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This page was generated on 2024-05-20 11:32:22 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4381
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Package 2094/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidySpatialExperiment 1.1.0  (landing page)
William Hutchison
Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 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)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for tidySpatialExperiment on kjohnson1


To the developers/maintainers of the tidySpatialExperiment package:
- 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: 2024-05-20 05:07:30 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 05:12:40 -0400 (Mon, 20 May 2024)
EllapsedTime: 310.0 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-mac-arm64/meat/tidySpatialExperiment.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* 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 5.347  0.177   5.828
* 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-mac-arm64/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-arm64/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: aarch64-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-arm64/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-arm64/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-arm64/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 
 24.686   0.763  25.539

Example timings

tidySpatialExperiment.Rcheck/tidySpatialExperiment-Ex.timings

nameusersystemelapsed
aggregate_cells5.3470.1775.828
arrange2.3510.0452.572
as_tibble2.3180.0432.593
bind_cols2.2250.0342.280
bind_rows2.2460.0342.293
count2.3020.0372.351
distinct2.1250.0332.165
ellipse2.0650.0352.132
extract1.8370.0351.952
filter2.2480.0332.290
formatting2.1380.0332.176
ggplot2.2640.0392.313
glimpse2.0860.0362.132
group_by2.1940.0372.271
inner_join2.3640.0342.404
join_features2.2860.0432.338
left_join2.3960.0342.439
mutate2.1590.0332.205
nest2.2640.0372.320
pivot_longer2.1600.0342.210
plot_ly2.1070.0512.173
pull2.0400.0412.161
rectangle2.1890.0342.235
rename2.3800.0362.427
right_join2.6270.0352.749
rowwise1.9290.0291.978
sample_n2.3510.0332.391
select1.6750.0331.732
separate2.2080.0352.257
slice2.1740.0332.214
summarise2.0980.0322.136
tbl_format_header0.0000.0000.001
unite2.1670.0322.205
unnest2.3510.0382.406