sigcheck 'clear_cluster' receive data failed error
0
0
Entering edit mode
@shamim-sarhadi-9395
Last seen 7.6 years ago

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 • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6