrewer_1.0-2  
parody_1.6.0        bioDist_1.20.0
  [6] KernSmooth_2.23-3   mvoutlier_1.4       flowViz_1.12.0      
flowCore_1.14.1     rrcov_1.0-01
[11] pcaPP_1.8-1         mvtnorm_0.9-9       robustbase_0.5-0-1  
Biobase_2.8.0       lattice_0.18-8
[16] outliers_0.13-2

loaded via a namespace (and not attached):
  [1] annotate_1.26.0      AnnotationDbi_1.10.1 DBI_0.2-5            
feature_1.2.4        geneplotter_1.26.0
  [6] graph_1.26.0         grid_2.11.1          ks_1.6.13            
MASS_7.3-6           RSQLite_0.9-1
[11] stats4_2.11.1        xtable_1.5-6
 >