I was trying to use monocle. I started with the monocle-vignette.R code. But as soon as I run the command newCellDataSet() my R session crashes. It happens in RStudio as well as in R sessions in command prompt. Could you please suggest how to solve it.
It's really weird, but monocle is crashing on me too, during a subsetting operation, or rather the assignment of the subsetting to a new variable.
I have an object called `bds` that I obtained from `buildBranchCellDataSet`.
bds <- buildBranchCellDataSet(HSMM, branch_point = 1)
Turns out, I can subset `bds` by rows, columns, or even both:
bds[1:10,] bds[,1:10] bds[1:10, 1:10]
but my R session crashes if I assign the output to a new variable:
bds2 <- bds[1:10, 1:10] *crash!*
I even cunningly tried to use .Last.value to get around the issue:
bds[1:10,] bds2 <- .Last.value *crash!*
Can anyone replicate this scenario?
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  splines stats4 parallel stats graphics grDevices utils  datasets methods base other attached packages:  monocle_2.5.0 DDRTree_0.1.5 irlba_2.2.1 VGAM_1.0-3  ggplot2_2.2.1 Biobase_2.37.2 BiocGenerics_0.23.0 Matrix_1.2-10 loaded via a namespace (and not attached):  Rcpp_0.12.12 compiler_3.4.0 RColorBrewer_1.1-2  plyr_1.8.4 bindr_0.1 tools_3.4.0  densityClust_0.2.1 Rtsne_0.13 tibble_1.3.3  gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1  rlang_0.1.1 igraph_1.0.1 HSMMSingleCell_0.111.0  bindrcpp_0.2 fastICA_1.2-1 stringr_1.2.0  dplyr_0.7.1 cluster_2.0.6 combinat_0.0-8  grid_3.4.0 glue_1.1.1 R6_2.2.2  qlcMatrix_0.9.5 pheatmap_1.0.8 limma_3.33.3  reshape2_1.4.2 magrittr_1.5 matrixStats_0.52.2  scales_0.4.1 assertthat_0.2.0 colorspace_1.3-2  stringi_1.1.5 lazyeval_0.2.0.9000 munsell_0.4.3  slam_0.1-40