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
