If I try to replicate the vignette of openCyto, I get following error with automatic gating:

gating(gt_tcell, gs)
error in UseMethod("alias") :
  no method for 'alias' for object class "gtPopulation"

trying to plot the hierarchy leads to:

> plot(gs[[1]])
error in as.double(y) :
  cannot coerce type 'S4' to vector of type 'double'

Any ideas what could go wrong ?

kind regards

Thomas

Here is the result of sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-suse-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8       
 [4] LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] pracma_1.7.0          data.table_1.9.2      openCyto_1.2.11       flowWorkspace_3.10.09
[5] gridExtra_0.9.1       ncdfFlow_2.10.30      flowViz_1.28.22       lattice_0.20-29      
[9] flowCore_1.30.7      

loaded via a namespace (and not attached):
 [1] Biobase_2.24.0        BiocGenerics_0.10.0   clue_0.3-48           cluster_1.15.3       
 [5] coda_0.16-1           colorspace_1.2-4      corpcor_1.6.7         DEoptimR_1.0-1       
 [9] digest_0.6.4          fda_2.4.3             flowClust_3.4.10      flowStats_3.22.6     
[13] GGally_0.4.8          ggplot2_1.0.0         graph_1.42.0          gtable_0.1.2         
[17] gtools_3.4.1          hexbin_1.27.0         IDPmisc_1.1.17        KernSmooth_2.23-12   
[21] ks_1.9.3              latticeExtra_0.6-26   MASS_7.3-35           Matrix_1.1-4         
[25] MCMCpack_1.3-3        misc3d_0.8-4          munsell_0.4.2         mvoutlier_2.0.5      
[29] mvtnorm_1.0-0         parallel_3.1.1        pcaPP_1.9-50          pls_2.4-3            
[33] plyr_1.8.1            proto_0.3-10          R.methodsS3_1.6.1     R.oo_1.18.0          
[37] R.utils_1.33.0        RBGL_1.41.0           RColorBrewer_1.0-5    Rcpp_0.11.3          
[41] reshape_0.8.5         reshape2_1.4          rgl_0.94.1131         Rgraphviz_2.8.1      
[45] robCompositions_1.9.0 robustbase_0.91-1     rrcov_1.3-4           scales_0.2.4         
[49] sgeostat_1.0-25       stats4_3.1.1          stringr_0.6.2         tools_3.1.1          
[53] XML_3.98-1.1          zlibbioc_1.10.0

The problem is solved. OpenCyto and data.table were loaded twice which they apparently did not like. It works now perfectly.