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

Karin Breuer kbreuer at bccrc.ca
Sat Jul 24 00:51:51 CEST 2010


Thanks for your reply, Nishant!

Yes, ImageMagic is available - below is the full output when I load 
flowQ. Unfortunately I can't try any other Windows machines because I 
don't have administrator rights. Which XServer have you set up with 
ImageMagick?

Thanks,
Karin

# 
-----------------------------------------------------------------------------------------------------------------------------
 > library(flowQ)
Loading required package: outliers
Loading required package: lattice
Loading required package: flowViz
Loading required package: flowCore
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. 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 1.0-01)

Attaching package: 'flowCore'

The following object(s) are masked from 'package:stats':

     alias, filter

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: mvoutlier
Loading required package: bioDist
Loading required package: KernSmooth
Loading required package: parody
Loading required package: tools
Loading required package: RColorBrewer
Loading required package: latticeExtra

Attaching package: 'latticeExtra'

The following object(s) are masked from 'package:flowViz':

     ecdfplot

Using ImageMagic library at .
(version 6.6.3)



On 10-07-23 02:29 PM, Nishant Gopalakrishnan wrote:
> 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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>>      
>    


-- 
Karin Breuer
Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada

Phone: +1 (604) 675-8000 x 7755



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