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Question: chipenrich - Error in .simpleInheritanceGeneric(fdef)
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gravatar for pierre-francois.roux
14 months ago by
France
pierre-francois.roux0 wrote:

Dear all,

I use chipenrich for quite a long time now, and it always worked perfectly fine.  But for any reason, while trying to run it now, I get the following error :

> library(chipenrich.data)
> library(chipenrich)
> 
> # Run ChipEnrich using an example dataset, assigning peaks to the nearest TSS, 
> # testing all Biocarta and Panther pathways
> data(peaks_E2F4)
> results = chipenrich(peaks_E2F4,method='chipenrich',locusdef='nearest_tss',
+                      genesets=c('biocarta_pathway','panther_pathway'),out_name=NULL)
Error in .simpleInheritanceGeneric(fdef) : 
  pile de noeuds débordée vers le haut
Erreur pendant l'emballage (wrapup) : pile de noeuds débordée vers le haut

As far as I understand (sorry, the error message is in French, but the translation would be something like "node stack overflow"), it's related to the parallel environment. But even when working only on one core (using the option n_cores = 1) i still get this error.

I tried again after making a fresh and clean install of R 3.3.1 but I am still getting the same message.

Has someone already experienced this kind of issue ?

 Thanks a lot,

Pierre-François

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] chipenrich.data_1.8.0                   plyr_1.8.4                              chipenrich_1.10.0                      
 [4] PWMEnrich.Hsapiens.background_4.6.0     PWMEnrich_4.8.2                         BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [7] BSgenome_1.40.1                         zoo_1.7-13                              ComplexHeatmap_1.10.2                  
[10] circlize_0.3.8                          org.Hs.eg.db_3.3.0                      TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.3
[13] GenomicFeatures_1.24.5                  AnnotationDbi_1.34.4                    Gviz_1.16.5                            
[16] edgeR_3.14.0                            limma_3.28.21                           pheatmap_1.0.8                         
[19] gplots_3.0.1                            ggplot2_2.1.0                           reshape2_1.4.1                         
[22] csaw_1.6.1                              rtracklayer_1.32.2                      R.utils_2.4.0                          
[25] R.oo_1.20.0                             R.methodsS3_1.7.1                       QuasR_1.12.0                           
[28] Rbowtie_1.12.0                          ShortRead_1.30.0                        GenomicAlignments_1.8.4                
[31] SummarizedExperiment_1.2.3              Biobase_2.32.0                          Rsamtools_1.24.0                       
[34] GenomicRanges_1.24.3                    GenomeInfoDb_1.8.7                      Biostrings_2.40.2                      
[37] XVector_0.12.1                          IRanges_2.6.1                           S4Vectors_0.10.3                       
[40] BiocParallel_1.6.6                      BiocGenerics_0.18.0                     BiocInstaller_1.22.3                   

loaded via a namespace (and not attached):
 [1] Hmisc_3.17-4                  AnnotationHub_2.4.2           splines_3.3.1                 TH.data_1.0-7                 digest_0.6.10                
 [6] ensembldb_1.4.7               htmltools_0.3.5               gdata_2.17.0                  magrittr_1.5                  cluster_2.0.4                
[11] matrixStats_0.50.2            sandwich_2.3-4                colorspace_1.2-6              RCurl_1.95-4.8                survival_2.39-5              
[16] VariantAnnotation_1.18.7      gtable_0.2.0                  zlibbioc_1.18.0               MatrixModels_0.4-1            GetoptLong_0.1.4             
[21] kernlab_0.9-24                evd_2.3-2                     shape_1.4.2                   rms_4.5-0                     prabclus_2.2-6               
[26] DEoptimR_1.0-6                SparseM_1.72                  scales_0.4.0                  mvtnorm_1.0-5                 DBI_0.5-1                    
[31] Rcpp_0.12.7                   xtable_1.8-2                  foreign_0.8-67                mclust_5.2                    Formula_1.2-1                
[36] httr_1.2.1                    RColorBrewer_1.1-2            fpc_2.1-10                    acepack_1.3-3.3               modeltools_0.2-21            
[41] XML_3.98-1.4                  flexmix_2.3-13                nnet_7.3-12                   locfit_1.5-9.1                labeling_0.3                 
[46] munsell_0.4.3                 tools_3.3.1                   RSQLite_1.0.0                 stringr_1.1.0                 knitr_1.14                   
[51] robustbase_0.92-6             caTools_1.17.1                dendextend_1.3.0              nlme_3.1-128                  whisker_0.3-2                
[56] mime_0.5                      quantreg_5.29                 biomaRt_2.28.0                Rhtslib_1.4.3                 interactiveDisplayBase_1.10.3
[61] statmod_1.4.26                stringi_1.1.1                 GenomicFiles_1.8.0            lattice_0.20-34               trimcluster_0.1-2            
[66] Matrix_1.2-7.1                GlobalOptions_0.0.10          data.table_1.9.6              bitops_1.0-6                  httpuv_1.3.3                 
[71] R6_2.1.3                      latticeExtra_0.6-28           hwriter_1.3.2                 KernSmooth_2.23-15            gridExtra_2.2.1              
[76] codetools_0.2-14              polspline_1.1.12              dichromat_2.0-0               MASS_7.3-45                   gtools_3.5.0                 
[81] seqLogo_1.38.0                chron_2.3-47                  openssl_0.9.4                 rjson_0.2.15                  multcomp_1.4-6               
[86] diptest_0.75-7                mgcv_1.8-15                   rpart_4.1-10                  class_7.3-14                  biovizBase_1.20.0
ADD COMMENTlink written 14 months ago by pierre-francois.roux0
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