sigcheck 'clear_cluster' receive data failed error
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Entering edit mode
@shamim-sarhadi-9395
Last seen 5 months ago
Germany

Hi

I am using sigcheck package to validate my signature I run these codes

library(breastCancerNKI)
library(SigCheck)
data(nki)
data(knownSignatures)
nki <- nki[,!is.na(nki$e.os)]
check <- sigCheck(nki, classes="e.os", survival="t.os",signature=mysignature,annotation="HUGO.gene.symbol",validationSamples=which(nki$series=="NKI2"))
nkiResults <- sigCheckAll(check, iterations=1000)

 

but I get this error: 

Error: stop worker failed:
 'clear_cluster' receive data failed:
 reached elapsed time limit

my sessioninfo:

 sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] SigCheck_2.4.0         survival_2.39-4        BiocParallel_1.6.2    
 [4] e1071_1.6-7            MLInterfaces_1.52.0    cluster_2.0.4         
 [7] annotate_1.50.0        XML_3.98-1.4           AnnotationDbi_1.34.3  
[10] IRanges_2.6.1          S4Vectors_0.10.1       Biobase_2.32.0        
[13] BiocGenerics_0.18.0    breastCancerNKI_1.10.0 BiocInstaller_1.22.3  

loaded via a namespace (and not attached):
 [1] mclust_5.2         rgl_0.95.1441      Rcpp_0.12.5        mvtnorm_1.0-5     
 [5] lattice_0.20-33    class_7.3-14       snow_0.4-1         gtools_3.5.0      
 [9] assertthat_0.1     digest_0.6.9       mime_0.4           R6_2.1.2          
[13] RSQLite_1.0.0      rda_1.0.2-2        diptest_0.75-7     gdata_2.17.0      
[17] kernlab_0.9-24     rpart_4.1-10       Matrix_1.2-6       splines_3.3.1     
[21] htmlwidgets_0.6    shiny_0.13.2       httpuv_1.3.3       base64enc_0.1-3   
[25] gbm_2.1.1          htmltools_0.3.5    nnet_7.3-12        tibble_1.0        
[29] threejs_0.2.2      dplyr_0.5.0        MASS_7.3-45        grid_3.3.1        
[33] jsonlite_0.9.22    xtable_1.8-2       DBI_0.4-1          magrittr_1.5      
[37] ggvis_0.4.2        hwriter_1.3.2      genefilter_1.54.2  flexmix_2.3-13    
[41] robustbase_0.92-6  pls_2.5-0          RColorBrewer_1.1-2 tools_3.3.1       
[45] fpc_2.1-10         trimcluster_0.1-2  DEoptimR_1.0-4     sfsmisc_1.1-0     
[49] prabclus_2.2-6     mlbench_2.1-1      modeltools_0.2-21 

Thanks in advance

 
sigchek software error • 1.1k views
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