Monocle causes R session to crash
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galib36 ▴ 10
@galib36-9138
Last seen 3.7 years ago
United Kingdom

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.

software error monocle • 1.5k views
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Exactly the same problem with me and several other people I know. My session info:

R Under development (unstable) (2016-10-20 r71540)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

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     datasets 
 [9] methods   base     

other attached packages:
[1] monocle_2.3.1       DDRTree_0.1.4       irlba_2.1.2         VGAM_1.0-3         
[5] ggplot2_2.2.1       Biobase_2.35.1      BiocGenerics_0.21.3 Matrix_1.2-8       

loaded via a namespace (and not attached):
 [1] igraph_1.0.1           Rcpp_0.12.10           cluster_2.0.5         
 [4] magrittr_1.5           munsell_0.4.3          colorspace_1.3-2      
 [7] lattice_0.20-34        R6_2.2.0               stringr_1.2.0         
[10] dplyr_0.5.0            plyr_1.8.4             tools_3.4.0           
[13] grid_3.4.0             gtable_0.2.0           DBI_0.6-1             
[16] matrixStats_0.52.1     assertthat_0.1         lazyeval_0.2.0        
[19] tibble_1.3.0           reshape2_1.4.2         RColorBrewer_1.1-2    
[22] HSMMSingleCell_0.109.0 slam_0.1-40            qlcMatrix_0.9.5       
[25] pheatmap_1.0.8         stringi_1.1.5          limma_3.31.20         
[28] fastICA_1.2-0          scales_0.4.1           combinat_0.0-8
RStudio version - 1.0.136
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Can you clarify exactly what you did? For instance, did you run the source code of vignette, e.g.,

fl = dir(system.file(package="monocle", "doc"), pattern=".R$", full=TRUE)
source(fl, echo=TRUE, max=Inf)

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?

 

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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.

sessionInfo()

R Under development (unstable) (2016-10-20 r71540)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

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_2.4.0       DDRTree_0.1.5       irlba_2.1.2        
[4] VGAM_1.0-3          ggplot2_2.2.1.9000  Biobase_2.36.2     
[7] BiocGenerics_0.22.0 Matrix_1.2-10      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10           RColorBrewer_1.1-2     plyr_1.8.4            
 [4] tools_3.4.0            densityClust_0.2.1     Rtsne_0.13            
 [7] tibble_1.3.3           gtable_0.2.0           lattice_0.20-34       
[10] rlang_0.1.1            igraph_1.0.1           HSMMSingleCell_0.110.0
[13] fastICA_1.2-0          stringr_1.2.0          dplyr_0.7.0           
[16] knitr_1.15.1           cluster_2.0.5          combinat_0.0-8        
[19] grid_3.4.0             glue_1.0.0             R6_2.2.0              
[22] qlcMatrix_0.9.5        pheatmap_1.0.8         limma_3.32.2          
[25] reshape2_1.4.2         magrittr_1.5           scales_0.4.1.9002     
[28] matrixStats_0.52.2     assertthat_0.2.0       colorspace_1.3-2      
[31] stringi_1.1.5          lazyeval_0.2.0         munsell_0.4.3         
[34] slam_0.1-40           

RStudio version: 1.0.143

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coletrap • 0
@coletrap-6766
Last seen 5.8 years ago

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.

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kevin.rue ▴ 300
@kevinrue-6757
Last seen 4 months ago
University of Oxford

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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