[BioC] Sudden Issue with add for lymphGate in flowCore

[Aric Gregson]

Hello,

I have an odd issue that I have been unable thus far to resolve. 
Literally overnight it has become impossible to add a lymphGate filter 
to a workFlow. This is specific for the lymphGate filter only, as any 
other type of filter works just fine. The error that I am receiving is 
shown after the Sweave output here. It happens regardless of whether 
the code is run in Sweave or manually in R. 

[snip]
10 : echo keep.source term verbatim (label = 
createWorkFlowBoundaryTransformLogicle)
11 : echo keep.source term verbatim (label = LiveDeadUVFilterAlt)
12 : keep.source term tex (label = summaryLive)
13 : echo keep.source term verbatim pdf (label = plotLiveDead)
14 : keep.source (label = LiveDeadUVFiltercd3)
15 : keep.source (label = plotLiveDeadcd3)
16 : echo keep.source term verbatim (label = singletfilterCreate)
17 : echo keep.source term verbatim pdf (label = plotSingletfilter)
18 : echo keep.source term verbatim (label = lymphocyteFilterCD4CD3)
19 : echo keep.source term verbatim (label = add.lymph.Gate)

Error:  chunk 19 (label = add.lymph.Gate) 
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "add", for signature 
"workFlow", "list"
In addition: Warning messages:
1: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
3: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
5: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
6: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
7: In readBin(con, dattype, n = (offsets["dataend"] - 
offsets["datastart"] +  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2


The only difference overnight is that I 'upgraded' the tcl/tk package 
on my computer. Since then I have reinstalled R and ran 
upgrade.packages for both R and Bioconductor, but the problem persists. 
I suspect I have not provided enough information here. Any ideas on how 
to figure this out would be greatly appreciated.

Thanks, Aric
-----------------

 sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: amd64-portbld-freebsd9.0 (64-bit)

locale:
[1] C

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

other attached packages:
 [1] xtable_1.6-0          Rgraphviz_1.30.1      flowQ_1.12.0         
 [4] latticeExtra_0.6-19   RColorBrewer_1.0-5    parody_1.10.0        
 [7] bioDist_1.24.1        KernSmooth_2.23-7     outliers_0.14        
[10] flowStats_1.13.0      cluster_1.14.1        mvoutlier_1.9.4      
[13] robCompositions_1.5.0 car_2.0-11            survival_2.36-10     
[16] nnet_7.3-1            compositions_1.10-2   energy_1.4-0         
[19] MASS_7.3-14           boot_1.3-2            tensorA_0.36         
[22] rgl_0.92.798          fda_2.2.7             zoo_1.7-6            
[25] flowWorkspace_0.99.22 IDPmisc_1.1.16        flowViz_1.16.0       
[28] lattice_0.19-33       flowCore_1.18.0       rrcov_1.3-01         
[31] pcaPP_1.9-44          mvtnorm_0.9-9991      robustbase_0.7-8     
[34] Biobase_2.12.2        XML_3.4-3             RBGL_1.29.0          
[37] graph_1.30.0          multicore_0.1-7       Rmpi_0.5-9           
[40] fortunes_1.4-2       

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.14.1 DBI_0.2-5            RSQLite_0.10.0      
[4] annotate_1.30.1      feature_1.2.8        geneplotter_1.30.0  
[7] ks_1.8.4             stats4_2.13.2