Multiple platform build/check report for BioC 3.20 - CHECK results for tidySpatialExperiment on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

CHECK results for tidySpatialExperiment on teran2

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: 1.2.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidySpatialExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidySpatialExperiment_1.2.0.tar.gz

StartedAt: 2024-11-20 10:44:19 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 10:47:41 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 202.2 seconds

RetCode: 0

Status: OK

CheckDir: tidySpatialExperiment.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidySpatialExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidySpatialExperiment_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/tidySpatialExperiment.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidySpatialExperiment’ version ‘1.2.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

tidySpatialExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tidySpatialExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘tidySpatialExperiment’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, saveRDS, 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] "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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] "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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] "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 39 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 14.423   0.835  15.249

Example timings

tidySpatialExperiment.Rcheck/tidySpatialExperiment-Ex.timings

name	user	system	elapsed
aggregate_cells	2.744	0.202	2.977
arrange	1.638	0.024	1.662
as_tibble	0.829	0.017	0.846
bind_cols	0.908	0.015	0.923
bind_rows	0.892	0.002	0.895
count	0.890	0.008	0.898
distinct	0.821	0.002	0.823
ellipse	0.871	0.006	0.877
extract	0.866	0.008	0.874
filter	0.887	0.002	0.889
formatting	0.854	0.003	0.858
gate	0.937	0.003	0.943
gate_interactive	0.804	0.004	0.808
gate_programmatic	0.941	0.005	0.946
ggplot	0.927	0.005	0.931
glimpse	0.818	0.010	0.829
group_by	0.860	0.006	0.869
inner_join	0.991	0.003	0.994
join_features	0.929	0.005	0.936
left_join	0.993	0.001	0.996
mutate	0.871	0.014	0.885
nest	0.890	0.009	0.900
pivot_longer	0.853	0.003	0.857
plot_ly	0.898	0.015	0.914
pull	0.855	0.010	0.867
rectangle	0.880	0.006	0.886
rename	0.966	0.007	0.974
right_join	1.003	0.006	1.010
rowwise	0.848	0.012	0.860
sample_n	0.987	0.010	0.998
select	0.899	0.005	0.907
separate	0.891	0.011	0.903
slice	0.905	0.013	0.920
summarise	0.847	0.011	0.859
tbl_format_header	0	0	0
unite	0.918	0.009	0.928
unnest	0.976	0.014	0.991