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xlucpu / MOVICS

Multi-Omics integration and VIsualization in Cancer Subtyping
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Error: C stack usage 7969424 is too close to the limit #3

Closed JianGuoZhou3 closed 3 years ago

JianGuoZhou3 commented 3 years ago 
> cmoic.brca <- getConsensusMOIC(moic.res.list = moic.res.list,
+                                fig.name      = "CONSENSUS HEATMAP",
+                                distance      = "euclidean",
+                                linkage       = "average")
Error: C stack usage  7969424 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969328 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969360 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969376 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969248 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969312 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969296 is too close to the limit
Graphics error: Plot rendering error

my PC information

 sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] dplyr_1.0.2         MOVICS_0.99.5       Biobase_2.50.0     
[4] BiocGenerics_0.36.0 kableExtra_1.3.1    knitr_1.30         

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1              CIMLR_1.0.0                
  [3] tableone_0.12.0             oompaData_3.1.1            
  [5] InterSIM_2.2.0              ggpmisc_0.3.6              
  [7] pkgmaker_0.32.2             tidyr_1.1.2                
  [9] ggplot2_3.3.2               bit64_4.0.5                
 [11] irlba_2.3.3                 DelayedArray_0.16.0        
 [13] data.table_1.13.2           RCurl_1.98-1.2             
 [15] doParallel_1.0.16           generics_0.1.0             
 [17] preprocessCore_1.52.0       cowplot_1.1.0              
 [19] RSQLite_2.2.1               shadowtext_0.0.7           
 [21] bit_4.0.4                   enrichplot_1.10.0          
 [23] webshot_0.5.2               xml2_1.3.2                 
 [25] SummarizedExperiment_1.20.0 assertthat_0.2.1           
 [27] viridis_0.5.1               xfun_0.19                  
 [29] hms_0.5.3                   evaluate_0.14              
 [31] caTools_1.18.0              readxl_1.3.1               
 [33] km.ci_0.5-2                 igraph_1.2.6               
 [35] DBI_1.1.0                   geneplotter_1.68.0         
 [37] stats4_4.0.2                purrr_0.3.4                
 [39] ellipsis_0.3.1              iClusterPlus_1.26.0        
 [41] ggpubr_0.4.0                backports_1.2.0            
 [43] permute_0.9-5               survey_4.0                 
 [45] geepack_1.3-1               annotate_1.68.0            
 [47] gridBase_0.4-7              RcppParallel_5.0.2         
 [49] MatrixGenerics_1.2.0        vctrs_0.3.4                
 [51] ggalluvial_0.12.2           Cairo_1.5-12.2             
 [53] maftools_2.6.0              jstable_1.0.0              
 [55] entropy_1.2.1               abind_1.4-5                
 [57] withr_2.3.0                 ggforce_0.3.2              
 [59] bdsmatrix_1.3-4             checkmate_2.0.0            
 [61] vegan_2.5-6                 mclust_5.4.6               
 [63] cluster_2.1.0               DOSE_3.16.0                
 [65] alluvial_0.1-2              CMScaller_0.99.2           
 [67] crayon_1.3.4                genefilter_1.72.0          
 [69] edgeR_3.32.0                pkgconfig_2.0.3            
 [71] tweenr_1.0.1                GenomeInfoDb_1.26.0        
 [73] nlme_3.1-148                rlang_0.4.8                
 [75] lifecycle_0.2.0             downloader_0.4             
 [77] registry_0.5-1              cellranger_1.1.0           
 [79] polyclip_1.10-0             GSVA_1.38.0                
 [81] matrixStats_0.57.0          PINSPlus_2.0.5             
 [83] pamr_1.56.1                 graph_1.68.0               
 [85] rngtools_1.5                Matrix_1.2-18              
 [87] KMsurv_0.1-5                carData_3.0-4              
 [89] heatmap.plus_1.3            boot_1.3-25                
 [91] zoo_1.8-8                   GlobalOptions_0.1.2        
 [93] png_0.1-7                   viridisLite_0.3.0          
 [95] rjson_0.2.20                oompaBase_3.2.9            
 [97] bitops_1.0-6                ConsensusClusterPlus_1.54.0
 [99] KernSmooth_2.23-17          blob_1.2.1                 
[101] shape_1.4.5                 stringr_1.4.0              
[103] qvalue_2.22.0               rstatix_0.6.0              
[105] S4Vectors_0.28.0            ggsignif_0.6.0             
[107] scales_1.1.1                memoise_1.1.0              
[109] graphite_1.36.0             GSEABase_1.52.0            
[111] magrittr_1.5                plyr_1.8.6                 
[113] gplots_3.1.0                zlibbioc_1.36.0            
[115] compiler_4.0.2              scatterpie_0.1.5           
[117] mogsa_1.24.0                RColorBrewer_1.1-2         
[119] lme4_1.1-25                 clue_0.3-57                
[121] DESeq2_1.30.0               XVector_0.30.0             
[123] patchwork_1.0.1             MASS_7.3-51.6              
[125] mgcv_1.8-31                 tidyselect_1.1.0           
[127] stringi_1.5.3               forcats_0.5.0              
[129] prettyGraphs_2.1.6          mitools_2.4                
[131] GOSemSim_2.16.1             locfit_1.5-9.4             
[133] ggrepel_0.8.2               survMisc_0.5.5             
[135] grid_4.0.2                  fastmatch_1.1-0            
[137] tools_4.0.2                 rio_0.5.16                 
[139] uuid_0.1-4                  circlize_0.4.11            
[141] rstudioapi_0.11             foreach_1.5.1              
[143] foreign_0.8-80              clusterRepro_0.9           
[145] coxme_2.2-16                gridExtra_2.3              
[147] farver_2.0.3                ggraph_2.0.3               
[149] digest_0.6.27               rvcheck_0.1.8              
[151] BiocManager_1.30.10         flexclust_1.4-0            
[153] FNN_1.1.3                   Rcpp_1.0.5                 
[155] GenomicRanges_1.42.0        car_3.0-10                 
[157] ClassDiscovery_3.3.12       broom_0.7.2                
[159] httr_1.4.2                  survminer_0.4.8            
[161] AnnotationDbi_1.52.0        ComplexHeatmap_2.7.1       
[163] colorspace_1.4-1            rvest_0.3.6                
[165] XML_3.99-0.5                IRanges_2.24.0             
[167] splines_4.0.2               statmod_1.4.35             
[169] graphlayouts_0.7.1          xtable_1.8-4               
[171] nloptr_1.2.2.2              SNFtool_2.3.0              
[173] tidygraph_1.2.0             corpcor_1.6.9              
[175] modeltools_0.2-23           ExPosition_2.8.23          
[177] R6_2.5.0                    ridge_2.7                  
[179] pillar_1.4.6                htmltools_0.5.0            
[181] NMF_0.23.0                  minqa_1.2.4                
[183] glue_1.4.2                  clusterProfiler_3.18.0     
[185] BiocParallel_1.24.1         class_7.3-17               
[187] codetools_0.2-16            aricode_1.0.0              
[189] fgsea_1.16.0                lattice_0.20-41            
[191] tibble_3.0.4                sva_3.38.0                 
[193] curl_4.3                    svd_0.5                    
[195] officer_0.3.15              gtools_3.8.2               
[197] IntNMF_1.2.0                zip_2.1.1                  
[199] GO.db_3.12.1                openxlsx_4.2.3             
[201] coca_1.1.0                  survival_3.1-12            
[203] limma_3.46.0                rmarkdown_2.5              
[205] munsell_0.5.0               DO.db_2.9                  
[207] GetoptLong_1.0.4            GenomeInfoDbData_1.2.4     
[209] iterators_1.0.13            labelled_2.7.0             
[211] impute_1.64.0               haven_2.3.1                
[213] reshape2_1.4.4              gtable_0.3.0

However,

according to those links: https://sr-c.github.io/2019/02/16/Error-C-stack-usage-is-too-close-to-the-limit/ https://github.com/LifeWorks/biojazz/issues/9

(base) [zhou@localhost strelka2]$ ulimit -s 16384
(base) [zhou@localhost strelka2]$ R --slave -e 'Cstack_info()["size"]'
    size 
15938355 
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -m unlimited
(base) [zhou@localhost strelka2]$ ulimit -s unlimited
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ conda activate strelka2
xlucpu commented 3 years ago

It doesn't seem to be the problem of MOVICS but your computer setup. I therefore close this issue.