Closed TJCooperIL closed 4 years ago
brgew
commented
4 years ago Hi, I am unable to reproduce this problem running Monocle3 develop branch on R 4.0.1 on Debian 10 and R 4.0.1 on an Ubuntu 20.04 virtual machine. I am concerned about it and I am interested in knowing if other people see this problem and/or have additional information or insight into it. Thank you.
anthonyxie
commented
4 years ago I'm also having a similar issue where learn_graph fails to complete.
The process stops here:
To reproduce: `library(monocle3) library(dplyr) expression_matrix <- readRDS(url("http://staff.washington.edu/hpliner/data/packer_embryo_expression.rds")) cell_metadata <- readRDS(url("http://staff.washington.edu/hpliner/data/packer_embryo_colData.rds")) gene_annotation <- readRDS(url("http://staff.washington.edu/hpliner/data/packer_embryo_rowData.rds"))
cds <- new_cell_data_set(expression_matrix, cell_metadata = cell_metadata, gene_metadata = gene_annotation)
cds <- preprocess_cds(cds, num_dim = 20); cds <- align_cds(cds, alignment_group = "batch", residual_model_formula_str = "~ bg.300.loading + bg.400.loading + bg.500.1.loading + bg.500.2.loading + bg.r17.loading + bg.b01.loading + bg.b02.loading")
cds <- reduce_dimension(cds)
ciliated_genes <- c("che-1", "hlh-17", "nhr-6", "dmd-6", "ceh-36", "ham-1")
plot_cells(cds, genes=ciliated_genes, label_cell_groups=FALSE, show_trajectory_graph=FALSE)
cds <- cluster_cells(cds)
cds <- learn_graph(cds, verbose=TRUE);
sessionInfo(): R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /share/software/user/open/openblas/0.2.19/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.0 monocle3_0.2.2.0 SingleCellExperiment_1.8.0
[4] SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1
[7] matrixStats_0.56.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[10] IRanges_2.20.2 S4Vectors_0.24.4 Biobase_2.46.0
[13] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] ggrepel_0.8.2 Rcpp_1.0.4.6 rsvd_1.0.3
[4] lattice_0.20-38 digest_0.6.25 assertthat_0.2.1
[7] RSpectra_0.16-0 R6_2.4.1 plyr_1.8.6
[10] ggplot2_3.3.2 pillar_1.4.4 zlibbioc_1.32.0
[13] rlang_0.4.6 rstudioapi_0.11 irlba_2.3.3
[16] Matrix_1.2-17 BiocNeighbors_1.4.2 labeling_0.3
[19] stringr_1.4.0 RCurl_1.98-1.2 munsell_0.5.0
[22] uwot_0.1.8 compiler_3.6.1 vipor_0.4.5
[25] BiocSingular_1.2.2 pkgconfig_2.0.3 ggbeeswarm_0.6.0
[28] tidyselect_1.1.0 tibble_3.0.1 gridExtra_2.3
[31] GenomeInfoDbData_1.2.2 batchelor_1.2.4 codetools_0.2-16
[34] viridisLite_0.3.0 crayon_1.3.4 bitops_1.0-6
[37] grid_3.6.1 gtable_0.3.0 lifecycle_0.2.0
[40] magrittr_1.5 scales_1.1.1 stringi_1.4.6
[43] farver_2.0.3 XVector_0.26.0 reshape2_1.4.4
[46] viridis_0.5.1 limma_3.42.2 scater_1.14.6
[49] DelayedMatrixStats_1.8.0 ellipsis_0.3.1 generics_0.0.2
[52] vctrs_0.3.1 RcppAnnoy_0.0.16 tools_3.6.1
[55] glue_1.4.1 beeswarm_0.2.3 purrr_0.3.4
[58] colorspace_1.4-1 `
brgew
commented
4 years ago Hi @anthonyxie,
Thank you for the example. Unfortunately, when I use those commands, Monocle3 runs without an error so I cannot debug this problem. For comparison, my sessionInfo() is
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS: /usr/local/R/R402_sse2/lib/R/lib/libRblas.so
LAPACK: /usr/local/R/R402_sse2/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.0 monocle3_0.2.2.0 testthat_2.3.2 SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.1 DelayedArray_0.14.0
[7] matrixStats_0.56.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 IRanges_2.22.1 S4Vectors_0.26.0 Biobase_2.48.0
[13] BiocGenerics_0.34.0 devtools_2.3.0 usethis_1.6.1
loaded via a namespace (and not attached):
[1] backports_1.1.7 plyr_1.8.6 igraph_1.2.5 lazyeval_0.2.2 splines_4.0.2 sp_1.4-2
[7] BiocParallel_1.22.0 listenv_0.8.0 ggplot2_3.3.1 scater_1.16.0 digest_0.6.25 htmltools_0.4.0
[13] viridis_0.5.1 gdata_2.18.0 fansi_0.4.1 magrittr_1.5 memoise_1.1.0 limma_3.44.1
[19] remotes_2.1.1 globals_0.12.5 gmodels_2.18.1 rsample_0.0.7 prettyunits_1.1.1 colorspace_1.4-1
[25] ggrepel_0.8.2 callr_3.4.3 crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.6.1 zoo_1.8-8
[31] glue_1.4.1 gtable_0.3.0 zlibbioc_1.34.0 XVector_0.28.0 pkgbuild_1.0.8 BiocSingular_1.4.0
[37] scales_1.1.1 pscl_1.5.5 pheatmap_1.0.12 DBI_1.1.0 Rcpp_1.0.4.6 viridisLite_0.3.0
[43] xtable_1.8-4 spData_0.3.5 units_0.6-7 spdep_1.1-3 rsvd_1.0.3 proxy_0.4-24
[49] htmlwidgets_1.5.1 httr_1.4.1 speedglm_0.3-2 RColorBrewer_1.1-2 ellipsis_0.3.1 farver_2.0.3
[55] pkgconfig_2.0.3 uwot_0.1.8 deldir_0.1-25 labeling_0.3 tidyselect_1.1.0 rlang_0.4.6
[61] reshape2_1.4.4 later_1.1.0.1 munsell_0.5.0 pbmcapply_1.5.0 tools_4.0.2 cli_2.0.2
[67] generics_0.0.2 batchelor_1.4.0 stringr_1.4.0 fastmap_1.0.1 processx_3.4.2 RhpcBLASctl_0.20-137
[73] fs_1.4.1 purrr_0.3.4 RANN_2.6.1 nlme_3.1-148 pbapply_1.4-2 future_1.17.0
[79] mime_0.9 slam_0.1-47 grr_0.9.5 compiler_4.0.2 rstudioapi_0.11 beeswarm_0.2.3
[85] plotly_4.9.2.1 e1071_1.7-3 tibble_3.0.1 stringi_1.4.6 ps_1.3.3 RSpectra_0.16-0
[91] desc_1.2.0 lattice_0.20-41 Matrix_1.2-18 classInt_0.4-3 vctrs_0.3.1 LearnBayes_2.15.1
[97] pillar_1.4.4 lifecycle_0.2.0 furrr_0.1.0 lmtest_0.9-37 RcppAnnoy_0.0.16 BiocNeighbors_1.6.0
[103] data.table_1.12.8 bitops_1.0-6 irlba_2.3.3 Matrix.utils_0.9.8 raster_3.1-5 httpuv_1.5.4
[109] R6_2.4.1 promises_1.1.1 KernSmooth_2.23-17 gridExtra_2.3 vipor_0.4.5 sessioninfo_1.1.1
[115] codetools_0.2-16 gtools_3.8.2 boot_1.3-25 MASS_7.3-51.6 assertthat_0.2.1 pkgload_1.1.0
[121] leidenbase_0.1.0 rprojroot_1.3-2 withr_2.2.0 GenomeInfoDbData_1.2.3 expm_0.999-4 grid_4.0.2
[127] coda_0.19-3 tidyr_1.1.0 class_7.3-17 DelayedMatrixStats_1.10.0 Rtsne_0.15 sf_0.9-4
[133] shiny_1.4.0.2 ggbeeswarm_0.6.0
I remain interested in understanding this problem...
I am grateful for your patience and assistance. Thank you.
TJCooperIL
commented
4 years ago After noticing additional instabilities + fatal errors in multiple R packages (in-addition to Monocle3), and despite all attempts to purge R from my system and cleanly reinstall it (the issues persisted), I resorted to a clean install of Ubuntu 20.04. Now everything is working. I can only suggest that there is an issue with the Ubuntu 19.10 -> Ubuntu 20.04 upgrade procedure, but this is outside the scope of Monocle3.
brgew
commented
4 years ago I appreciate the feedback. Thank you.
Describe the bug When running learn_graph (from master + devel branches), on the vignette sample data or my own (both small and large subsets), the process does not complete. It definitely runs, consuming 12% of CPU (1 core). On occasion, running learn_graph will cause a fatal error in RStudio.
The process stops here:
To Reproduce
sessionInfo():
Additional context Add any other context about the problem here.