Entering edit mode
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