[BioC] flowQ qaProcess fails to run in both Windows and Mac OS: What am I doing wrong?

[Jason Eriksen [guest]]

Hi everyone,

I am a newcomer to R and Bioconductor. I have been working to set up flow cytometry packages for analysis of data from our instrument. For a native R package, I've installed flowCore, flowQ, flowViz and flowStats libaries, and have been following along with the tutorials (i.e. file:///C:/Program%20Files/R/R-2.15.3/library/flowQ/doc/DataQualityAssessment.pdf).

However, despite best efforts, and trying installs in both Windows and Linux, the qaProcess fails to run in the flowQ library. It looks like there might be a missing library, but frankly I'm stumped as to how to procede. 

I would greatly appreciate your advice!

Jason

Here is an example, taken from the flowCore tutorial, where the program fails and generates an error. I have little idea what these errors mean.

> library(flowQ)
> data(GvHD)
> GvHD <- GvHD[1:10]
> dest <- file.path(tempdir(), "flowQ")
> qp1 <- qaProcess.cellnumber(GvHD, outdir=dest, cFactor=0.75)
creating summary plots...Error in if (scaleFac != 1) newDims <- dims * scaleFac : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: running command 'C:\Windows\system32\cmd.exe /c identify "C:/Users/jeriksen/AppData/Local/Temp/RtmpyWMjlk/flowQ/images/rQ2ZMUQHWQ/summary.pdf"' had status 1 
2: In .local(.Object, ...) : NAs introduced by coercion


 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)

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     grid      splines   stats     graphics  grDevices
 [7] utils     datasets  methods   base     

other attached packages:
 [1] flowQ_1.18.0          latticeExtra_0.6-24   RColorBrewer_1.0-5   
 [4] parody_1.16.0         bioDist_1.30.0        KernSmooth_2.23-10   
 [7] outliers_0.14         flowStats_1.16.0      flowWorkspace_1.4.0  
[10] hexbin_1.26.2         IDPmisc_1.1.17        flowViz_1.22.0       
[13] XML_3.96-1.1          RBGL_1.34.0           graph_1.36.2         
[16] Cairo_1.5-2           cluster_1.14.4        mvoutlier_1.9.9      
[19] sgeostat_1.0-25       robCompositions_1.6.3 car_2.0-16           
[22] nnet_7.3-6            compositions_1.30-1   energy_1.5.0         
[25] MASS_7.3-23           boot_1.3-7            tensorA_0.36         
[28] rgl_0.93.935          fda_2.3.4             Matrix_1.0-12        
[31] lattice_0.20-15       zoo_1.7-9             flowCore_1.24.2      
[34] rrcov_1.3-3           pcaPP_1.9-49          mvtnorm_0.9-9994     
[37] robustbase_0.9-7      Biobase_2.18.0        BiocGenerics_0.4.0   
[40] BiocInstaller_1.8.3  

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.7 DBI_0.2-6           
 [4] feature_1.2.8        geneplotter_1.36.0   IRanges_1.16.6      
 [7] ks_1.8.12            parallel_2.15.3      RSQLite_0.11.3      
[10] stats4_2.15.3        xtable_1.7-1 

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