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

[Nishant Gopalakrishnan]

Hi Karin,

I tried your example  with R 2.11.1 , flowQ 1.8.0  and Image magic 6.6.3
on Windows XP, but was unable to reproduce the error you got. 
Do you have Image magic available on your system path ? .

Nishant

#--------------------------------------------------------------------------
Using ImageMagic library at .
(version 6.6.3)
> 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)
> g
QA process image information
> g <- qaGraph(imageDir=idir, empty=TRUE)
> g
QA process image information
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

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

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

other attached packages:
 [1] flowQ_1.8.0         latticeExtra_0.6-11 RColorBrewer_1.0-2
 [4] parody_1.6.0        bioDist_1.20.0      KernSmooth_2.23-3 
 [7] mvoutlier_1.4       flowViz_1.12.0      flowCore_1.14.1   
[10] rrcov_1.0-01        pcaPP_1.8-1         mvtnorm_0.9-92    
[13] 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_1.26.1      AnnotationDbi_1.10.2 DBI_0.2-5          
 [4] feature_1.2.4        geneplotter_1.26.0   graph_1.26.0       
 [7] grid_2.11.1          ks_1.6.13            MASS_7.3-6         
[10] RSQLite_0.9-1        stats4_2.11.1        xtable_1.5-6

On 07/19/2010 01:18 PM, Karin Breuer wrote:
> 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
> >
>
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