Rstudio crashes when running monocole
Entering edit mode
Assa Yeroslaviz ★ 1.5k
Last seen 8 days ago


i am trying to run the monocole package on my macBook, but when running the command 

CellData <- monocle::newCellDataSet(ddata, phenoData = pdata, featureData = fdata)

Rstudio just crashes without any warnings at all. 

I have read that monocole doesn't work with too many genes. the d object  is a 894x255 matrix, which supposedly should work with monocole.

Any ideas, why this is happening?

Is it a macBook problem or there is something wrong with the data?



> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.4 (Sierra)
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] R.utils_2.5.0 R.oo_1.21.0 R.methodsS3_1.7.1 Seurat_1.4.0.14
[5] cowplot_0.7.0 SLICER_0.2.0 alphahull_2.1 lle_1.1
[9] snowfall_1.84-6.1 snow_0.4-2 MASS_7.3-47 scatterplot3d_0.3-40
[13] igraph_1.0.1 destiny_2.0.8 monocle_2.2.0 DDRTree_0.1.4
[17] irlba_2.1.2 VGAM_1.0-3 ggplot2_2.2.1 Biobase_2.34.0
[21] BiocGenerics_0.20.0 Matrix_1.2-8 M3Drop_1.0.0 numDeriv_2016.8-1
[25] TSCAN_1.12.0

loaded via a namespace (and not attached):
[1] backports_1.0.5 Hmisc_4.0-2 RcppEigen_0.
[4] sn_1.5-0 plyr_1.8.4 lazyeval_0.2.0
[7] shinydashboard_0.5.3 sp_1.2-4 fastICA_1.2-0
[10] digest_0.6.12 foreach_1.4.3 htmltools_0.3.6
[13] viridis_0.4.0 lars_1.2 gdata_2.17.0
[16] memoise_1.1.0 magrittr_1.5 checkmate_1.8.2
[19] tensor_1.5 cluster_2.0.6 mixtools_1.1.0
[22] ROCR_1.0-7 limma_3.30.13 tripack_1.3-8
[25] matrixStats_0.52.2 xts_0.9-7 colorspace_1.3-2
[28] dplyr_0.5.0 RCurl_1.95-4.8 lme4_1.1-13
[31] spatstat_1.50-0 iterators_1.0.8 survival_2.41-3
[34] zoo_1.8-0 ape_4.1 polyclip_1.6-1
[37] gtable_0.2.0 MatrixModels_0.4-1 car_2.1-4
[40] kernlab_0.9-25 prabclus_2.2-6 DEoptimR_1.0-8
[43] abind_1.4-5 SparseM_1.77 VIM_4.7.0
[46] scales_0.4.1 sgeostat_1.0-27 pheatmap_1.0.8
[49] mvtnorm_1.0-6 DBI_0.6-1 Rcpp_0.12.10
[52] viridisLite_0.2.0 xtable_1.8-2 laeken_0.4.6
[55] htmlTable_1.9 tclust_1.2-3 foreign_0.8-68
[58] proxy_0.4-16 mclust_5.2.3 Formula_1.2-1
[61] tsne_0.1-3 vcd_1.4-3 htmlwidgets_0.8
[64] FNN_1.1 gplots_3.0.1 RColorBrewer_1.1-2
[67] fpc_2.1-10 acepack_1.4.1 modeltools_0.2-21
[70] XML_3.98-1.6 flexmix_2.3-14 nnet_7.3-12
[73] deldir_0.1-14 caret_6.0-76 AnnotationDbi_1.36.2
[76] reshape2_1.4.2 munsell_0.4.3 tools_3.3.1
[79] RSQLite_1.1-2 ranger_0.7.0 splancs_2.01-40
[82] stringr_1.2.0 goftest_1.1-1 ModelMetrics_1.1.0
[85] knitr_1.15.1 robustbase_0.92-7 caTools_1.17.1
[88] pbapply_1.3-2 nlme_3.1-131 mime_0.5
[91] quantreg_5.33 slam_0.1-40 biomaRt_2.30.0
[94] pbkrtest_0.4-7 e1071_1.6-8 spatstat.utils_1.4-1
[97] smoother_1.1 tibble_1.3.0 statmod_1.4.29
[100] stringi_1.1.5 lattice_0.20-35 trimcluster_0.1-2
[103] nloptr_1.0.4 HSMMSingleCell_0.108.0 combinat_0.0-8
[106] lmtest_0.9-35 data.table_1.10.4 bitops_1.0-6
[109] httpuv_1.3.3 R6_2.2.0 latticeExtra_0.6-28
[112] KernSmooth_2.23-15 gridExtra_2.2.1 IRanges_2.8.2
[115] codetools_0.2-15 boot_1.3-19 gtools_3.5.0
[118] assertthat_0.2.0 mnormt_1.5-5 qlcMatrix_0.9.5
[121] S4Vectors_0.12.2 diptest_0.75-7 mgcv_1.8-17
[124] grid_3.3.1 rpart_4.1-11 class_7.3-14
[127] minqa_1.2.4 segmented_0.5-1.4 Rtsne_0.13
[130] TTR_0.23-1 bbmle_1.0.19 shiny_1.0.3
[133] base64enc_0.1-3
monocole single-cell rstudio • 704 views

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