tmp_dir not deleting after R session ends

[eliza-barkan]

The tmp_dir files are not deleting after an R session ends. I believe they are supposed to delete themselves after they are no longer stored in memory but it doesn't seem like this is happening.

suppressPackageStartupMessages({
  library(ggplot2)
  library(tibble)
  library(tidyr)
  library(dplyr)
  library(googledrive)
  library(splines)
  library(plotly)
  library(viridis)
  library(data.table)
  library(DelayedArray)
  library(htmlwidgets)
  library(stringr)
  library(monocle3)
  library(devtools)

  # maddys
  library(usethis)
  library(SingleCellExperiment)
  library(IRanges)
  library(Biobase)
  library(ggplot2)
  library(msigdbr)
  library(SummarizedExperiment)
  library(S4Vectors)
  library(BiocGenerics)
  library(GenomicRanges)
  library(MatrixGenerics)
  library(GenomeInfoDb)
  library(matrixStats)

  library(Rgraphviz)
  library(PLNmodels)
  library(garnett)
  library(hooke) # use instead of load_all()
  library(splines)

  DelayedArray:::set_verbose_block_processing(TRUE)
  options(DelayedArray.block.size=1e9)
})

cds = load_monocle_objects("path to dir")

# plot genes
plot_genes = c("gene1","gene2")

for (g in plot_genes){
plot_cells(cds, x = 1, y = 3,  genes = g,
           label_cell_groups = F, show_trajectory_graph = F,
           cell_size = 0.8, cell_stroke = 0, alpha = 0.8, norm_method = "log", scale_to_range = F) +
  scale_color_viridis_c() +
  theme_void() +
  theme(legend.position = "right")

  ggsave(paste0("fig_all_", g, "-expr_umap.png"),
       dpi = 1400,
       height = 2.5,
       width = 4,
       bg = "transparent")
}

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.3.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] splines   stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] BPCells_0.1.0               dplyr_1.1.4
 [3] hooke_0.0.1                 PLNmodels_1.1.0
 [5] monocle3_1.4.11             SingleCellExperiment_1.16.0
 [7] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1
 [9] GenomeInfoDb_1.30.1         Biobase_2.54.0
[11] stringr_1.5.1               htmlwidgets_1.6.4
[13] tidyr_1.3.0                 devtools_2.4.3
[15] usethis_2.2.2               DelayedArray_0.20.0
[17] IRanges_2.28.0              S4Vectors_0.32.4
[19] MatrixGenerics_1.6.0        matrixStats_1.2.0
[21] BiocGenerics_0.40.0         Matrix_1.6-4
[23] data.table_1.14.10          viridis_0.6.4
[25] viridisLite_0.4.2           plotly_4.10.3
[27] ggplot2_3.4.4              

loaded via a namespace (and not attached):
 [1] nlme_3.1-153           bitops_1.0-7           fs_1.6.3
 [4] lubridate_1.8.0        bit64_4.0.5            RcppAnnoy_0.0.21
 [7] httr_1.4.7             tools_4.1.2            utf8_1.2.4
[10] R6_2.5.1               DBI_1.2.1              lazyeval_0.2.2
[13] colorspace_2.1-0       withr_2.5.2            tidyselect_1.2.0
[16] gridExtra_2.3          processx_3.8.3         bit_4.0.5
[19] compiler_4.1.2         graph_1.72.0           cli_3.6.2
[22] scales_1.3.0           callr_3.7.3            digest_0.6.34
[25] minqa_1.2.6            XVector_0.34.0         coro_1.0.3
[28] pkgconfig_2.0.3        htmltools_0.5.7        parallelly_1.36.0
[31] lme4_1.1-35.1          sessioninfo_1.2.2      fastmap_1.1.1
[34] rlang_1.1.3            torch_0.12.0           RSQLite_2.2.9
[37] generics_0.1.3         jsonlite_1.8.8         RCurl_1.98-1.14
[40] magrittr_2.0.3         GenomeInfoDbData_1.2.7 Rcpp_1.0.12
[43] munsell_0.5.0          fansi_1.0.6            terra_1.7-46
[46] lifecycle_1.0.4        stringi_1.8.3          MASS_7.3-55
[49] zlibbioc_1.40.0        pkgbuild_1.4.3         plyr_1.8.9
[52] blob_1.2.2             grid_4.1.2             parallel_4.1.2
[55] listenv_0.9.0          crayon_1.5.2           lattice_0.20-45
[58] Biostrings_2.62.0      KEGGREST_1.34.0        ps_1.7.5
[61] pillar_1.9.0           igraph_1.6.0           boot_1.3-28
[64] future.apply_1.11.1    codetools_0.2-18       pkgload_1.3.3
[67] glue_1.7.0             remotes_2.4.2.1        png_0.1-8
[70] vctrs_0.6.5            nloptr_2.0.3           gtable_0.3.4
[73] purrr_1.0.2            assertthat_0.2.1       future_1.33.1
[76] cachem_1.0.8           tidygraph_1.3.0        glassoFast_1.0.1
[79] RSpectra_0.16-1        tibble_3.2.1           AnnotationDbi_1.56.2
[82] memoise_2.0.1          corrplot_0.92          globals_0.16.2
[85] ellipsis_0.3.2