constantAmateur
commented
2 years ago This is an issue with the writeMM function which comes from the package Matrix. It very much looks like an issue with lack of memory, but as I did not write this function I suggest you contact the authors of the Matrix package for more guidance.
Hi, I get the following error while writing the results:
Error in writeMM(x, file = mhandle) : Cholmod error 'error reading/writing file' at file ../Check/cholmod_write.c, line 635
I have already tried gc() and setting the memory limit. But still get same error.
session info: R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /usr/local/lib64/R/lib/libRblas.so LAPACK: /usr/local/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] stats graphics grDevices utils datasets methods base
other attached packages: [1] Matrix_1.3-4 SeuratObject_4.0.2 Seurat_4.0.3 SoupX_1.5.2
loaded via a namespace (and not attached): [1] nlme_3.1-149 matrixStats_0.59.0 spatstat.sparse_2.0-0 [4] RcppAnnoy_0.0.18 RColorBrewer_1.1-2 httr_1.4.2
[7] sctransform_0.3.2 tools_4.0.3 utf8_1.2.1
[10] R6_2.5.0 irlba_2.3.3 rpart_4.1-15
[13] KernSmooth_2.23-17 uwot_0.1.10 mgcv_1.8-33
[16] DBI_1.1.1 lazyeval_0.2.2 colorspace_2.0-2
[19] tidyselect_1.1.1 gridExtra_2.3 compiler_4.0.3
[22] plotly_4.9.4.1 scales_1.1.1 lmtest_0.9-38
[25] spatstat.data_2.1-0 ggridges_0.5.3 pbapply_1.4-3
[28] goftest_1.2-2 stringr_1.4.0 digest_0.6.27
[31] spatstat.utils_2.2-0 pkgconfig_2.0.3 htmltools_0.5.1.1
[34] parallelly_1.27.0 fastmap_1.1.0 htmlwidgets_1.5.3
[37] rlang_0.4.11 shiny_1.6.0 generics_0.1.0
[40] zoo_1.8-9 jsonlite_1.7.2 ica_1.0-2
[43] dplyr_1.0.7 magrittr_2.0.1 patchwork_1.1.1
[46] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[49] abind_1.4-5 reticulate_1.20 lifecycle_1.0.0
[52] stringi_1.7.3 MASS_7.3-53 Rtsne_0.15
[55] plyr_1.8.6 grid_4.0.3 parallel_4.0.3
[58] listenv_0.8.0 promises_1.2.0.1 ggrepel_0.9.1
[61] crayon_1.4.1 miniUI_0.1.1.1 deldir_0.2-10
[64] lattice_0.20-41 cowplot_1.1.1 splines_4.0.3
[67] tensor_1.5 pillar_1.6.1 igraph_1.2.6
[70] spatstat.geom_2.2-2 future.apply_1.7.0 reshape2_1.4.4
[73] codetools_0.2-16 leiden_0.3.8 glue_1.4.2
[76] data.table_1.14.0 png_0.1-7 vctrs_0.3.8
[79] httpuv_1.6.1 gtable_0.3.0 RANN_2.6.1
[82] purrr_0.3.4 spatstat.core_2.3-0 polyclip_1.10-0
[85] tidyr_1.1.3 scattermore_0.7 future_1.21.0
[88] assertthat_0.2.1 ggplot2_3.3.5 mime_0.11
[91] xtable_1.8-4 later_1.2.0 survival_3.2-7
[94] viridisLite_0.4.0 tibble_3.1.2 cluster_2.1.0
[97] globals_0.14.0 fitdistrplus_1.1-5 ellipsis_0.3.2
[100] ROCR_1.0-11