std::bad_alloc error #62
Description
I am getting a std::bad_alloc error when I run optimizeRetGroup. I have 995G of ram on my machine and when I watch in htop it never goes over 12G so I am stumped as to what is going on.
Code:
library(here)
library(xcms)
library(RColorBrewer)
library(IPO)
datapath <- here("data", "msdata")
datafiles <- list.files(datapath, recursive = TRUE, full.names = TRUE, pattern = paste("\\.", "mzXML", "$", sep=''))
datafiles <- datafiles[grep("pos", datafiles)]
exp_design <- read.csv(here("data", "experimental_design.csv"))
exp_design <- exp_design[grep("pos", exp_design$charge),]
peakpickingParameters.cent <- getDefaultXcmsSetStartingParams("centWave")
resultPeakpicking_cent <- optimizeXcmsSet(files = datafiles,
params = peakpickingParameters.cent,
nSlaves = 2,
subdir = "results/centWave")
optimizedXcmsSetObject <- resultPeakpicking_cent$best_settings$xset
retcorGroupParameters <- getDefaultRetGroupStartingParams()
resultRetcorGroup <- optimizeRetGroup(xset = optimizedXcmsSetObject, params = retcorGroupParameters, nSlaves = 2, subdir = "results/centWave", plot = TRUE)
I get the following error:
> resultRetcorGroup <- optimizeRetGroup(xset = optimizedXcmsSetObject, params = retcorGroupParameters, nSlaves = 2, subdir = "results/centWave", plot = TRUE)
starting new DoE with:
distFunc: cor_opt
gapInit: c(0, 0.4)
gapExtend: c(2.1, 2.7)
profStep: c(0.7, 1)
plottype: none
response: 1
factorDiag: 2
factorGap: 1
localAlignment: 0
retcorMethod: obiwarp
bw: c(22, 38)
minfrac: c(0.3, 0.7)
mzwid: c(0.015, 0.035)
minsamp: 1
max: 50
center: 1
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Error in unserialize(node$con) : error reading from connection
>
> terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
This then results in a core dump.
session Info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /local/cluster/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /local/cluster/R-3.5.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] IPO_1.8.0 CAMERA_1.38.0 rsm_2.10
[4] RColorBrewer_1.1-2 xcms_3.4.0 MSnbase_2.8.0
[7] ProtGenerics_1.14.0 S4Vectors_0.20.0 mzR_2.16.0
[10] Rcpp_1.0.0 BiocParallel_1.16.0 Biobase_2.42.0
[13] BiocGenerics_0.28.0 here_0.1
loaded via a namespace (and not attached):
[1] lattice_0.20-35 rprojroot_1.3-2 digest_0.6.18
[4] foreach_1.4.4 plyr_1.8.4 backports_1.1.2
[7] acepack_1.4.1 mzID_1.20.0 ggplot2_3.1.0
[10] pillar_1.3.0 zlibbioc_1.28.0 rlang_0.3.0.1
[13] lazyeval_0.2.1 data.table_1.11.8 rstudioapi_0.8
[16] rpart_4.1-13 Matrix_1.2-14 checkmate_1.8.5
[19] preprocessCore_1.44.0 splines_3.5.0 stringr_1.3.1
[22] foreign_0.8-71 htmlwidgets_1.3 igraph_1.2.2
[25] munsell_0.5.0 compiler_3.5.0 pkgconfig_2.0.2
[28] base64enc_0.1-3 multtest_2.38.0 pcaMethods_1.74.0
[31] htmltools_0.3.6 nnet_7.3-12 tibble_1.4.2
[34] gridExtra_2.3 htmlTable_1.12 RANN_2.6
[37] Hmisc_4.1-1 IRanges_2.16.0 codetools_0.2-15
[40] XML_3.98-1.16 crayon_1.3.4 MASS_7.3-51.1
[43] grid_3.5.0 MassSpecWavelet_1.48.0 RBGL_1.58.0
[46] gtable_0.2.0 affy_1.60.0 magrittr_1.5
[49] scales_1.0.0 ncdf4_1.16 graph_1.60.0
[52] stringi_1.2.4 impute_1.56.0 affyio_1.52.0
[55] doParallel_1.0.14 limma_3.38.2 latticeExtra_0.6-28
[58] robustbase_0.93-3 Formula_1.2-3 iterators_1.0.10
[61] tools_3.5.0 DEoptimR_1.0-8 survival_2.43-1
[64] colorspace_1.3-2 cluster_2.0.7-1 BiocManager_1.30.3
[67] vsn_3.50.0 MALDIquant_1.18 knitr_1.20
Any help would be much appreciated!
Thank you!