Dear all!

I am trying to move my flow analysis to Bioconductor's flow packages, but I ran into trouble.

I can create a GatingSet object and properly apply my gating steps manually or use openCyto to do it for me, but getPopStats() with format="wide" fails spectacularly (see below for the full traceback).

Here is a reproducible example:

library(flowWorkspace)
data(GvHD)

dat <- GvHD[1:4]
gs <- GatingSet(dat)
gate <- rectangleGate(filterId="randomGate", .gate=list("FSC-H"=c(250, 500), "SSC-H"=c(200, 400)))
add(gs, gate)
getPopStats(gs, format="long") # works
getPopStats(gs, format="wide") # breaks

Actually, it breaks even when I do not add the gate at all, but call getPopStats on the empty GatingSet. Is this a problem with the package, or is it on my end only? Thank you for your ideas!

VT

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] flowWorkspace_3.16.9      gridExtra_2.0.0          
[3] ncdfFlow_2.16.0           BH_1.58.0-1              
[5] RcppArmadillo_0.6.400.2.2 flowViz_1.34.0           
[7] lattice_0.20-33           flowCore_1.36.4          

loaded via a namespace (and not attached):
 [1] pcaPP_1.9-60        Rcpp_0.12.2         DEoptimR_1.0-4     
 [4] RColorBrewer_1.1-2  flowUtils_1.34.0    tools_3.2.3        
 [7] zlibbioc_1.16.0     jsonlite_0.9.19     gtable_0.1.2       
[10] graph_1.48.0        DBI_0.3.1           Rgraphviz_2.14.0   
[13] parallel_3.2.3      mvtnorm_1.0-3       hexbin_1.27.1      
[16] stringr_1.0.0       dplyr_0.4.3         cluster_2.0.3      
[19] IDPmisc_1.1.17      stats4_3.2.3        grid_3.2.3         
[22] robustbase_0.92-5   Biobase_2.30.0      data.table_1.9.6   
[25] rrcov_1.3-8         R6_2.1.1            XML_3.98-1.3       
[28] RBGL_1.46.0         latticeExtra_0.6-26 magrittr_1.5       
[31] corpcor_1.6.8       MASS_7.3-45         BiocGenerics_0.16.1
[34] RUnit_0.4.31        assertthat_0.1      KernSmooth_2.23-15
[37] stringi_1.0-1       chron_2.3-47     

The traceback can be found at http://pastebin.com/KQWiYLQv

I got rid of the compilation error after downgrading the BH package to 1.58.0-1, which got bumped to 1.60 during an auto-update. Neither flowCore nor flowWorkspace seem to currently like this.

After recompilation, I also got rid of the segfault, so I guess that fixed itself. Thanks for your input, though!

You need to run

recompute(gs)

after any gate is added.