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 >> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Karin Breuer Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada Phone: +1 (604) 675-8000 x 7755