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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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Segmentation fault #156

Closed Santos22903 closed 3 years ago

Santos22903 commented 3 years ago

Dear MAST team,

I am getting a segmentation fault when running the summary command on the fit object:

summaryCond <- summary(zlmCond,doLRT="ConditionPAH") Combining coefficients and standard errors Calculating log-fold changes realloc(): invalid pointer caught segfault address 0xa0000006, cause 'memory not mapped'

realloc(): invalid pointer

caught segfault address 0x30, cause 'memory not mapped' Abort (core dumped)

I tried it on a different server, the error message ended differently, but started with the same realloc() problem. Could you please help me get rid of the segfault. My sessionInfo is:

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8

Matrix products: default BLAS: /opt/R-4.0.3/lib64/R/lib/libRblas.so LAPACK: /opt/R-4.0.3/lib64/R/lib/libRlapack.so

locale: [1] C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] MAST_1.16.0 SingleCellExperiment_1.12.0 [3] SummarizedExperiment_1.20.0 Biobase_2.50.0 [5] GenomicRanges_1.42.0 GenomeInfoDb_1.26.4 [7] IRanges_2.24.1 S4Vectors_0.28.1 [9] BiocGenerics_0.36.0 MatrixGenerics_1.2.1 [11] matrixStats_0.58.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.6 plyr_1.8.6 compiler_4.0.3 [4] pillar_1.5.1 XVector_0.30.0 bitops_1.0-6 [7] tools_4.0.3 zlibbioc_1.36.0 lifecycle_1.0.0 [10] tibble_3.1.0 gtable_0.3.0 lattice_0.20-41 [13] pkgconfig_2.0.3 rlang_0.4.10 Matrix_1.3-2 [16] DBI_1.1.1 DelayedArray_0.16.2 GenomeInfoDbData_1.2.4 [19] dplyr_1.0.5 stringr_1.4.0 generics_0.1.0 [22] vctrs_0.3.6 tidyselect_1.1.0 grid_4.0.3 [25] glue_1.4.2 data.table_1.14.0 R6_2.5.0 [28] fansi_0.4.2 reshape2_1.4.4 purrr_0.3.4 [31] ggplot2_3.3.3 magrittr_2.0.1 scales_1.1.1 [34] ellipsis_0.3.1 assertthat_0.2.1 abind_1.4-5 [37] colorspace_2.0-0 utf8_1.2.1 stringi_1.5.3 [40] RCurl_1.98-1.3 munsell_0.5.0 crayon_1.4.1

Thank you

gfinak commented 3 years ago

MAST doesn't have any compiled code to cause such a segfault. This is likely in some downstream package.