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.
Without having more information (version of R, version of RStudio, sessionInfo()), It's going to be difficult to troubleshoot this. Crashes in the past often have been ameliorated by upgrading everything Monocle depends on.
Hi all,
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`.
Basically:
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?
Many thanks
Kevin
For information:
> 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: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats4 parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] monocle_2.5.0 DDRTree_0.1.5 irlba_2.2.1 VGAM_1.0-3 [5] ggplot2_2.2.1 Biobase_2.37.2 BiocGenerics_0.23.0 Matrix_1.2-10 loaded via a namespace (and not attached): [1] Rcpp_0.12.12 compiler_3.4.0 RColorBrewer_1.1-2 [4] plyr_1.8.4 bindr_0.1 tools_3.4.0 [7] densityClust_0.2.1 Rtsne_0.13 tibble_1.3.3 [10] gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 [13] rlang_0.1.1 igraph_1.0.1 HSMMSingleCell_0.111.0 [16] bindrcpp_0.2 fastICA_1.2-1 stringr_1.2.0 [19] dplyr_0.7.1 cluster_2.0.6 combinat_0.0-8 [22] grid_3.4.0 glue_1.1.1 R6_2.2.2 [25] qlcMatrix_0.9.5 pheatmap_1.0.8 limma_3.33.3 [28] reshape2_1.4.2 magrittr_1.5 matrixStats_0.52.2 [31] scales_0.4.1 assertthat_0.2.0 colorspace_1.3-2 [34] stringi_1.1.5 lazyeval_0.2.0.9000 munsell_0.4.3 [37] slam_0.1-40
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version 2.3.6
Exactly the same problem with me and several other people I know. My session info:
RStudio version - 1.0.136Can you clarify exactly what you did? For instance, did you run the source code of vignette, e.g.,
or did you copy-and-paste commands from the vignette into your R session? Can you also cut and paste the running code being echoed to the screen at the time of the crash?
Sorry, Martin, just noticed your question. We had this problem when running our course: http://hemberg-lab.github.io/scRNA.seq.course/pseudotime-analysis.html
Namely, if I run this in RStudio (on any system):
library(monocle) deng <- readRDS("deng.rds") cellLabels <- colnames(deng) d <- deng[1:1000, ] d <- d[!duplicated(rownames(d)), ] colnames(d) <- 1:ncol(d) geneNames <- rownames(d) rownames(d) <- 1:nrow(d) pd <- data.frame(timepoint = cellLabels) pd <- new("AnnotatedDataFrame", data=pd) fd <- data.frame(gene_short_name = geneNames) fd <- new("AnnotatedDataFrame", data=fd) dCellData <- newCellDataSet(d, phenoData = pd, featureData = fd, expressionFamily = tobit())RStudio will crash after the last line of code. Deng dataset can be downloaded from here: https://github.com/hemberg-lab/scRNA.seq.course/raw/master/deng/deng.rds
Running the vignette as you proposed seems ok.
RStudio version: 1.0.143