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

[Dan Tenenbaum]

On Mon, May 6, 2013 at 1:56 PM, Jason Eriksen [guest]
<guest at bioconductor.org> wrote:
>
> 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.
>

Which operating systems did you try it on? Your subject line says
Windows and Mac OS, but your email says Windows and Linux. (Note that
flowQ support in Windows was dropped in Bioconductor releases
subsequent to the one you are using).

> 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
>
>

This suggests that perhaps ImageMagick is not installed. It needs to
be installed with the directory containing its executables (identify,
convert, etc) in your PATH.

Dan


>  -- 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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