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This page was generated on 2024-05-03 11:38:57 -0400 (Fri, 03 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4660
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4391
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4422
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2091/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidySpatialExperiment 1.1.0  (landing page)
William Hutchison
Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024)
git_url: https://git.bioconductor.org/packages/tidySpatialExperiment
git_branch: devel
git_last_commit: 55489cc
git_last_commit_date: 2024-04-30 11:53:47 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for tidySpatialExperiment on merida1


To the developers/maintainers of the tidySpatialExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidySpatialExperiment.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: tidySpatialExperiment
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidySpatialExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidySpatialExperiment_1.1.0.tar.gz
StartedAt: 2024-05-02 12:46:24 -0400 (Thu, 02 May 2024)
EndedAt: 2024-05-02 12:57:15 -0400 (Thu, 02 May 2024)
EllapsedTime: 651.2 seconds
RetCode: 0
Status:   OK  
CheckDir: tidySpatialExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidySpatialExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidySpatialExperiment_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/tidySpatialExperiment.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidySpatialExperiment’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tidySpatialExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
select_helper: no visible global function definition for ‘all_of’
join_features,SpatialExperiment: no visible binding for global variable
  ‘index’
Undefined global functions or variables:
  all_of index
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
aggregate_cells 10.264  0.274  11.946
right_join       6.234  0.078   7.641
left_join        5.447  0.055   6.127
sample_n         5.433  0.063   6.603
rename           5.378  0.059   6.105
inner_join       5.360  0.061   6.051
unnest           5.340  0.057   5.857
join_features    5.141  0.056   5.843
count            5.110  0.056   5.809
nest             5.090  0.063   5.894
filter           5.074  0.071   5.729
bind_rows        5.081  0.057   5.723
plot_ly          4.998  0.132   5.858
ggplot           5.051  0.062   5.669
bind_cols        5.052  0.056   5.691
arrange          5.015  0.085   5.665
extract          5.009  0.058   6.004
mutate           4.967  0.060   5.757
rectangle        4.935  0.056   5.631
slice            4.892  0.063   5.767
separate         4.894  0.060   5.742
unite            4.890  0.063   5.436
pivot_longer     4.865  0.055   5.600
ellipse          4.857  0.061   5.478
group_by         4.834  0.065   5.500
as_tibble        4.812  0.060   5.443
rowwise          4.783  0.058   6.052
distinct         4.775  0.062   5.371
formatting       4.776  0.059   5.633
glimpse          4.759  0.057   5.371
pull             4.736  0.059   5.580
summarise        4.719  0.060   5.305
select           4.685  0.054   5.691
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/tidySpatialExperiment.Rcheck/00check.log’
for details.

Installation output

tidySpatialExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidySpatialExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘tidySpatialExperiment’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidySpatialExperiment)

Tests output

tidySpatialExperiment.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tidySpatialExperiment)
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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':

    I, expand.grid, unname

Loading required package: IRanges
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

Loading required package: tidySingleCellExperiment

Attaching package: 'tidySpatialExperiment'

The following object is masked from 'package:tidySingleCellExperiment':

    unnest_single_cell_experiment

> 
> test_check("tidySpatialExperiment")

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# Features=50 | Cells=99 | Assays=counts
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 47.453   1.819  55.076

Example timings

tidySpatialExperiment.Rcheck/tidySpatialExperiment-Ex.timings

nameusersystemelapsed
aggregate_cells10.264 0.27411.946
arrange5.0150.0855.665
as_tibble4.8120.0605.443
bind_cols5.0520.0565.691
bind_rows5.0810.0575.723
count5.1100.0565.809
distinct4.7750.0625.371
ellipse4.8570.0615.478
extract5.0090.0586.004
filter5.0740.0715.729
formatting4.7760.0595.633
ggplot5.0510.0625.669
glimpse4.7590.0575.371
group_by4.8340.0655.500
inner_join5.3600.0616.051
join_features5.1410.0565.843
left_join5.4470.0556.127
mutate4.9670.0605.757
nest5.0900.0635.894
pivot_longer4.8650.0555.600
plot_ly4.9980.1325.858
pull4.7360.0595.580
rectangle4.9350.0565.631
rename5.3780.0596.105
right_join6.2340.0787.641
rowwise4.7830.0586.052
sample_n5.4330.0636.603
select4.6850.0545.691
separate4.8940.0605.742
slice4.8920.0635.767
summarise4.7190.0605.305
tbl_format_header0.0000.0010.001
unite4.8900.0635.436
unnest5.3400.0575.857