'memory not mapped' error when running monocole
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 9 weeks ago
Munich, Germany

Hi,

when trying to analyse time-sereis analysis of single-cells RNASeq with monocole, my R session crashes, when I try to get the structure of my CellDataSet object. 

This is the script I am using ( it is a minimal example I created for the reproduction of the error message):

library(monocle)
library(SLICER)
set.seed(1)

d <- readRDS("d.RDS")
cellLabels <- readRDS("celllables.RDS")

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 <- monocle::newCellDataSet(d, phenoData = pd, featureData = fd)

When calling the dCellData it works nicely, but when trying to see the structure the session aborts (s. below for error message)

Is there a reason for that?

thanks

Assa

 

> str(dCellData)

Formal class 'CellDataSet' [package "monocle"] with 19 slots

  ..@ reducedDimS          : num[0 , 0 ]

  ..@ reducedDimW          : num[0 , 0 ]

  ..@ reducedDimA          : num[0 , 0 ]

  ..@ reducedDimK          : num[0 , 0 ]

  ..@ minSpanningTree      :

*** caught segfault ***

address 0x11000002, cause 'memory not mapped'

Traceback:

1: base::.Call(.NAME, ...)

2: .Call("R_igraph_is_directed", graph, PACKAGE = "igraph")

3: is_directed(object)

4: paste(sep = "", "IGRAPH ", c("U", "D")[is_directed(object) +     1], c("-", "N")[is_named(object) + 1], c("-", "W")[is_weighted(object) +     1], c("-", "B")[is_bipartite(object) + 1], " ", vcount(object),     " ", ecount(object), " -- ")

5: .print.header(x)

6: print.igraph(object, full = TRUE, ...)

7: str.igraph(obj, ...)

8: str(obj, ...)

9: (function (...) str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L),     nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE),     give.head = quote(TRUE), width = quote(80L), envir = quote(NULL),     strict.width = quote("no"), formatNum = quote(function (x,         ...)     format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99),     give.length = quote(TRUE), nest.lev = quote(2), indent.str = quote("  .. .."))

10: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)

11: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev +     1, indent.str = paste(indent.str, ".."))

12: str.default(obj, ...)

13: str(obj, ...)

14: (function (...) str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L),     nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE),     give.head = quote(TRUE), width = quote(80L), envir = quote(<environment>),     strict.width = quote("no"), formatNum = quote(function (x,         ...)     format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99),     comp.str = quote("@ "), no.list = quote(TRUE), give.length = quote(TRUE),     indent.str = quote("  .."), nest.lev = quote(1))

15: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)

16: strSub(a, comp.str = "@ ", no.list = TRUE, give.length = give.length,     indent.str = paste(indent.str, ".."), nest.lev = nest.lev +         1)

17: str.default(dCellData)

18: str(dCellData)

Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace

Selection:

 

___________________________________

 

> R.version

               _                          

platform       x86_64-apple-darwin15.6.0  

arch           x86_64                     

os             darwin15.6.0               

system         x86_64, darwin15.6.0       

status                                    

major          3                          

minor          4.0                        

year           2017                       

month          04                         

day            21                         

svn rev        72570                      

language       R                          

version.string R version 3.4.0 (2017-04-21)

nickname       You Stupid Darkness       

> sessionInfo()

R version 3.4.0 (2017-04-21)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: OS X El Capitan 10.11.6

Matrix products: default

BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:

[1] C/UTF-8/C/C/C/C

attached base packages:

[1] splines   stats4    parallel  stats     graphics  grDevices utils   

[8] datasets  methods   base    

other attached packages:

[1] SLICER_0.2.0         alphahull_2.1        lle_1.1            

[4] snowfall_1.84-6.1    snow_0.4-2           MASS_7.3-47        

[7] scatterplot3d_0.3-40 igraph_1.0.1         monocle_2.4.0      

[10] DDRTree_0.1.5        irlba_2.1.2          VGAM_1.0-3         

[13] ggplot2_2.2.1        Biobase_2.36.0       BiocGenerics_0.22.0

[16] Matrix_1.2-10      

loaded via a namespace (and not attached):

[1] slam_0.1-40            reshape2_1.4.2         lattice_0.20-35      

[4] colorspace_1.3-2       spatstat.utils_1.4-1   fastICA_1.2-0        

[7] mgcv_1.8-17            R.oo_1.21.0            spatstat_1.50-0      

[10] DBI_0.6-1              R.utils_2.5.0          sp_1.2-4             

[13] RColorBrewer_1.1-2     HSMMSingleCell_0.110.0 matrixStats_0.52.2   

[16] sgeostat_1.0-27        plyr_1.8.4             stringr_1.2.0        

[19] munsell_0.4.3          combinat_0.0-8         gtable_0.2.0         

[22] R.methodsS3_1.7.1      Rcpp_0.12.10           tensor_1.5           

[25] scales_0.4.1           limma_3.32.2           densityClust_0.2.1   

[28] abind_1.4-5            deldir_0.1-14          tripack_1.3-8        

[31] stringi_1.1.5          Rtsne_0.13             qlcMatrix_0.9.5      

[34] dplyr_0.5.0            splancs_2.01-40        polyclip_1.6-1       

[37] grid_3.4.0             tools_3.4.0            goftest_1.1-1        

[40] magrittr_1.5           lazyeval_0.2.0         tibble_1.3.0         

[43] cluster_2.0.6          pheatmap_1.0.8         assertthat_0.2.0     

[46] rpart_4.1-11           R6_2.2.0               nlme_3.1-131         

[49] compiler_3.4.0       

 

monocole memory CellDataSet • 592 views
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