[BUG/Question] What's the layer annotation variable in the spe object? #89

sluan-jh · 2024-10-15T18:50:34Z

Hello,

Since fetch_data returns error on my machine, I manually downloaded data from the https link for type == "sce" in the fetch_data() function and converted the downloaded sce to spe using sce_to_spe().

>fetch_data(type = "spe")
snapshotDate(): 2024-04-29
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'

When I try to replicate the example code below:

vis_clus(
    spe = spe,
    clustervar = "spatialLIBD",
    sampleid = "151673",
    colors = libd_layer_colors,
    ... = " DLPFC Human Brain Layers\nMade with research.libd.org/spatialLIBD/"
)

I couldn't find a variable named "spatialLIBD" in the colData, but it seems using the column "layer_guess_reordered_short" produces the same result.

Is "layer_guess_reordered_short" the annotation of the layers?

Session info is attached below in case it's helpful

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2024-10-15
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-8     2024-09-12 [1] CRAN (R 4.4.1)
 AnnotationDbi          1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationHub          3.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 attempt                0.3.1     2020-05-03 [1] CRAN (R 4.4.1)
 basilisk             * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 basilisk.utils         1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beachmat               2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.4.0)
 benchmarkme            1.0.8     2022-06-12 [1] CRAN (R 4.4.1)
 benchmarkmeData        1.0.4     2020-04-23 [1] CRAN (R 4.4.1)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache        * 2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocIO                 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager            1.30.25   2024-08-28 [1] CRAN (R 4.4.1)
 BiocNeighbors          1.22.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocParallel           1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocSingular           1.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocVersion            3.19.1    2024-04-17 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.1)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.1)
 bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 bslib                  0.8.0     2024-07-29 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 config                 0.3.2     2023-08-30 [1] CRAN (R 4.4.1)
 cowplot                1.1.3     2024-01-22 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   5.2.2     2024-08-26 [1] CRAN (R 4.4.1)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.4.1)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr               * 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DelayedMatrixStats     1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 dir.expiry             1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.4.1)
 dotCall64              1.2       2024-10-04 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 DT                     0.33      2024-04-04 [1] CRAN (R 4.4.1)
 edgeR                  4.2.1     2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 ExperimentHub          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 fields                 16.3      2024-09-30 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.4.1)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.12    2024-10-10 [1] Bioconductor
 GenomicAlignments      1.40.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 GenomicRanges        * 1.56.1    2024-06-12 [1] Bioconductor 3.19 (R 4.4.0)
 ggbeeswarm             0.7.2     2023-04-29 [1] CRAN (R 4.4.1)
 ggplot2                3.5.1     2024-04-23 [1] CRAN (R 4.4.1)
 ggrepel                0.9.6     2024-09-07 [1] CRAN (R 4.4.1)
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.4.1)
 golem                  0.5.1     2024-08-27 [1] CRAN (R 4.4.1)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.4.1)
 gtable                 0.3.5     2024-04-22 [1] CRAN (R 4.4.1)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.4.1)
 htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                 1.6.15    2024-03-26 [1] CRAN (R 4.4.1)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.1)
 IRanges              * 2.38.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.4.1)
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.4.1)
 jquerylib              0.1.4     2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite               1.8.8     2023-12-04 [1] CRAN (R 4.4.1)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
 later                  1.3.2     2023-12-06 [1] CRAN (R 4.4.1)
 lattice                0.22-6    2024-03-20 [2] CRAN (R 4.4.1)
 lazyeval               0.2.2     2019-03-15 [1] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.1)
 limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 lobstr               * 1.1.2     2022-06-22 [1] CRAN (R 4.4.1)
 locfit                 1.5-9.10  2024-06-24 [1] CRAN (R 4.4.1)
 magick                 2.8.5     2024-09-20 [1] CRAN (R 4.4.1)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.1)
 maps                   3.4.2     2023-12-15 [1] CRAN (R 4.4.1)
 Matrix               * 1.7-0     2024-04-26 [2] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 matrixStats          * 1.4.1     2024-09-08 [1] CRAN (R 4.4.1)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.1)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.4.0)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.4.1)
 paletteer              1.6.0     2024-01-21 [1] CRAN (R 4.4.1)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.1)
 plotly                 4.10.4    2024-01-13 [1] CRAN (R 4.4.1)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 promises               1.3.0     2024-04-05 [1] CRAN (R 4.4.1)
 purrr                  1.0.2     2023-08-10 [1] CRAN (R 4.4.1)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.1)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.1)
 raster               * 3.6-26    2023-10-14 [1] CRAN (R 4.4.1)
 RColorBrewer           1.1-3     2022-04-03 [1] CRAN (R 4.4.0)
 Rcpp                   1.0.13    2024-07-17 [1] CRAN (R 4.4.1)
 RCurl                  1.98-1.16 2024-07-11 [1] CRAN (R 4.4.1)
 readr                * 2.1.5     2024-01-10 [1] CRAN (R 4.4.1)
 rematch2               2.1.2     2020-05-01 [1] CRAN (R 4.4.1)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.4.1)
 reticulate           * 1.39.0    2024-09-05 [1] CRAN (R 4.4.1)
 rjson                  0.2.23    2024-09-16 [1] CRAN (R 4.4.1)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.1)
 Rsamtools              2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.1)
 rstudioapi             0.16.0    2024-03-24 [1] CRAN (R 4.4.1)
 rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.4.1)
 rtracklayer            1.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 S4Vectors            * 0.42.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 sass                   0.4.9     2024-03-15 [1] CRAN (R 4.4.1)
 ScaledMatrix           1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 scales                 1.3.0     2023-11-28 [1] CRAN (R 4.4.1)
 scater                 1.32.1    2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 scuttle                1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.1)
 shiny                  1.9.1     2024-08-01 [1] CRAN (R 4.4.1)
 shinyWidgets           0.8.7     2024-09-23 [1] CRAN (R 4.4.1)
 SingleCellExperiment * 1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sp                   * 2.1-4     2024-04-30 [1] CRAN (R 4.4.1)
 spam                   2.11-0    2024-10-03 [1] CRAN (R 4.4.1)
 SparseArray            1.4.8     2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 sparseMatrixStats      1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 spatialLIBD          * 1.16.2    2024-05-28 [1] Bioconductor 3.19 (R 4.4.1)
 statmod                1.5.0     2023-01-06 [1] CRAN (R 4.4.1)
 SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 terra                  1.7-78    2024-05-22 [1] CRAN (R 4.4.1)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.1)
 tidyr                  1.3.1     2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.1)
 tzdb                   0.4.0     2023-05-12 [1] CRAN (R 4.4.1)
 UCSC.utils             1.0.0     2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.1)
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 vipor                  0.4.7     2023-12-18 [1] CRAN (R 4.4.1)
 viridis                0.6.5     2024-01-29 [1] CRAN (R 4.4.1)
 viridisLite            0.4.2     2023-05-02 [1] CRAN (R 4.4.1)
 withr                  3.0.1     2024-07-31 [1] CRAN (R 4.4.1)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.4.1)
 XVector                0.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 yaml                   2.3.10    2024-07-26 [1] CRAN (R 4.4.1)
 zellkonverter        * 1.14.1    2024-06-26 [1] Bioconductor 3.19 (R 4.4.0)
 zlibbioc               1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)

 [1] C:/Users/Shu Luan/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Thank you!

The text was updated successfully, but these errors were encountered:

lcolladotor · 2024-10-15T19:03:53Z

Hi,

Since you are not using fetch_data() you are missing these internal steps

spatialLIBD/R/fetch_data.R

Lines 336 to 345 in c82c789

    
           .update_sce <- function(sce) { 
        
               ## Rename here the default cluster we want to show in the shiny app 
        
               sce$spatialLIBD <- sce$layer_guess_reordered_short 
        
               ## Add ManualAnnotation which was formerly called Layer, then drop Layer 
        
               sce$ManualAnnotation <- sce$Layer 
        
               sce$Layer <- NULL 
        
               return(sce) 
        
           }

.

I haven't heard of this error before and would need more information, like the output of traceback().

Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'

Maybe it's an issue with Windows 10 x64 but well, I'm not sure.

Best,
Leo

sluan-jh · 2024-10-15T19:13:16Z

Hi Leo,

That makes sense now. Thank you!

For the bug, here's the traceback:

> fetch_data(type = "spe")
snapshotDate(): 2024-04-29
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'
> traceback()
8: get_ram()
7: enough_ram()
6: fetch_data("sce", destdir = destdir, eh = eh)
5: is(sce, "SingleCellExperiment")
4: stopifnot(is(sce, "SingleCellExperiment"))
3: check_sce(sce)
2: sce_to_spe(fetch_data("sce", destdir = destdir, eh = eh))
1: fetch_data(type = "spe")

Best,
Shu

lcolladotor · 2024-10-15T21:01:24Z

I see, looks like

spatialLIBD/R/enough_ram.R

Line 23 in c82c789

ram <- get_ram()

is failing for you. It's from

spatialLIBD/R/enough_ram.R

Line 12 in c82c789

#' @importFrom benchmarkme get_ram

.

What is the output of the following for you?

## Reproduce error
benchmarkme::get_ram()
traceback()

## R Session info
options(width = 120)
sessioninfo::session_info()

It might be worth reporting the output of this at https://github.com/csgillespie/benchmarkme. Looks like csgillespie/benchmarkme#49 might be related, which coincidentally (aka suspicious now) was also reported by a Windows 10 user.

Best,
Leo

sluan-jh · 2024-10-15T21:35:00Z

Hi Leo,

This is the output of the code you provided.

> ## Reproduce error
> benchmarkme::get_ram()
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'
> traceback()
1: benchmarkme::get_ram()
> ## R Session info
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2024-10-15
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-8     2024-09-12 [1] CRAN (R 4.4.1)
 AnnotationDbi          1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationHub          3.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 attempt                0.3.1     2020-05-03 [1] CRAN (R 4.4.1)
 basilisk             * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 basilisk.utils         1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beachmat               2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.4.0)
 benchmarkme            1.0.8     2022-06-12 [1] CRAN (R 4.4.1)
 benchmarkmeData        1.0.4     2020-04-23 [1] CRAN (R 4.4.1)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache        * 2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocIO                 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager            1.30.25   2024-08-28 [1] CRAN (R 4.4.1)
 BiocNeighbors          1.22.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocParallel           1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocSingular           1.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocVersion            3.19.1    2024-04-17 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.1)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.1)
 bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 bslib                  0.8.0     2024-07-29 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 config                 0.3.2     2023-08-30 [1] CRAN (R 4.4.1)
 cowplot                1.1.3     2024-01-22 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   5.2.2     2024-08-26 [1] CRAN (R 4.4.1)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.4.1)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr               * 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DelayedMatrixStats     1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 dir.expiry             1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.4.1)
 dotCall64              1.2       2024-10-04 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 DT                     0.33      2024-04-04 [1] CRAN (R 4.4.1)
 edgeR                  4.2.1     2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 ExperimentHub          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 fields                 16.3      2024-09-30 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.4.1)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.12    2024-10-10 [1] Bioconductor
 GenomicAlignments      1.40.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 GenomicRanges        * 1.56.1    2024-06-12 [1] Bioconductor 3.19 (R 4.4.0)
 ggbeeswarm             0.7.2     2023-04-29 [1] CRAN (R 4.4.1)
 ggplot2                3.5.1     2024-04-23 [1] CRAN (R 4.4.1)
 ggrepel                0.9.6     2024-09-07 [1] CRAN (R 4.4.1)
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.4.1)
 golem                  0.5.1     2024-08-27 [1] CRAN (R 4.4.1)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.4.1)
 gtable                 0.3.5     2024-04-22 [1] CRAN (R 4.4.1)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.4.1)
 htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                 1.6.15    2024-03-26 [1] CRAN (R 4.4.1)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.1)
 IRanges              * 2.38.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.4.1)
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.4.1)
 jquerylib              0.1.4     2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite               1.8.8     2023-12-04 [1] CRAN (R 4.4.1)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
 later                  1.3.2     2023-12-06 [1] CRAN (R 4.4.1)
 lattice                0.22-6    2024-03-20 [2] CRAN (R 4.4.1)
 lazyeval               0.2.2     2019-03-15 [1] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.1)
 limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 lobstr               * 1.1.2     2022-06-22 [1] CRAN (R 4.4.1)
 locfit                 1.5-9.10  2024-06-24 [1] CRAN (R 4.4.1)
 magick                 2.8.5     2024-09-20 [1] CRAN (R 4.4.1)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.1)
 maps                   3.4.2     2023-12-15 [1] CRAN (R 4.4.1)
 Matrix               * 1.7-0     2024-04-26 [2] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 matrixStats          * 1.4.1     2024-09-08 [1] CRAN (R 4.4.1)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.1)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.4.0)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.4.1)
 paletteer              1.6.0     2024-01-21 [1] CRAN (R 4.4.1)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.1)
 plotly                 4.10.4    2024-01-13 [1] CRAN (R 4.4.1)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 promises               1.3.0     2024-04-05 [1] CRAN (R 4.4.1)
 purrr                  1.0.2     2023-08-10 [1] CRAN (R 4.4.1)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.1)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.1)
 raster               * 3.6-26    2023-10-14 [1] CRAN (R 4.4.1)
 RColorBrewer           1.1-3     2022-04-03 [1] CRAN (R 4.4.0)
 Rcpp                   1.0.13    2024-07-17 [1] CRAN (R 4.4.1)
 RCurl                  1.98-1.16 2024-07-11 [1] CRAN (R 4.4.1)
 readr                * 2.1.5     2024-01-10 [1] CRAN (R 4.4.1)
 rematch2               2.1.2     2020-05-01 [1] CRAN (R 4.4.1)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.4.1)
 reticulate           * 1.39.0    2024-09-05 [1] CRAN (R 4.4.1)
 rjson                  0.2.23    2024-09-16 [1] CRAN (R 4.4.1)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.1)
 Rsamtools              2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.1)
 rstudioapi             0.16.0    2024-03-24 [1] CRAN (R 4.4.1)
 rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.4.1)
 rtracklayer            1.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 S4Vectors            * 0.42.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 sass                   0.4.9     2024-03-15 [1] CRAN (R 4.4.1)
 ScaledMatrix           1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 scales                 1.3.0     2023-11-28 [1] CRAN (R 4.4.1)
 scater                 1.32.1    2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 scuttle                1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.1)
 shiny                  1.9.1     2024-08-01 [1] CRAN (R 4.4.1)
 shinyWidgets           0.8.7     2024-09-23 [1] CRAN (R 4.4.1)
 SingleCellExperiment * 1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sp                   * 2.1-4     2024-04-30 [1] CRAN (R 4.4.1)
 spam                   2.11-0    2024-10-03 [1] CRAN (R 4.4.1)
 SparseArray            1.4.8     2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 sparseMatrixStats      1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 spatialLIBD          * 1.16.2    2024-05-28 [1] Bioconductor 3.19 (R 4.4.1)
 statmod                1.5.0     2023-01-06 [1] CRAN (R 4.4.1)
 SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 terra                  1.7-78    2024-05-22 [1] CRAN (R 4.4.1)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.1)
 tidyr                  1.3.1     2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.1)
 tzdb                   0.4.0     2023-05-12 [1] CRAN (R 4.4.1)
 UCSC.utils             1.0.0     2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.1)
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.4.1)
 vipor                  0.4.7     2023-12-18 [1] CRAN (R 4.4.1)
 viridis                0.6.5     2024-01-29 [1] CRAN (R 4.4.1)
 viridisLite            0.4.2     2023-05-02 [1] CRAN (R 4.4.1)
 withr                  3.0.1     2024-07-31 [1] CRAN (R 4.4.1)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.4.1)
 XVector                0.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 yaml                   2.3.10    2024-07-26 [1] CRAN (R 4.4.1)
 zellkonverter        * 1.14.1    2024-06-26 [1] Bioconductor 3.19 (R 4.4.0)
 zlibbioc               1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)

 [1] C:/Users/Shu Luan/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

lcolladotor · 2024-10-22T12:44:47Z

Thanks @sluan-jh! Well, we now need to wait for a response about csgillespie/benchmarkme#49.

lcolladotor · 2024-12-12T19:58:18Z

Hi @sluan-jh,

At csgillespie/benchmarkme#49 (comment) someone reported that this was no longer an issue with OS: Windows 11 x64 version 24H2 (KB5046617).

Can you try upgrading your winOS to that version and checking if the issue has been resolved for you too?

Thanks!
Leo

sluan-jh · 2024-12-12T22:38:35Z

Hi @lcolladotor,

I have tried the fetch() function again and now it's working.
What's interesting is that I didn't update my winOS.

> library(spatialLIBD)
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet,
    colCollapse, colCounts, colCummaxs,
    colCummins, colCumprods, colCumsums, colDiffs,
    colIQRDiffs, colIQRs, colLogSumExps,
    colMadDiffs, colMads, colMaxs, colMeans2,
    colMedians, colMins, colOrderStats, colProds,
    colQuantiles, colRanges, colRanks, colSdDiffs,
    colSds, colSums2, colTabulates, colVarDiffs,
    colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys,
    rowAvgsPerColSet, rowCollapse, rowCounts,
    rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs,
    rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
    rowMeans2, rowMedians, rowMins, rowOrderStats,
    rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates,
    rowVarDiffs, rowVars, rowWeightedMads,
    rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame,
    basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get,
    grep, grepl, intersect, is.unsorted, lapply,
    Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff,
    table, tapply, union, unique, unsplit,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view
    with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and
    for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

> fetch_data(type = "spe")
snapshotDate(): 2024-04-29
C:\Users\Shu Luan\AppData\Local/R/cache/R/BiocFileCache
  does not exist, create directory? (yes/no): yes
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
  |===============================================| 100%
  |===============================================| 100%

2024-12-12 15:39:33.19272 loading file C:\Users\Shu Luan\AppData\Local/R/cache/R/BiocFileCache/32f029485674_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
class: SpatialExperiment 
dim: 33538 47681 
metadata(0):
assays(2): counts logcounts
rownames(33538): ENSG00000243485 ENSG00000237613
  ... ENSG00000277475 ENSG00000268674
rowData names(9): source type ... gene_search
  is_top_hvg
colnames(47681): AAACAACGAATAGTTC-1
  AAACAAGTATCTCCCA-1 ... TTGTTTCCATACAACT-1
  TTGTTTGTGTAAATTC-1
colData names(69): sample_id Cluster ... array_row
  array_col
reducedDimNames(6): PCA TSNE_perplexity50 ...
  TSNE_perplexity80 UMAP_neighbors15
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : pxl_col_in_fullres
  pxl_row_in_fullres
imgData names(4): sample_id image_id data
  scaleFactor

> ## R Session info
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2024-12-12
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-8     2024-09-12 [1] CRAN (R 4.4.1)
 AnnotationDbi          1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationHub          3.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 attempt                0.3.1     2020-05-03 [1] CRAN (R 4.4.1)
 beachmat               2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.4.0)
 benchmarkme            1.0.8     2022-06-12 [1] CRAN (R 4.4.1)
 benchmarkmeData        1.0.4     2020-04-23 [1] CRAN (R 4.4.1)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocIO                 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager            1.30.25   2024-08-28 [1] CRAN (R 4.4.2)
 BiocNeighbors          1.22.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocParallel           1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocSingular           1.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocVersion            3.19.1    2024-04-17 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.5.0     2024-09-20 [1] CRAN (R 4.4.2)
 bit64                  4.5.2     2024-09-22 [1] CRAN (R 4.4.2)
 bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 bslib                  0.8.0     2024-07-29 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 config                 0.3.2     2023-08-30 [1] CRAN (R 4.4.1)
 cowplot                1.1.3     2024-01-22 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   6.0.0     2024-11-05 [1] CRAN (R 4.4.2)
 data.table             1.16.2    2024-10-10 [1] CRAN (R 4.4.2)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr                 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DelayedMatrixStats     1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.4.1)
 dotCall64              1.2       2024-10-04 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 DT                     0.33      2024-04-04 [1] CRAN (R 4.4.1)
 edgeR                  4.2.2     2024-10-16 [1] Bioconductor 3.19 (R 4.4.1)
 ExperimentHub          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 fields                 16.3      2024-09-30 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.4.1)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.12    2024-10-10 [1] Bioconductor
 GenomicAlignments      1.40.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 GenomicRanges        * 1.56.2    2024-10-09 [1] Bioconductor 3.19 (R 4.4.1)
 ggbeeswarm             0.7.2     2023-04-29 [1] CRAN (R 4.4.1)
 ggplot2                3.5.1     2024-04-23 [1] CRAN (R 4.4.1)
 ggrepel                0.9.6     2024-09-07 [1] CRAN (R 4.4.1)
 glue                   1.8.0     2024-09-30 [1] CRAN (R 4.4.2)
 golem                  0.5.1     2024-08-27 [1] CRAN (R 4.4.1)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.4.1)
 gtable                 0.3.6     2024-10-25 [1] CRAN (R 4.4.2)
 htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                 1.6.15    2024-03-26 [1] CRAN (R 4.4.1)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.1)
 IRanges              * 2.38.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.4.1)
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.4.1)
 jquerylib              0.1.4     2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite               1.8.9     2024-09-20 [1] CRAN (R 4.4.2)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
 later                  1.4.1     2024-11-27 [1] CRAN (R 4.4.2)
 lattice                0.22-6    2024-03-20 [2] CRAN (R 4.4.1)
 lazyeval               0.2.2     2019-03-15 [1] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.1)
 limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 locfit                 1.5-9.10  2024-06-24 [1] CRAN (R 4.4.1)
 magick                 2.8.5     2024-09-20 [1] CRAN (R 4.4.1)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.1)
 maps                   3.4.2.1   2024-11-10 [1] CRAN (R 4.4.2)
 Matrix                 1.7-0     2024-04-26 [2] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 matrixStats          * 1.4.1     2024-09-08 [1] CRAN (R 4.4.1)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.1)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.4.0)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.4.1)
 paletteer              1.6.0     2024-01-21 [1] CRAN (R 4.4.1)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.1)
 plotly                 4.10.4    2024-01-13 [1] CRAN (R 4.4.1)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 promises               1.3.2     2024-11-28 [1] CRAN (R 4.4.2)
 purrr                  1.0.2     2023-08-10 [1] CRAN (R 4.4.1)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.1)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.1)
 RColorBrewer           1.1-3     2022-04-03 [1] CRAN (R 4.4.0)
 Rcpp                   1.0.13-1  2024-11-02 [1] CRAN (R 4.4.2)
 RCurl                  1.98-1.16 2024-07-11 [1] CRAN (R 4.4.1)
 rematch2               2.1.2     2020-05-01 [1] CRAN (R 4.4.1)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.4.1)
 rjson                  0.2.23    2024-09-16 [1] CRAN (R 4.4.1)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.1)
 Rsamtools              2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.1)
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 rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.4.1)
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 scuttle                1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.1)
 shiny                  1.9.1     2024-08-01 [1] CRAN (R 4.4.1)
 shinyWidgets           0.8.7     2024-09-23 [1] CRAN (R 4.4.1)
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 spam                   2.11-0    2024-10-03 [1] CRAN (R 4.4.1)
 SparseArray            1.4.8     2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 sparseMatrixStats      1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 spatialLIBD          * 1.16.2    2024-05-28 [1] Bioconductor 3.19 (R 4.4.1)
 statmod                1.5.0     2023-01-06 [1] CRAN (R 4.4.1)
 stringi                1.8.4     2024-05-06 [1] CRAN (R 4.4.0)
 stringr                1.5.1     2023-11-14 [1] CRAN (R 4.4.1)
 SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.1)
 tidyr                  1.3.1     2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.1)
 UCSC.utils             1.0.0     2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.1)
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.4.1)
 vipor                  0.4.7     2023-12-18 [1] CRAN (R 4.4.1)
 viridis                0.6.5     2024-01-29 [1] CRAN (R 4.4.1)
 viridisLite            0.4.2     2023-05-02 [1] CRAN (R 4.4.1)
 withr                  3.0.2     2024-10-28 [1] CRAN (R 4.4.2)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.4.1)
 XVector                0.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 yaml                   2.3.10    2024-07-26 [1] CRAN (R 4.4.1)
 zlibbioc               1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)

 [1] C:/Users/Shu Luan/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

I'm not sure how this problem was fixed. If you need more information, please feel free to let me know!

Best regards,
Shu

lcolladotor mentioned this issue Oct 15, 2024

get_ram() cannot retrieve RAM csgillespie/benchmarkme#49

Open

lcolladotor added the bug-on-dependency label Oct 22, 2024

lcolladotor mentioned this issue Oct 22, 2024

[BUG] Fail to obtain the spe data of DLPFC #79

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[BUG/Question] What's the layer annotation variable in the spe object? #89

[BUG/Question] What's the layer annotation variable in the spe object? #89

sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 15, 2024

sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 15, 2024

sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 22, 2024

lcolladotor commented Dec 12, 2024

sluan-jh commented Dec 12, 2024

[BUG/Question] What's the layer annotation variable in the spe object? #89

[BUG/Question] What's the layer annotation variable in the spe object? #89

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sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 15, 2024

sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 15, 2024

sluan-jh commented Oct 15, 2024

lcolladotor commented Oct 22, 2024

lcolladotor commented Dec 12, 2024

sluan-jh commented Dec 12, 2024